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1,799 results on '"The James Hutton Institute"'

1. Broccoli Ileo Study

Author: University of Reading and The James Hutton Institute
Published: 2019

2. Phylogenomics and the rise of the angiosperms

Author: Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Royal Botanic Gardens, Kew. U. K., Villum Fonden. Denmark, Aarhus University. Denmark, James Hutton Institute. U. K., National Institute of Agricultural Botany (NIAB). U. K., Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Arista Palmero, Montserrat, Ariza Molina, María Jesús, Arroyo Marín, Juan, De Castro Mateo, Alejandra, Escudero Lirio, Marcial, Valle García, José Carlos del, Baker, William J., Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Royal Botanic Gardens, Kew. U. K., Villum Fonden. Denmark, Aarhus University. Denmark, James Hutton Institute. U. K., National Institute of Agricultural Botany (NIAB). U. K., Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Arista Palmero, Montserrat, Ariza Molina, María Jesús, Arroyo Marín, Juan, De Castro Mateo, Alejandra, Escudero Lirio, Marcial, Valle García, José Carlos del, and Baker, William J.
Abstract: Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5,6,7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
Published: 2024

3. Healthier and Sustainable Food Systems: Integrating Underutilised Crops in a ‘Theory of Change Approach’

Author: European Commission, Fundação para a Ciência e a Tecnologia (Portugal), James Hutton Institute, Scottish Government, Pinto, Elisabete, Ferreira, Helena, Santos, Carla S., da Silva, Marta Nunes, Styles, David, Migliorini, Paola, Ntatsi, Georgia, Karkanis, Anestis, Brémaud, Marie Fleur, de Mey, Yann, Meuwissen, Miranda, Petrusan, Janos Istvan, Smetana, Sergiy, Silva, Beatriz, Marie Krenz, Lina Maja, Pleissner, Daniel, Profeta, Adriano, Debeljak, Marko, Ivanovska, Aneta, Balázs, Bálint, Rubiales, Diego, Hawes, Cathy, Iannetta, Pietro P.M., Vasconcelos, Marta W., European Commission, Fundação para a Ciência e a Tecnologia (Portugal), James Hutton Institute, Scottish Government, Pinto, Elisabete, Ferreira, Helena, Santos, Carla S., da Silva, Marta Nunes, Styles, David, Migliorini, Paola, Ntatsi, Georgia, Karkanis, Anestis, Brémaud, Marie Fleur, de Mey, Yann, Meuwissen, Miranda, Petrusan, Janos Istvan, Smetana, Sergiy, Silva, Beatriz, Marie Krenz, Lina Maja, Pleissner, Daniel, Profeta, Adriano, Debeljak, Marko, Ivanovska, Aneta, Balázs, Bálint, Rubiales, Diego, Hawes, Cathy, Iannetta, Pietro P.M., and Vasconcelos, Marta W.
Abstract: Increasingly, consumers are paying attention to healthier food diets, “healthy” food attributes (such as “freshness”, “naturalness” and “nutritional value”), and the overall sustainability of production and processing methods. Other significant trends include a growing demand for regional and locally produced/supplied and less processed food. To meet these demands, food production and processing need to evolve to preserve the raw material and natural food properties while ensuring such sustenance is healthy, tasty, and sustainable. In parallel, it is necessary to understand the influence of consumers’ practices in maintaining the beneficial food attributes from purchasing to consumption. The whole supply chain must be resilient, fair, diverse, transparent, and economically balanced to make different food systems sustainable. This chapter focuses on the role of dynamic value chains using biodiverse, underutilised crops to improve food system resilience and deliver foods with good nutritional and health properties while ensuring low environmental impacts, and resilient ecosystem functions.
Published: 2023

4. Design guide for on-farm demonstrations

Author: ACTA - Les Instituts Techniques Agricoles, ILVO - Flanders Research Institute for Agriculture, Fisheries an, JHI - James Hutton Institute, BioSens Institut, ACTA - Les Instituts Techniques Agricoles, ILVO - Flanders Research Institute for Agriculture, Fisheries an, JHI - James Hutton Institute, and BioSens Institut
Abstract: The FarmDemo Training Kit supports the organisation of successful farm demonstrations. It collects many interesting tools, guidelines and videos that can help farmers and other farm organisers in organising successful farm demonstrations. The Training Kit will inspire them to uplift their future demonstration events, whether on-farm or online. The Training Kit offers an overview of the most important elements to be considered for preparing, delivering, and evaluating demonstrations on the farm. The FarmDemo Training Kit supports the skills enhancement and capacity building of farm demo organisers. It enables the practical implementation of innovative demo practices on the farm and increases the awareness of the value of farmer-to-farmer exchanges during farm demonstrations.
Published: 2022

5. Design guide for virtual demonstrations

Author: ACTA - Les Instituts Techniques Agricoles, ILVO - Flanders Research Institute for Agriculture, Fisheries an, JHI - James Hutton Institute, BioSens Institut, ACTA - Les Instituts Techniques Agricoles, ILVO - Flanders Research Institute for Agriculture, Fisheries an, JHI - James Hutton Institute, and BioSens Institut
Abstract: The FarmDemo Training Kit supports the organisation of successful farm demonstrations. It collects many interesting tools, guidelines and videos that can help farmers and other farm organisers in organising successful farm demonstrations. The Training Kit will inspire them to uplift their future demonstration events, whether on-farm or online. The Training Kit offers an overview of the most important elements to be considered for preparing, delivering, and evaluating demonstrations on the farm. The FarmDemo Training Kit supports the skills enhancement and capacity building of farm demo organisers. It enables the practical implementation of innovative demo practices on the farm and increases the awareness of the value of farmer-to-farmer exchanges during farm demonstrations.
Published: 2022

6. Understanding values beyond carbon in the Woodland Carbon Code in Scotland

Author: James Hutton Institute, Ovando Pol, Paola [0000-0001-6915-5826], Vergunst, Jo [0000-0002-7585-1286], Koronca, James, Ovando Pol, Paola, Vergunst, Jo, James Hutton Institute, Ovando Pol, Paola [0000-0001-6915-5826], Vergunst, Jo [0000-0002-7585-1286], Koronca, James, Ovando Pol, Paola, and Vergunst, Jo
Abstract: Many governments and organisations are encouraging carbon dioxide capture in woodlands through the creation of markets that commodify forest carbon. These schemes can connect different values in local landscapes and global environmental responses to climate change, which go beyond increasing the cost-effectiveness of carbon offsetting. In this paper we use the UK Woodland Carbon Code (WCC) to explore the values and meanings brought to the WCC by landowners, forest developers and carbon buyers, with a focus on Scotland. Our analysis presents quantitative and qualitative evidence of different values coexisting among the participants of the WCC, accommodating both conservation oriented woodland expansion projects and those driven by income diversification. The former mainly use non-commercial native broadleaf species and the latter combine commercial non-native conifer plantation with different levels of native broadleaves whilst remaining non-viable economically. WCC participants convey different values and meanings of forest carbon, transcending commodity value as tradeable offsets to encompass other environmental and social outcomes. We argue that the WCC works by encoding and enabling the exchange of different values, which for proponents is a positive feature that captures the diverse co-benefits of woodland. Critics of carbon offsets, meanwhile, may see these shifts in value as a form of greenwashing that benefits carbon buyers. We argue that research into the effects of carbon offset schemes should incorporate both material and symbolic processes that go beyond carbon itself.
Published: 2022

7. A global database of soil nematode abundance and functional group composition

Author: DOB Ecology, Netherlands Organization for Scientific Research, Ministerio de Economía y Competitividad (España), National Science Foundation (US), European Commission, Natural Environment Research Council (UK), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), German Research Foundation, Ministry of Science and Higher Education of the Russian Federation, Chinese Academy of Sciences, National Natural Science Foundation of China, German Academic Exchange Service, National Foundation for Science and Technology Development (Vietnam), National Key Research and Development Program (China), European Research Council, Bureau of Animal and Plant Health Inspection and Quarantine (Taiwan), Russian Foundation for Basic Research, James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, Hoogen, Johan van den, Geisen, Stefan, Wall, Diana H., Wardle, David A., Traunspurger, Walter, Goede, Ron G. M. de, Adams, Byron J., Ahmad, Wasim, Ferris, Howard, Bardgett, Richard D., Bonkowski, Michael, Campos-Herrera, Raquel, Cares, Juvenil E., Caruso, Tancredi, Brito Caixeta, Larissa de, Chen, Xiaoyun, Costa, Sofia R., Creamer, Rachel, Cunha Castro, José Mauro da, Dam, Marie, Djigal, Djibril, Escuer, Miguel, Griffiths, Bryan S., Gutiérrez, Carmen, Hohberg, Karin, Kalinkina, Daria, Kardol, Paul, Kergunteuil, Alan, Korthals, Gerard, Krashevska, Valentyna, Kudrin, Alexey A., Li, Qi, Liang, Wenju, Magilton, Matthew, Marais, Mariette, Rodríguez Martín, José Antonio, Matveeva, Elizaveta, Mayad, El Hassan, Mzough, E., Mulder, Christian, Mullin, Peter, Neilson, Roy, Nguyen, T. A. Duong, Nielsen, Uffe N., Okada, Hiroaki, Palomares Rius, Juan E., Pan, Kaiwen, Peneva, Vlada, Pellissier, Loïc, Pereira da Silva, Julio Carlos, Pitteloud, Camille, Powers, Thomas O., Powers, Kirsten, Quist, Casper W., Rasmann, Sergio, Sánchez-Moreno, Sara, Scheu, Stefan, Setälä, Heikki, Sushchuk, Anna, Tiunov, Alexei V., Trap, Jean, Vestergård, Mette, Villenave, Cecile, Waeyenberge, Lieven, Wilschut, Rutger, Wright, Daniel G., Keith, Aidan M., Yang, Jiue-in, Schmidt, Olaf, Bouharroud, R., Ferji, Z., Putten, Wim H. van der, Routh, Devin, Crowther, Thomas Ward, DOB Ecology, Netherlands Organization for Scientific Research, Ministerio de Economía y Competitividad (España), National Science Foundation (US), European Commission, Natural Environment Research Council (UK), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), German Research Foundation, Ministry of Science and Higher Education of the Russian Federation, Chinese Academy of Sciences, National Natural Science Foundation of China, German Academic Exchange Service, National Foundation for Science and Technology Development (Vietnam), National Key Research and Development Program (China), European Research Council, Bureau of Animal and Plant Health Inspection and Quarantine (Taiwan), Russian Foundation for Basic Research, James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, Hoogen, Johan van den, Geisen, Stefan, Wall, Diana H., Wardle, David A., Traunspurger, Walter, Goede, Ron G. M. de, Adams, Byron J., Ahmad, Wasim, Ferris, Howard, Bardgett, Richard D., Bonkowski, Michael, Campos-Herrera, Raquel, Cares, Juvenil E., Caruso, Tancredi, Brito Caixeta, Larissa de, Chen, Xiaoyun, Costa, Sofia R., Creamer, Rachel, Cunha Castro, José Mauro da, Dam, Marie, Djigal, Djibril, Escuer, Miguel, Griffiths, Bryan S., Gutiérrez, Carmen, Hohberg, Karin, Kalinkina, Daria, Kardol, Paul, Kergunteuil, Alan, Korthals, Gerard, Krashevska, Valentyna, Kudrin, Alexey A., Li, Qi, Liang, Wenju, Magilton, Matthew, Marais, Mariette, Rodríguez Martín, José Antonio, Matveeva, Elizaveta, Mayad, El Hassan, Mzough, E., Mulder, Christian, Mullin, Peter, Neilson, Roy, Nguyen, T. A. Duong, Nielsen, Uffe N., Okada, Hiroaki, Palomares Rius, Juan E., Pan, Kaiwen, Peneva, Vlada, Pellissier, Loïc, Pereira da Silva, Julio Carlos, Pitteloud, Camille, Powers, Thomas O., Powers, Kirsten, Quist, Casper W., Rasmann, Sergio, Sánchez-Moreno, Sara, Scheu, Stefan, Setälä, Heikki, Sushchuk, Anna, Tiunov, Alexei V., Trap, Jean, Vestergård, Mette, Villenave, Cecile, Waeyenberge, Lieven, Wilschut, Rutger, Wright, Daniel G., Keith, Aidan M., Yang, Jiue-in, Schmidt, Olaf, Bouharroud, R., Ferji, Z., Putten, Wim H. van der, Routh, Devin, and Crowther, Thomas Ward
Abstract: As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
Published: 2020

8. Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida

Author: Department of Agriculture (US), Agriculture and Agri-Food Canada, Scottish Government, James Hutton Institute, Ministerio de Educación, Cultura y Deporte (España), Duceppe, Marc-Olivier, Lafond-Lapalme, Joël, Palomares Rius, Juan E., Sabeh, Michaël, Blok, Vivian C., Moffett, Peter, Mimee, Benjamin, Department of Agriculture (US), Agriculture and Agri-Food Canada, Scottish Government, James Hutton Institute, Ministerio de Educación, Cultura y Deporte (España), Duceppe, Marc-Olivier, Lafond-Lapalme, Joël, Palomares Rius, Juan E., Sabeh, Michaël, Blok, Vivian C., Moffett, Peter, and Mimee, Benjamin
Abstract: Potato cyst nematodes (PCNs), Globodera rostochiensis and G. pallida, cause important economic losses. They are hard to manage because of their ability to remain dormant in soil for many years. Although general knowledge about these plant parasitic nematodes has considerably increased over the past decades, very little is known about molecular events involved in cyst dormancy and hatching, two key steps of their development. Here, we have studied the progression of PCN transcriptomes from dry cysts to hatched juveniles using RNA-Seq. We found that several cell detoxification-related genes were highly active in the dry cysts. Many genes linked to an increase of calcium and water uptake were up-regulated during transition from dormancy to hydration. Exposure of hydrated cysts to host plant root exudates resulted in different transcriptional response between species. After 48 h of exposure, G. pallida cysts showed no significant modulation of gene expression while G. rostochiensis had 278 differentially expressed genes. The first G. rostochiensis significantly up-regulated gene was observed after 8 h and was coding for a transmembrane metalloprotease. This enzyme is able to activate/inactivate peptide hormones and could be involved in a cascade of events leading to hatching. Several known effector genes were also up-regulated during hatching.
Published: 2017

9. Mitochondrial genome diversity in dagger and needle nematodes (Nematoda: Longidoridae)

Author: Junta de Andalucía, European Commission, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, Palomares Rius, Juan E., Cantalapiedra-Navarrete, C., Archidona-Yuste, Antonio, Blok, Vivian C., Castillo, Pablo, Junta de Andalucía, European Commission, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, Palomares Rius, Juan E., Cantalapiedra-Navarrete, C., Archidona-Yuste, Antonio, Blok, Vivian C., and Castillo, Pablo
Abstract: Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12.7 kb, respectively. Up to date, the mt genome of X. pachtaicum is the smallest genome found in Nematoda. The four mt genomes contain 12 protein-coding genes (viz. cox1-3, nad1-6, nad4L, atp6 and cob) and two ribosomal RNA genes (rrnL and rrnS), but the atp8 gene was not detected. These mt genomes showed a gene arrangement very different within the Longidoridae species sequenced, with the exception of very closely related species (X. americanum and X. rivesi). The sizes of non-coding regions in the Longidoridae nematodes were very small and were present in a few places in the mt genome. Phylogenetic analysis of all coding genes showed a closer relationship between Longidorus and Paralongidorus and different phylogenetic possibilities for the three Xiphinema species.
Published: 2017

10. Social equity in governance of ecosystem services: synthesis from European treeline areas

Author: European Commission, European Cooperation in Science and Technology, James Hutton Institute, University of Oulu, Sarkki, Simo, Alados, Concepción L., Zhyla, Tetiana, European Commission, European Cooperation in Science and Technology, James Hutton Institute, University of Oulu, Sarkki, Simo, Alados, Concepción L., and Zhyla, Tetiana
Abstract: Achieving social equity among local stakeholders should be a key objective for ecosystem service (ES) governance in Europe's ecologically fragile treeline areas. The ES literature tends to be biased towards distributional equity and market-based instruments when assessing social equity of ES governance. In this study, we analyze a wide range of social equity procedures that have been applied in Europe, using 11 synthesized case studies of governance-related challenges and 75 proposals for governance enhancement from 8 European countries provided by researchers with expertise on treeline area governance. The proposals were grouped by inductive clustering into 10 procedural or distributional equity-related policy recommendations: (1) increase stakeholder collaboration, (2) balance interactions between horizontal and vertical governance levels, (3) increase ES education, (4) use science to guide decisions, (5) start collaboration at an early stage, (6) enhance transparency, (7) aim to mitigate negative impacts, (8) use an ES approach to identify synergistic goals for governance, (9) enhance balanced multi-functional land use, and (10) use market-based instruments to balance benefits and costs deriving from governance decisions. Finally, we discuss 5 more general proposals on how regulatory and market-based approaches could be linked to enhance both procedural and distributional equity of treeline area governance.
Published: 2017

11. Geographic coordinates, environmental and genetic data for 256 wild barley accessions

Author: Russell, J. (Cell And Molecular Sciences, The James Hutton Institute. Invergowrie, Scotland (UK)), Dawson, I.K. (Cell And Molecular Sciences, The James Hutton Institute. Invergowrie, Scotland (UK)), Booth, A. (Cell And Molecular Sciences, The James Hutton Institute. Invergowrie, Scotland (UK)), Waugh, R. (Cell And Molecular Sciences, The James Hutton Institute. Invergowrie, Scotland (UK)), Van Zonneveld, M. (Regional Office For The Americas, Bioversity International, Cali, Colombia), and Steffenson, B. (Department Of Plant Pathology, University Of Minnesota, Saint Paul, Minnesota (USA))
Published: 2014
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12. Unusual features of pomoviral RNA movement

Author: Cell and Molecular Sciences, Invergowrie, Dundee, DD2 5DA , Scotland / UK - The James Hutton Institute, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland / UK - Cell and Molecular Sciences, UCL - SST/ELI/ELIM - Applied Microbiology, Uppsala BioCentre, Swedish University of Agricultural Sciences, Uppsala, Sweden - Department of Plant Biology and Forest Genetics, Torrance, Lesley, Wright, Kathryn M., Crutzen, François, Cowan, Graham H., Lukhovitskaya, Nina I., Cell and Molecular Sciences, Invergowrie, Dundee, DD2 5DA , Scotland / UK - The James Hutton Institute, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland / UK - Cell and Molecular Sciences, UCL - SST/ELI/ELIM - Applied Microbiology, Uppsala BioCentre, Swedish University of Agricultural Sciences, Uppsala, Sweden - Department of Plant Biology and Forest Genetics, Torrance, Lesley, Wright, Kathryn M., Crutzen, François, Cowan, Graham H., and Lukhovitskaya, Nina I.
Abstract: Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of coat protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2 and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement.
Published: 2011

13. Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate

Author: Ministerio de Educación, Cultura y Deporte (España), James Hutton Institute, Scottish Government, Palomares Rius, Juan E., Hedley, Pete, Cock, Peter J., Morris, Jenny A., Jones, John T., Blok, Vivian C., Ministerio de Educación, Cultura y Deporte (España), James Hutton Institute, Scottish Government, Palomares Rius, Juan E., Hedley, Pete, Cock, Peter J., Morris, Jenny A., Jones, John T., and Blok, Vivian C.
Abstract: Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest including hatching inhibition and dauer stages are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in an anhydrobiotic state, with unhatched nematode persisting for extended periods of time inside the cyst in the absence of the host. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G. pallida to hydration and following exposure to tomato root diffusate (RD) using microarray gene expression analysis encompassing a broad set of genes. For the quiescent eggs, 547 genes showed differential expression following hydration vs. hydratation and RD (H-RD) treatment whereas 708 genes showed differential regulation for the diapaused eggs following these treatments. The comparison between hydrated quiescent and diapaused eggs showed marked differences, with 2,380 genes that were differentially regulated compared with 987 genes following H-RD. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long-term survival. Transport activity is highly up-regulated following H-RD and few genes were coincident between both kinds of eggs. With the quiescent eggs, the majority of genes were related to ion transport (mainly sodium), while the diapaused eggs showed a major diversity of transporters (amino acid transport, ion transport, acetylcholine or other molecules).
Published: 2016

14. Analyzing Lateral Root Development : How to Move Forward

Author: University of Nottingham - Division of Plant and Crop Sciences, James Hutton Institute - Invergowrie, United Kingdom, VIB - Department of Plant Systems Biology, Ghent, Belgium, Universidad de Extremadure - Facultad de Ciencias, Spain, Utrecht University - Molecular Genetics, Utrecht, The Netherlands, Oberlin College - Biology Department, Ohio, Institut National de la Recherche Agronomique - Laboratoire des Symbioses Tropicales et Méditerranéennes, Montpellier, France, University of Bonn - Institute of Crop Science and Resource Conservation, Germany, UCL - SST/ELI/ELIA - Agronomy, De Smet, Ive, White, Philip J., Bengough, A. Glyn, Dupuy, Lionel, Parizot, Boris, Casimiro, Ilda, Heidstra, Renze, Laskowski, Marta, Lepetit, Marc, Hochholdinger, Frank, Draye, Xavier, University of Nottingham - Division of Plant and Crop Sciences, James Hutton Institute - Invergowrie, United Kingdom, VIB - Department of Plant Systems Biology, Ghent, Belgium, Universidad de Extremadure - Facultad de Ciencias, Spain, Utrecht University - Molecular Genetics, Utrecht, The Netherlands, Oberlin College - Biology Department, Ohio, Institut National de la Recherche Agronomique - Laboratoire des Symbioses Tropicales et Méditerranéennes, Montpellier, France, University of Bonn - Institute of Crop Science and Resource Conservation, Germany, UCL - SST/ELI/ELIA - Agronomy, De Smet, Ive, White, Philip J., Bengough, A. Glyn, Dupuy, Lionel, Parizot, Boris, Casimiro, Ilda, Heidstra, Renze, Laskowski, Marta, Lepetit, Marc, Hochholdinger, Frank, and Draye, Xavier
Abstract: Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.
Published: 2012

15. Characterisation of auxin-signalling genes involved in root development in barley

Author: Ghent University - VIB Department of Plant Systems Biology, The James Hutton Institute - Genetics, University of Nottingham - Centre for Plant Integrative Biology, UCL - SST/ELI/ELIA - Agronomy, Orman, Beata, Draye, Xavier, Beeckman, Tom, Waugh, Robbie, Bennett, Malcolm, Ghent University - VIB Department of Plant Systems Biology, The James Hutton Institute - Genetics, University of Nottingham - Centre for Plant Integrative Biology, UCL - SST/ELI/ELIA - Agronomy, Orman, Beata, Draye, Xavier, Beeckman, Tom, Waugh, Robbie, and Bennett, Malcolm
Published: 2012

16. Insights into the genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and its molecular determinism in rice

Author: Hue Thi Nguyen, Sophie Mantelin, Cuong Viet Ha, Mathias Lorieux, John T. Jones, Chung Duc Mai, Stéphane Bellafiore, Scottish Funding Council, University of St Andrews. School of Biology, University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. St Andrews Bioinformatics Unit, LMI RICE, Agricultural Genetics Institute, Institut de Recherche pour le Développement (IRD), Agricultural Genetics Institute (AGI), University of Science and Technology of Hanoi (USTH), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Vietnam National University of Agriculture (VNUA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), The James Hutton Institute, University of St Andrews [Scotland], Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Consultative Group for International Agricultural Research Program on rice-agrifood systems (CRP-RICE, 20172022), French National Institute for Sustainable Development (IRDFrance), International Join Laboratory (LMI-Rice 2) in Vietnam, SFC ODA GCRF award via the University of St Andrews, United Kingdom, and James Hutton Institute receives funding from the Rural and Environment Science and Analytical Services Division of the Scottish Government.
Subjects: EXPRESSION, salicylic acid, Genetic determinism, Resistance, NDAS, AFRICAN RICE, Plant Science, QH426 Genetics, resistance, SB Plant culture, DISEASE RESISTANCE, MA GENE, ROOT-KNOT NEMATODE, incompatible interaction, QH426, SB, [SDV.GEN]Life Sciences [q-bio]/Genetics, DEFENSE RESPONSE, Incompatible interaction, rice, Biology and Life Sciences, food and beverages, Salicylic acid, Root-knot nematode (Meloidogyne graminicola), SALICYLIC-ACID, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, genetic determinism, hypersensitive response (HR), CELL-DEATH, Hypersensitive response (HR), H2O2 ACCUMULATION, ORYZA-SATIVA, Rice, root-knot nematode (Meloidogyne graminicola)
Abstract: This research and HN were funded by the Consultative Group for International Agricultural Research Program on rice-agrifood systems (CRP-RICE, 2017–2022), the French National Institute for Sustainable Development (IRD–France), and the International Join Laboratory (LMI-Rice 2) in Vietnam. Funding for some parts of this work was also provided through an SFC ODA GCRF award via the University of St Andrews, United Kingdom. The James Hutton Institute receives funding from the Rural and Environment Science and Analytical Services Division of the Scottish Government. Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed. Publisher PDF
Published: 2022
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17. Pollinator monitoring more than pays for itself

Author: Rory S. O'Connor, Richard Comont, Mark Jitlal, Michael Edwards, Jodey Peyton, Kelvin Balcombe, Andy J. Musgrove, Paul Lee, Alison Bailey, Simon G. Potts, Michael P.D. Garratt, Martin Harvey, Adam J. Vanbergen, Tom D. Breeze, Roger Morris, Tom Brereton, Cathy Hawes, Catherine M. Jones, Stuart P. M. Roberts, Nick J. B. Isaac, David B. Roy, Helen E. Roy, Claire Carvell, Cuong Q. Tang, William E. Kunin, School of Agriculture, Policy and Development, University of Reading, Department Land Management and Systems, Lincoln University, Lincoln, New Zealand, Butterfly Conservation, Wareham, Bumblebee Conservation Trust, Edwards Ecological and Data Services Ltd, Wallingford, UK, School of Environment, Earth and Ecosystem Sciences [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), The James Hutton Institute, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Queen Mary University of London (QMUL), Buglife the Invertebrate Conservation Trust, Orton Waterville, UK, Department of Biology, Leeds University, Leeds, UK, Hymettus, Wallingford, UK, Hoverfly Recording Scheme, Wallingford, UK, British Trust for Ornithology (BTO), NatureMetrics, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UK Centre for Ecology HydrologyScottish GovernmentWelsh GovernmentUK Research & Innovation (UKRI)Natural Environment Research Council (NERC) NE/R016429/1, School of Agriculture, Policy and Development, University of Reading, Reading, UK, Butterfly Conservation, Wareham, UK, Bumblebee Conservation Trust, Stirling, UK, School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK, The James Hutton Institute, Dundee, UK, CENTRE FOR ECOLOGY AND HYDROLOGY WALLINGFORD UK, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., British Trust for Ornithology, Thetford, UK, and NatureMetrics Ltd, Egham, UK
Subjects: 0106 biological sciences, Pollination, [SDE.MCG]Environmental Sciences/Global Changes, power analysis, ecological economics, pollination services, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Pollinator, Economic cost, Baseline (configuration management), science polic, biodiversity policy, Service (business), Data collection, Ecology, Cost–benefit analysis, business.industry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 010604 marine biology & hydrobiology, Environmental resource management, 15. Life on land, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Data quality, biodiversity monitoring, [SDE]Environmental Sciences, pollinators, Business, cost–benefit analysis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.1. Resilient pollination services depend on sufficient abundance of pollinating insects over time. Currently, however, most knowledge about the status and trends of pollinators is based on changes in pollinator species richness and distribution only.2. Systematic, long-term monitoring of pollinators is urgently needed to provide baseline information on their status, to identify the drivers of declines and to inform suitable response measures.3. Power analysis was used to determine the number of sites required to detect a 30% change in pollinator populations over 10 years. We then evaluated the full economic costs of implementing four national monitoring schemes in the UK: (a) professional pollinator monitoring, (b) professional pollination service monitoring, (c) volunteer collected pan traps and (d) volunteer focal floral observations. These costs were compared to (a) the costs of implementing separate, expert-designed research and monitoring networks and (b) the economic benefits of pollination services threatened by pollinator loss.4. Estimated scheme costs ranged from £6,159/year for a 75-site volunteer focal flower observation scheme to £2.7 M/year for an 800-site professional pollination service monitoring network. The estimated research costs saved using the site network as research infrastructure range from £1.46–4.17 M/year. The economic value of UK crop yield lost following a 30% decline in pollinators was estimated at ~£188 M/year.5. Synthesis and applications. We evaluated the full costs of running pollinator monitoring schemes against the economic benefits to research and society they provide. The annual costs of monitoring are
Published: 2021
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18. A global database of soil nematode abundance and functional group composition

Author: Qi Li, Byron J. Adams, Christian Mulder, Larissa de Brito Caixeta, Bryan S. Griffiths, Roy Neilson, Karin Hohberg, Thomas O. Powers, Daniel G. Wright, Camille Pitteloud, Mette Vestergård, Richard D. Bardgett, David A. Wardle, Aidan M. Keith, Sergio Rasmann, Tancredi Caruso, Alan Kergunteuil, Devin Routh, Alexei V. Tiunov, Djibril Djigal, Juvenil Enrique Cares, Alexey A. Kudrin, Juan E. Palomares Rius, Rachid Bouharroud, Jean Trap, Gerard W. Korthals, Stefan Scheu, Kirsten Powers, José Mauro da Cunha e Castro, Lieven Waeyenberge, Marie Dam, Wasim Ahmad, Paul Kardol, E. Mzough, Walter Traunspurger, Cécile Villenave, El Hassan Mayad, Michael Bonkowski, Carmen Gutiérrez, Stefan Geisen, Rachel Creamer, Olaf Schmidt, Zahra Ferji, Uffe N. Nielsen, Valentyna Krashevska, Miguel Escuer, Xiaoyun Chen, Júlio Carlos Pereira da Silva, Ron G.M. de Goede, Sofia R. Costa, Loïc Pellissier, Matthew Magilton, Vlada Peneva, Wim H. van der Putten, Peter Mullin, Daria Kalinkina, E. M. Matveeva, Thomas W. Crowther, Rutger A. Wilschut, José Antonio Rodríguez Martín, Mariette Marais, Diana H. Wall, Hiroaki Okada, Anna Sushchuk, Johan van den Hoogen, Heikki Setälä, Raquel Campos-Herrera, Jiue-in Yang, Casper W. Quist, Wenju Liang, Kaiwen Pan, Sara Sanchez Moreno, Howard Ferris, T. A. Duong Nguyen, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Department of Biology [Fort Collins], Colorado State University [Fort Collins] (CSU), Nanyang Technological University [Singapour], Universität Bielefeld = Bielefeld University, Wageningen University and Research [Wageningen] (WUR), Brigham Young University (BYU), Aligarh Muslim University, University of California [Davis] (UC Davis), University of California (UC), University of Manchester [Manchester], University of Cologne, Instituto de Ciencias de la Vid y el Vino (ICVV), Universidad de La Rioja (UR)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Institute of Biology of the University of Neuchâtel, Université de Neuchâtel (UNINE), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013-43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849)., DOB Ecology, Netherlands Organization for Scientific Research, Ministerio de Economía y Competitividad (España), National Science Foundation (US), European Commission, Natural Environment Research Council (UK), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), German Research Foundation, Ministry of Science and Higher Education of the Russian Federation, Chinese Academy of Sciences, National Natural Science Foundation of China, German Academic Exchange Service, National Foundation for Science and Technology Development (Vietnam), National Key Research and Development Program (China), European Research Council, Bureau of Animal and Plant Health Inspection and Quarantine (Taiwan), Russian Foundation for Basic Research, James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, University of California, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Data Descriptor, Nematoda, Ecosystem ecology, Biome, 010501 environmental sciences, computer.software_genre, 01 natural sciences, Soil, Abundance (ecology), Data and Information, lcsh:Science, biology, Ecology, Biodiversity, Soil Biology, PE&RC, Biosystematiek, Computer Science Applications, Biogeography, 1181 Ecology, evolutionary biology, Composition (visual arts), Statistics, Probability and Uncertainty, Information Systems, Statistics and Probability, Biogeochemical cycle, EXTRACTION, Geospatial analysis, Soil test, Library and Information Sciences, Education, Life Science, Animals, Functional group (ecology), Life Below Water, Bodembiologie, Ecosystem, 0105 earth and related environmental sciences, 15. Life on land, biology.organism_classification, Nematode, Biology and Microbiology, 13. Climate action, Nematoda/classification, Biosystematics, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Animal Distribution, 010606 plant biology & botany
Abstract: As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/ M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013- 43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849).
Published: 2020
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19. FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

Author: Cock, Peter [The James Hutton Institute, Dundee (United Kingdom)]
Published: 2016
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20. The functional trait spectrum of European temperate grasslands

Author: Bernard Amiaud, Nadejda A. Soudzilovskaia, Helge Bruelheide, Costantino Bonomi, Bruno Enrico Leone Cerabolini, Maria Tudela‐Isanta, Pietro P. M. Iannetta, Sabina Burrascano, Jitka Klimešová, Kinga Öllerer, Joseph M. Craine, Vladimir G. Onipchenko, Emma Ladouceur, Andrea Mondoni, Frédérique Louault, Borja Jiménez-Alfaro, Peter Poschlod, Vanessa Minden, Johannes H. C. Cornelissen, Ladouceur, Emma, German Centre for Integrative Biodiversity Research (iDiv), Museo delle Scienze, German Centre for Integrative Biodiversity Research, Academy of Sciences of the Czech Republic, Università degli Studi di Roma 'La Sapienza' [Rome], Department of Ecology and Conservation Biology, University of Regensburg, Department of Earth and Environmental Sciences, Université Catholique de Louvain (UCL), Ecological Sciences, James Hutton Institute (JHI), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Department of Theoretical and Applied Sciences, Università degli Studi dell' Insubria, Department of Ecological Science [Amsterdam], Vrije Universiteit [Brussels] (VUB), Jonah Ventures, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Oldenburg, Institute of Biology Bucharest, Romanian Academy, Moscow State University, Leiden University, Universidad de Oviedo, European Union (EU) 607785, Systems Ecology, Biology, European Commission, Czech Academy of Sciences [Prague] (CAS), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Université Catholique de Louvain = Catholic University of Louvain (UCL), The James Hutton Institute, and Vrije Universiteit Brussel (VUB)
Subjects: 0106 biological sciences, regeneration niche, caractère fonctionnel, seed traits, Biodiversité et Ecologie, clonality, Plant Science, Biology, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, species pool, Grassland, Biodiversity and Ecology, specialist species, Altitude, functional traits, germination, grasslands, trait spectrum, clonalité, Regeneration (ecology), SDG 15 - Life on Land, 2. Zero hunger, geography, geography.geographical_feature_category, caractères fonctionnels, prairie, niche de régénération, bassin d'espèces, spectre des caractères, Ecology, grasslands regeneration, clonalite, food and beverages, 15. Life on land, niche, Habitat, Disturbance (ecology), Trait, Ordination, grassland, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: Questions: What is the functional trait variation of European temperate grasslands and how does this reflect global patterns of plant form and function? Do habitat specialists show trait differentiation across habitat types?. Location: Europe. Methods: We compiled 18 regeneration and non-regeneration traits for a continental species pool consisting of 645 species frequent in five grassland types. These grassland types are widely distributed in Europe but differentiated by altitude, soil bedrock and traditional long-term management and disturbance regimes. We evaluated the multivariate trait space of this entire species pool and compared multi-trait variation and mean trait values of habitat specialists grouped by grassland type. Results: The first dimension of the trait space accounted for 23% of variation and reflected a gradient between fast-growing and slow-growing plants. Plant height and SLA contributed to both the first and second ordination axes. Regeneration traits mainly contributed to the second and following dimensions to explain 56% of variation across the first five axes. Habitat specialists showed functional differences between grassland types mainly through non-regeneration traits. Conclusions: The trait spectrum of plants dominating European temperate grasslands is primarily explained by growth strategies which are analogous to the trait variation observed at the global scale, and secondly by regeneration strategies. Functional differentiation of habitat specialists across grassland types is mainly related to environmental filtering linked with altitude and disturbance. This filtering pattern is mainly observed in non-regeneration traits, while most regeneration traits demonstrate multiple strategies within the same habitat type., EL, BJA, MTI, AM, PI and CB acknowledge the research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013 under REA grant agreement no. 607785, as a part of the NAtive Seed Science TEchnology and Conservation (NASSTEC) Initial Training Network (ITN). BJA was further funded by the Marie Curie Clarín‐COFUND program of the Principality of Asturias and the European Union (ACB17‐26). BJA and HB acknowledge support from the German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig funded by the German Research Foundation (DFTG FZT 118) through the sPlot research platform. PI acknowledges support from the Rural & Environment Science & Analytical Services Division of the Scottish Government. KÖ thanks RO1567‐IBB03/2018 for financial support.
Published: 2019
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21. Whole genome analyses suggests that Burkholderiasensu lato contains two additional novel genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae

Author: Ethan A. Humm, Ann M. Hirsch, Philip S. Poole, Chrizelle W. Beukes, Fábio Bueno dos Reis Junior, Marcel Lafos, Stephanus N. Venter, Paulina Estrada-de los Santos, Nicole Shapiro, Belén Chávez-Ramírez, Euan K. James, Marike Palmer, Marcelo F. Simon, Matthew B. Crook, William B. Whitman, Eduardo Gross, Emma Theodora Steenkamp, Noor Ullah Khan, Marta Maluk, Leah Briscoe, Monique Arrabit, Paulina Estrada-de los Santos, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológica, Marike Palmer, University of Pretoria, Belén Chávez-Ramírez, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Chrizelle Beukes, University of Pretoria, Emma T. Steenkamp, University of Pretoria, Leah Briscoe, University of California, Noor Khan, University of California, Marta Maluk, The James Hutton Institute, Marcel Lafos, The James Hutton Institute, Ethan Humm, University of California, Monique Arrabit, University of California, Matthew Crook, Weber State University, Eduardo Gross, Santa Cruz State University, MARCELO FRAGOMENI SIMON, Cenargen, FABIO BUENO DOS REIS JUNIOR, CPAC, William B. Whitman, University of Georgia, Nicole Shapiro, Walnut Creek, Philip S. Poole, University of Oxford, Ann M. Hirsch, University of California, Stephanus N. Venter, University of Pretoria, and Euan K. James, The James Hutton Institute.
Subjects: 0301 basic medicine, Burkholderiaceae, food.ingredient, Mimosa, Análise Comparativa, lcsh:QH426-470, Burkholderia, root nodulation, Biology, Genome, Paraburkholderia, Article, 03 medical and health sciences, diazotrophy, food, Sensu, parasitic diseases, Genetics, Caballeronia, Genetics (clinical), symbionts, Genoma, Phylogenetic tree, Rhizopus, fungi, Genes conservados, 15. Life on land, Robbsia, biology.organism_classification, 16S ribosomal RNA, bacterial infections and mycoses, lcsh:Genetics, 030104 developmental biology, Filogenia, Taxonomy (biology)
Abstract: Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4&ndash, 7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits&mdash, diazotrophy and/or symbiotic nodulation, and pathogenesis&mdash, were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-&agrave, vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.
Published: 2018
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22. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Author: Zhang, Runxuan, Calixto, Cristiane P.G., Marquez, Yamile, Venhuizen, Peter, Tzioutziou, Nikoleta A., Guo, Wenbin, Spensley, Mark, Entizne, Juan Carlos, Lewandowska, Dominika, ten Have, Sara, Frei dit Frey, Nicolas, Hirt, Heribert, James, Allan B., Nimmo, Hugh G., Barta, Andrea, Kalyna, Maria, Brown, John W.S., Informatics and Computational Sciences, The James Hutton Institute, Plant Sciences Division, College of Life Sciences, University of Dundee, Max Perutz Labs, University of Vienna [Vienna], The Donnelly Centre, University of Toronto, Cell and Molecular Sciences, Centre for Gene Regulation and Expression, School of Life Sciences Dundee, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université d'Evry Val d'Essonne, Institute of MoleculCell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Department of Applied Genetics and Cell Biology, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K013661/1, BB/K006568/1, BB/K006835/1], Scottish Government Rural and Environment Science and Analytical Services division (RESAS), Austrian Science Fund (FWF) [P26333, DK W1207], LABEX Saclay Plant Sciences, BBSRC EASTBIO PhD studentships, European Alternative Splicing Network of Excellence (EURASNET) [LSHG-CT-2005-518238], James Hutton Institute, Max F. Perutz Laboratories, Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paul Sabatier - Toulouse 3 ( UPS ), Institut des Sciences des Plantes de Paris-Saclay ( IPS2 ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), University of Natural Resources and Life Sciences, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, RNA, Untranslated, Transcription, Genetic, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, [SDV]Life Sciences [q-bio], Arabidopsis, Sequence analysis, Genetic Variation, Reproducibility of Results, Genes, Insect, Data Resources and Analyses, Reference Values, Transcriptome, Alternative splicing
Abstract: Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
Published: 2017
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23. Similar estimates of temperature impacts on global wheat yield by three independent methods

Author: Frank Ewert, Jakarat Anothai, P. V. Vara Prasad, Davide Cammarano, Curtis D. Jones, Elias Fereres, Margarita Garcia-Vila, Soora Naresh Kumar, Eckart Priesack, Phillip D. Alderman, Andrew J. Challinor, Reimund P. Rötter, Alex C. Ruane, Christian Folberth, Gerrit Hoogenboom, Pierre Martre, Roberto C. Izaurralde, Fulu Tao, Pramod K. Aggarwal, Mohamed Jabloun, Jordi Doltra, Joshua Elliott, Christoph Müller, Bing Liu, Iurii Shcherbak, Jeffrey W. White, Bruno Basso, Senthold Asseng, Pierre Stratonovitch, Peter J. Thorburn, Claas Nendel, Taru Palosuo, Joost Wolf, Ann-Kristin Koehler, Thilo Streck, Jørgen E. Olesen, David B. Lobell, Kurt Christian Kersebaum, Delphine Deryng, L. A. Hunt, Garry O'Leary, Katharina Waha, Giacomo De Sanctis, Daniel Wallach, Yan Zhu, James W. Jones, Elke Stehfest, Mikhail A. Semenov, Christian Biernath, Claudio O. Stöckle, Thomas A. M. Pugh, Matthew P. Reynolds, Enli Wang, Bruce A. Kimball, Erwin Schmid, Iwan Supit, Zhigan Zhao, Michael J. Ottman, Sebastian Gayler, Cynthia Rosenzweig, Ehsan Eyshi Rezaei, Gerard W. Wall, National Engineering and Technology Center for Information Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Potsdam Institute for Climate Impact Research (PIK), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Leibniz Association, Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], Computation Institute, Loyola University of Chicago, Department of Environmental Earth System Science and Center on Food Security and the Environment, Stanford University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, CGIAR Research Program on Climate Change, Agriculture and Food Security, Borlaug Institute for South Asia, CIMMYT, Consultative Group on International Agricultural Research (CGIAR), Department of Plant and Soil Sciences, Mississippi State University [Mississippi], Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University (PSU), Department of Geological Sciences, University of Oregon [Eugene], W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Institute of Soil Ecology [Neuherberg] (IBOE), Helmholtz-Zentrum München (HZM), The James Hutton Institute, Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, CGIAR-ESSP Program on Climate Change, Agriculture and Food Security, International Center for Tropical Agriculture, European Commission - Joint Research Centre [Ispra] (JRC), Cantabrian Agricultural Research and Training Centre, Department of Agronomy, Purdue University [West Lafayette], Department of Geography, University of Liverpool, Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Institute of Soil Science and Land Evaluation, University of Hohenheim, AgWeatherNet Program, Washington State University (WSU), Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], US Arid-Land Agricultural Research Center, United States Department of Agriculture, Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Landscape & Water Sciences, Department of Environment of Victoria, The School of Plant Sciences, University of Arizona, Natural resources institute Finland, Institute of Ecology, German Research Center for Environmental Health, Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung (IMK-IFU), Karlsruher Institut für Technologie (KIT), School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Birmingham Institute of Forest Research (BIFoR), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Center for Development Research (ZEF), Environmental Impacts Group, Georg-August-University [Göttingen], Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Computational and Systems Biology Department, Rothamsted Research, Biotechnology and Biological Sciences Research Council, Netherlands Environmental Assessment Agency, Department of Biological Systems Engineering, University of Wisconsin-Madison, PPS, WSG and CALM, Wageningen University and Research [Wageningen] (WUR), Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences [Beijing] (CAS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), USDA-ARS, Arid-Land Agricultural Research Center, China Agricultural University (CAU), National High-Tech Research and Development Program of China (2013AA100404), the National Natural Science Foundation of China (31271616, 31611130182, 41571088 and 31561143003), the National Research Foundation for the Doctoral Program of Higher Education of China (20120097110042), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), China Scholarship Council., IFPRI through the Global Futures and Strategic Foresight project, the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), the CGIAR Research Program on Wheat, the Agricultural Model Intercomparison and Improvement Project (AgMIP), Agricultural & Biological Engineering Department, University of Florida [Gainesville], Institute of Crop Science and Resource Conservation, University of Bonn-Division of Plant Nutrition, Stanford University [Stanford], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Prince of Songkla University, Texas A&M AgriLife Research and Extension Center, Natural Resources Institute Finland, Georg-August-Universität Göttingen, Wageningen University and Research Center (WUR), China Agricultural University, Division of Plant Nutrition-University of Bonn, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), University of Florida, Potsdam Institute for Climate Impact Research ( PIK ), Leibniz Centre for Agricultural Landscape Research, Institute for Landscape Biogeochemistry, Center for Climate Systems Research [New York] ( CCSR ), Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), Institut National de la Recherche Agronomique ( INRA ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), NASA Goddard Institute for Space Studies ( GISS ), NASA Goddard Space Flight Center ( GSFC ), Consultative Group on International Agricultural Research ( CGIAR ), W.K. Kellogg Biological Station, Institute of Soil Ecology [Neuherberg] ( IBOE ), Helmholtz-Zentrum München ( HZM ), James Hutton Institute, Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, European Commission - Joint Research Centre [Ispra] ( JRC ), International Institute for Applied Systems Analysis ( IIASA ), Washington State University ( WSU ), Texas A and M University ( TAMU ), Leibniz Centre for Agricultural Landscape Research (ZALF), Centre for Environment Science and Climate Resilient Agriculture ( CESCRA ), Indian Agricultural Research Institute ( IARI ), Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung ( IMK-IFU ), Karlsruher Institut für Technologie ( KIT ), School of Geography, Earth & Environmental Science and Birmingham Institute of Forest Research, University of Birmingham, International Maize and Wheat Improvement Center ( CIMMYT ), Bonn Universität [Bonn], University of Natural Resources and Life Sciences, University of Wisconsin-Madison [Madison], Wageningen University and Research Center ( WUR ), Chinese Academy of Sciences [Beijing] ( CAS ), Commonwealth Scientific and Industrial Research Organisation, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Université de Toulouse (UT)-Université de Toulouse (UT), Helmholtz Zentrum München = German Research Center for Environmental Health, Natural Resources Institute Finland (LUKE), Georg-August-University = Georg-August-Universität Göttingen, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Biotechnology and Biological Sciences Research Council (BBSRC), and Institute of geographical sciences and natural resources research [CAS] (IGSNRR)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, régression statistique, 010504 meteorology & atmospheric sciences, impact sur le rendement, klim, Atmospheric sciences, 01 natural sciences, incertitude, wheat, uncertainty, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 2. Zero hunger, changement climatique, Regression analysis, statistical regression, simulation, PE&RC, [ SDE.MCG ] Environmental Sciences/Global Changes, sécurité alimentaire, Plant Production Systems, modèle de récolte, Yield (finance), comparaison de modèles, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, Environmental Science (miscellaneous), Earth System Science, blé, température, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, réchauffement climatique, global change, 0105 earth and related environmental sciences, Hydrology, WIMEK, Global temperature, business.industry, Crop yield, Global warming, Climate Resilience, 13. Climate action, Agriculture, Klimaatbestendigheid, Plantaardige Productiesystemen, Environmental science, Leerstoelgroep Aardsysteemkunde, Climate model, business, Social Sciences (miscellaneous), 010606 plant biology & botany
Abstract: The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security. The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security.
Published: 2016
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24. Temperature effects on fish production across a natural thermal gradient

Author: O'Gorman, EJ, Ólafsson, OP, Demars, BOL, Friberg, N, Guðbergsson, G, Hannesdóttir, ER, Jackson, MC, Johansson, LS, McLaughlin, OB, Ólafsson, JS, Woodward, G, Gíslason, GM, Department of Life Sciences [Trieste], Università degli studi di Trieste, Institute of Life and Environmental Sciences, University of Iceland, The James Hutton Institute, Norwegian Institute for Water Research (NIVA), Institute of Freshwater Fisheries, Centre for Invasion Biology, Department of Zoology and Entomology, University of Pretoria (UPSpace), Department of Bioscience, Aarhus University [Aarhus], Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), NERC [NE/L011840/1, NE/I009280/2], Royal Society [RG140601], British Ecological Society [4009-4884], Fisheries Society of the British Isles, Grand Challenges in Ecosystems, Environment initiative at Imperial College London, Scottish Government Rural and Environment Science and Analytical Services (RESAS), Salmonid Fisheries Management Fund in Reykjavik, Assistantship and Research Funds from the University of Iceland [GMG2006, GMG2007], Department of Life Sciences, Universita di Trieste, James Hutton Institute, Norwegian Institute of Water Research, University of Pretoria ( UPSpace ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Líf- og umhverfisvísindadeild (HÍ), Faculty of Life and Environmental Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, Natural Environment Research Council (NERC), and The Royal Society
Subjects: Hengill, Food Chain, Trout, Tilraunir, [SDV]Life Sciences [q-bio], 05 Environmental Sciences, Iceland, Vistfræði, Salmo trutta fario, PIT tag, Silungur, Arctic, FRESH-WATER ECOSYSTEMS, FOOD-WEB STRUCTURE, GEOTHERMALLY HEATED STREAM, Animals, Primary Research Article, TROUT SALMO-TRUTTA, freshwater, Ecosystem, natural experiment, BODY-SIZE, CLIMATE-CHANGE, Ecology, [ SDV ] Life Sciences [q-bio], Temperature, mark‐recapture, 06 Biological Sciences, Primary Research Articles, ONCORHYNCHUS-MYKISS, Diet, EMERGING AQUATIC INSECTS, YELLOWSTONE-NATIONAL-PARK, Vatn, JUVENILE BROWN TROUT, ecosystem services, mark-recapture
Abstract: Global warming is widely predicted to reduce the biomass production of top predators, or even result in species loss.Several exceptions to this expectation have been identiﬁed, however, and it is vital that we understand the underlyingmechanisms if we are to improve our ability to predict future trends. Here, we used a natural warming experiment inIceland and quantitative theoretical predictions to investigate the success of brown trout as top predators across astream temperature gradient (4–25 °C). Brown trout are at the northern limit of their geographic distribution in thissystem, with ambient stream temperatures below their optimum for maximal growth, and above it in the warmeststreams. A ﬁve-month mark-recapture study revealed that population abundance, biomass, growth rate, and produc-tion of trout all increased with stream temperature. We identiﬁed two mechanisms that contributed to theseresponses: (1) trout became more selective in their diet as stream temperature increased, feeding higher in the foodweb and increasing in trophic position; and (2) trophic transfer through the food web was more efﬁcient in the war-mer streams. We found little evidence to support a third potential mechanism: that external subsidies would play amore important role in the diet of trout with increasing stream temperature. Resource availability was also ampliﬁedthrough the trophic levels with warming, as predicted by metabolic theory in nutrient-replete systems. These resultshighlight circumstances in which top predators can thrive in warmer environments and contribute to our knowledgeof warming impacts on natural communities and ecosystem functioning., The authors are supported by grants awarded by NERC (NE/L011840/1 and NE/I009280/2), the Royal Society (RG140601), the British Ecological Society (4009-4884), the Fisheries Society of the British Isles, the Grand Challenges in Ecosystems and the Environment initiative at Imperial College London, the Scottish Government Rural and Environment Science and Analytical Services (RESAS), the Salmonid Fisheries Management Fund in Reykjavik, and Assistantship and Research Funds from the University of Iceland (GMG2006, GMG2007)., Ritrýnt tímarit
Published: 2016
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25. What are heritage values? Integrating natural and cultural heritage into environmental valuation

Author: Elaine Azzopardi, Jasper O. Kenter, Juliette Young, Chris Leakey, Seb O'Connor, Simone Martino, Wesley Flannery, Lisa P. Sousa, Dimitra Mylona, Katia Frangoudes, Irène Béguier, Maria Pafi, Arturo Rey da Silva, Jacob Ainscough, Manos Koutrakis, Margarida Ferreira da Silva, Cristina Pita, University of York [York, UK], University College of Wales [Aberystwyth], Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), NatureScot Perth UK, University of Leeds, Leeds, UK, The James Hutton Institute, Aberdeen, UK, Queen's University [Belfast] (QUB), Civil Engineering Department, University of Aveiro, Aveiro, Portugal, Center for East Crete, Greece, University of Brest, Brest, France, Parc Naturel Régional du Golfe du Morbihan France, University of Edinburgh France, University, Lancaster, UK, Environment and Development (IIED), London, UK, PERICLES has received funding from the European CommissionUnion's Horizon 2020 Research and Innovation programme underGrant Agreement No. 770504. EA was supported by the UK NaturalEnvironment Research Council (NE/S00713X/1). LS and CP acknowledge FCT/MCTES for the financial support to CESAM (UIDP/50017/2020+UIDB/50017/2020), through national funds. MFS acknowledges the Portuguese Foundation for Science and Technology(FCT) for her PhD Grant (SFRH/BD/145485/2019) and FCT/MCTESfor the financial support to GOVCOPP (UIDB/04058/2020)+(UIDP/04058/2020), through national funds., and European Project: 770504,PERICLES
Subjects: plural values, [SDV]Life Sciences [q-bio], participatory research, Life Framework of Values, ecosystem services, nature's contributions to people, Ecology, Evolution, Behavior and Systematics, culture, heritage
Abstract: International audience; There are strong links between heritage and the environment yet, heritage is not fully included in existing ecosystem-based frameworks. Different understandings of heritage values exist, and heritage values are not yet related to key value categories in environmental values research.To address this gap and facilitate a common values-based approach, we develop a novel framework that links heritage and environmental values. First, we expand the understanding of heritage values by linking heritage to key environmental value categories. We then use the Life Framework of Values to show how heritage features in the different ways in which people relate to the world.The resulting heritage values framework is operationalised by applying it to six case examples drawn from participatory research on the governance of European coastal and maritime heritage.We found that the environment was not only considered to be a setting for heritage but was itself valued as heritage in different ways; that heritage is not extrinsic to the environment but is also a way in which people see meaning in the environment; and that multiple value frames and types were involved in shaping this perspective. The results highlight important discrepancies between stakeholders' perspectives and existing management approaches.Applying the framework shows the ways in which heritage and nature are entwined by providing a structure for elucidating what can be valued as heritage, what values can inform heritage values and how heritage values feature in human–nature relations.
Published: 2022
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26. Paraburkholderia atlantica is the main rhizobial symbiont of Mimosa spp. in ultramafic soils in the Brazilian Cerrado biome

Author: Clemente Batista Soares Neto, Paula Rose Almeida Ribeiro, Paulo Ivan Fernandes-Júnior, Leide Rovenia Miranda de Andrade, Jerri Edson Zilli, Ieda Carvalho Mendes, Helson Mario Martins do Vale, Euan Kevin James, Fábio Bueno dos Reis Junior, CLEMENTE BATISTA SOARES NETO, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, PAULA ROSE ALMEIDA RIBEIRO, PAULO IVAN FERNANDES JUNIOR, CPATSA, LEIDE ROVENIA MIRANDA DE ANDRADE, CPAC, JERRI EDSON ZILLI, CNPAB, IEDA DE CARVALHO MENDES, CPAC, HELSON MARIO MARTINS DO VALE, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, EUAN KEVIN JAMES, The James Hutton Institute, Invergowrie, UK, and FABIO BUENO DOS REIS JUNIOR, CPAC.
Subjects: Bioma Cerrado, Solo, Soil, Paraburkholderia atlantica, Bactéria, Nitrogen fixation, Mimosa spp, Soil Science, Cerrado, Plant Science, Fixação de Nitrogênio
Abstract: Aim to evaluate the occurrence, the characterization and identity of nodulating bacteria in symbiosis with Mimosa spp. in the ultramafic massif of Barro Alto, Goiás state, Brazil. Made available in DSpace on 2022-06-15T15:19:21Z (GMT). No. of bitstreams: 1 Paraburkholderia-atlantica-is-the-main-rhizobial-symbiont-2022.pdf: 1199919 bytes, checksum: 665ad3d4500ad286057cb9fb81e4b430 (MD5) Previous issue date: 2022 On-line.
Published: 2022
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27. Multi-purpose PVX : presentation and expression of enzymes and VLPs

Author: Burnett, David Alexander, Tilsner, Jens, Goss, Rebecca J., University of St Andrews. School of Biology, University of St Andrews. School of Chemistry, and James Hutton Institute
Subjects: FOS: Nanotechnology, Plant virus, Enzymatic nanoparticles, Nanotechnology, Viral nanoparticles, PVX
Abstract: Viral nanoparticles represent ideal nanomaterials, they replicate to high numbers, self-assemble into defined structures, and have many options for functionalisation. Presentation of heterologous peptides and proteins on the surface of nanoparticles is an area of growing research interest with far-ranging applications from vaccines to biocatalysts. Plant viral particles represent ideal candidates for this purpose as they are non-infectious to humans, replicate to extremely high titres and can be produced relatively cheaply. This study aims to investigate the potential of Potato virus X (PVX) as a platform for the presentation of enzymes in order to generate catalytically active nanoparticles. Presentation of enzymes on nanoparticles has the potential to increase the stability, reusability, and reaction rate of presented enzymes. This thesis also aims to investigate the ability of PVX to provide whole plant systemic overexpression of heterologous proteins and viral like particles. The knowledge gained is important to further development of plant viral nanoparticles as a technology and to the utilisation of PVX as a nanomaterial.
Published: 2023

28. Field testing of IPM-based cropping systems: a diversity of experimental approaches in Europe

Author: Lechenet, Martin, Deytieux, Violaine, Antichi, Daniele, Aubertot, Jean-Noel, Bàrberi, Paolo, Bertrand, Michel, Cellier, Vincent, Charles, Raphaël, Colnenne-David, Caroline, Dachbrodt-Saaydeh, Silke, Debaeke, Philippe, Doré, Thierry, Farcy, Pascal, Fernández-Quintanilla, César, Grandeau, Gilles, Hawes, Cathy, Jouy, lionel, Justes, Eric, Kierzek, Roman, Kudsk, Per, Lamichhane, Jay Ram, Mazzoncini, Marco, Melander, Bo, Moonen, Anna Camilla, Newton, Adrian C, Nolot, Jean Marie, Panozzo, Silvia, retaureau, patrick, Sattin, Maurizio, Schwarz, Juergen, toque, clotilde, Vasileiadis, Vasileios, Munier-Jolain, Nicolas, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Domaine expérimental d'Époisses (DIJ EPOISSES), Institut National de la Recherche Agronomique (INRA), Centro di Ricerche Agro-Ambientali Enrico Avanzi (CIRAA), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute of Life Sciences, Scuola Superiore Sant'Anna [Pisa], Agronomie, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institute for Plant Production Sciences, Agroscope, Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), The James Hutton Institute, ARVALIS - Institut du végétal [Paris], Weed Science and Plant Protection Department, National Research Institute Władysława Węgorka, Aarhus University [Aarhus], Unité Impacts Ecologiques des Innovations en Production Végétale (ECO-INNOV), Institute of agroenvironmental and forest biology (CNR-IBAF), Doré, Thierry, Domaine expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Domaine expérimental d'Époisses ( DIJ EPOISSES ), Institut National de la Recherche Agronomique ( INRA ), Centro di Ricerche Agro-Ambientali Enrico Avanzi ( CIRAA ), Università di Pisa, AGrosystèmes et développement terrItoRial ( AGIR ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Julius Kühn Institute ( JKI ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), James Hutton Institute, Unité Impacts Ecologiques des Innovations en Production Végétale ( ECO-INNOV ), and Institute of agroenvironmental and forest biology ( CNR-IBAF )
Subjects: [SDV] Life Sciences [q-bio], [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience; Integrated Pest Management (IPM) emphasizes physical and biological regulation strategies to control pests while reducing the reliance on pesticides. It is often based on combinations of control measures, because each available alternative measure might have a moderate efficiency. Field experiments are required to analyse the interactions between control measures, and to evaluate the sustainability of IPM-based cropping systems (CS). A network of European agronomists managing field experiments at the CS level was set recently, aiming at sharing data and expertise to enhance our knowledge on IPM. Comparing methodologies highlighted a diversity of approaches in CS design and experimental layouts. This diversity is partly related with the research context and objectives. Some experiments intend to explore really innovative strategies and gain scientific knowledge about how such innovative CS behave, while others aim at providing quickly adoptable solutions for local farmers. In some research programs, the experiment is part of the CS design process, and tested CS are regularly revised, while in other cases CS are kept stable across years so as to be able to evaluate cumulative long term effects. The concept of CS itself is viewed differently across scientists, and this affects protocols: some consider each CS as a sequence of techniques, which has to be similar across repetitions, others define a CS as a set of decision-making rules that allows a flexibility in the actual sequences of techniques. The main difference among experiments differentiates factorial layouts from systemic approaches: factorial experiments make it possible to quantify the effects of each IPM factor, and to analyse the interactions, without particular attention for the consistency among components constituting each CS. On the contrary, system approach focuses on the overall evaluation of CS designed with a great attention paid to their consistency, hence maximizing the chance to meet the system objectives (in the case of IPM, to use little amount of pesticide while maintaining the CS sustainability). Such field experiments are costly, so preliminary reflections defining the experimental strategy have a critical importance. Networking at the European level may constitute a useful exchange platform with potential scientific added value.
Published: 2015

29. WHEALBI: Wheat and barley legacy for breeding improvement; A EU-FP7 Project to link genomics and agronomy

Author: Charmet, Gilles, Stein, Nils, Russell, Joanne, Waugh, Robbie, Cattivelli, Luigi, Bink, Marco, Keller, Beat, Lage, Jacob, Morris, Nathan, Crepieux, Sebastien, Lagendijk, Emmanuelle, Pendu, Ronan, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Leibniz Institute of Plant Genetics and Crop Plant Research, The James Hutton Institute, Consiglio per la Ricerca e Sperimentazione in Agricoltura, DLO-Research Institute for Plant Protection, Universität Zürich, KWS-UK, National Institute of Agricultural Botany (NIAB), ARCADIA International, INRA-transfert SA, James Hutton Institute (JHI), ProdInra, Archive Ouverte, INRA Transfert, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV] Life Sciences [q-bio], blé dur, [SDV]Life Sciences [q-bio], hard wheat, orge
Abstract: Book of abstracts, p. 108Book of abstracts, p. 108; WHEALBI: Wheat and barley legacy for breeding improvement; A EU-FP7 Project to link genomics and agronomy. Recent progress in drought tolerance: from genetics to modelling
Published: 2015

30. World's soils are under threat

Author: Dan Pennock, Suk Young Hong, Gan-Lin Zhang, F.O. Nachtergaele, Martin Yemefack, Isaurinda Baptista, Abdullah Alshankiti, Victor Chude, Pavel Krasilnikov, Luca Montanarella, David Espinosa-Victoria, Helaina Black, Dominique Arrouays, Jon Hempel, Marta Camps Arbestain, Sayed Kazem Alavipanah, Mohamed Badraoui, Ronald Vargas, Elsiddig A.E. Elsheikh, Maria de Lourdes Mendonça-Santos, Kazuyuki Yagi, Miguel Angel Taboada, Julio Alegre, Neil McKenzie, Tekalign Mamo, Mikha Singh Aulakh, Carlos Henríquez, Pisoot Vijarnsorn, Jaroslava Sobocka, European Commission - Joint Research Centre [Ispra] (JRC), College of Agriculture and Bioresources, University of Saskatchewan [Saskatoon] (U of S), Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Institut national de la recherche agronomique [Maroc] (INRA Maroc), National Programme for Food Security, Instituto Nacional de Invesgaçao e Desenvolvimento Agrario (INIDA), Ministry of Agriculture, International Institute of Tropical Agriculture, Institut de Recherche Agricole pour le Développement [Yaoundé] (IRAD), Banda University of Agriculture & Technology, National Institute of Agro-Environmental Sciences (NIAES), National Academy of Agricultural Science, Chaipattana Foundation, State Key Laboratory of Soil and Sustainable Agriculture, InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), Ecological Sciences Group, The James Hutton Institute, Eurasian Center for Foof Security, Lomonosov Moscow State University (MSU), Institute of Biology, Karelian Research Center, National Agricultural and Food Centre, Soil Science and Conservation Research Institute, Departemento de Suelos, National Agrarian University, Centro de Investigaciones Agronómicas (CIAS), Universidad Nacional de Costa Rica, The National Centre of Soil Research, Brazilian Agricultural Research Corporation (Embrapa), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Instituto de Suelos, Colegio de Postgraduados (CP), International Center for Biosaline Agriculture (ICBA), Department of Remote Sensing and GIS, University of Tehran, Department of Soil & Environment Sciences, University of Khartoum, NRCS National Soil Survey Center, United States Department of Agriculture, Institute of Agriculture and Environment, Food and Agriculture Organization of the United Nations, European Commission, CSIRO, Institut National de la Recherche Agronomique du Maroc (INRA), International Institute of Tropical Agriculture (IITA), Banda University of Agriculture and Technology, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences [Changchun Branch] (CAS), Unité INFOSOL (ORLEANS INFOSOL), Eurasian Center for Food Security, Departamento de Suelos, Universidad Autónoma de Chapingo, Colegio de Postgraduados, USDA-NRCS ational Soil Survey Center, Food and Agricultural Organization (FAO), International Institute of Tropical Agriculture (IITA-DRC), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Universidad Autónoma de Chapingo (UACh), FAO Sub-regional Office for Eastern Africa [Addis Ababa, Ethiopie] (FAO), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Institut de Recherche Agricole pour le Développement (IRAD), LUCA MONTANARELLA, European Commission, DANIEL JON PENNOCK, University of Saskatchewan, NEIL MCKENZIE, CSIRO Agriculture Flagship, MOHAMED BADRAOUI, INRA, VICTOR CHUDE, National Programme for Food Security, ISAURINDA BAPTISTA, Instituto Nacional de Investigação e Desenvolvimento Agrário, TEKALIGN MAMO, Ministry of Agriculture, Ethiopia, MARTIN YEMEFACK, International Institute of Tropical Agriculture, MIKHA SINGH AULAKH, Banda University of Agriculture & Technology, KAZUYUKI YAGI, National Institute for Agro-Environmental Sciences, SUK YOUNG HONG, National Academy of Agricultural Science, PISOOT VIJARNSORN, Chaipattana Foundation, Bangkok, GAN-LIN ZHANG, Chinese Academy of Sciences, DOMINIQUE ARROUAYS, INRA, HELAINA BLACK, The James Hutton Institute, Craigiebuckler, PAVEL KRASILNIKOV, Lomonosov Moscow State University, JAROSLAVA SOBOCKÁ, Soil Science and Conservation Research Institute, Bratislava, JULIO ALEGRE, National Agrarian University, La Molina, Peru, CARLOS ROBERTO HENRIQUEZ, Universidad de Costa Rica, San Pedro, MARIA DE LOURDES M SANTOS BREFIN, CNPS, MIGUEL TABOADA, Instituto de Suelos and CONICET, CIRN, INTA, DAVID ESPINOSA-VICTORIA, Colegio de Postgraduados, Mexico City, ABDULLAH ALSHANKITI, International Center for Biosaline Agriculture (ICBA), Dubai, SAYED KAZEM ALAVIPANAH, University of Tehran, Iran, ELSIDDIG AHMED EL MUSTAFA ELSHEIKH, University of Khartoum, Republic of the Sudan, JON HEMPEL, USDA-NRCS National Soil Survey Center, MARTA CAMPS ARBESTAIN, Institute of Agriculture and Environment, Massey Agriculture, FREDDY NACHTERGAELE, FAO, and RONALD VARGAS, FAO.
Subjects: Soil biodiversity, [SDV]Life Sciences [q-bio], Soil Science, 010501 environmental sciences, 01 natural sciences, 050601 international relations, sciences du sol, No-till farming, soil degradation, Intergovernmental Technical Panel on Soils, Environmental protection, Soil retrogression and degradation, Soil governance, soil resources, lcsh:Environmental sciences, 0105 earth and related environmental sciences, lcsh:GE1-350, 2. Zero hunger, Soil health, lcsh:QE1-996.5, 05 social sciences, Environmental engineering, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, menace, 6. Clean water, 0506 political science, lcsh:Geology, soil sciences, Solo, soil threat, Water quality, GlobalSoilMap, Agricultural soil science, CIENCIAS AGRÍCOLAS, purl.org/becyt/ford/4.1 [https], Soil erosion, 040103 agronomy & agriculture, Soils, 0401 agriculture, forestry, and fisheries, Environmental science, Recurso do solo, Soil fertility, Agricultura, Silvicultura y Pesca, Ciencias del Suelo, purl.org/becyt/ford/4 [https]
Abstract: The Intergovernmental Technical Panel on Soils has completed the first State of the World’s Soil Resources Report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils - the regions where the most food insecurity among us are found - while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved - the regional assessments in the State of the World’s Soil Resources Report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier. Fil: Montanarella, Luca. European Commission Joint Research Centre; Fil: Pennock, Daniel Jon. University of Saskatchewan; Canadá Fil: McKenzie, Neil. Csiro Agriculture Flagship, Brisbane; Australia Fil: Badraoui, Mohamed. Institut National de la Recherche Agronomique, Morocco; Fil: Chude, Victor. National Programme For Food Security; Nigeria Fil: Baptista, Isaurinda. Instituto Nacional de Investigação e Desenvolvimento Agrário; Cabo Verde Fil: Mamo, Tekalign. Ministry of Agriculture; Etiopía Fil: Yemefack, Martin. International Institute Of Tropical Agriculture Yaounde; Fil: Aulakh, Mikha Singh. Banda University Of Agriculture And Technology; India Fil: Yagi, Kazuyuki. Institute For Agro-environmental Sciences, Naro; Fil: Hong, Suk Young. Rural Development Administration; Fil: Vijarnsorn, Pisoot. Chaipattana Foundation; Fil: Zhang, Gan-Lin. Chinese Academy of Sciences; República de China Fil: Arrouays, Dominique. Institut National de la Recherche Agronomique. InfoSol Unit; Francia Fil: Black, Helaina. The James Hutton Institute; Reino Unido Fil: Krasilnikov, Pavel. Lomonosov Moscow State University; Fil: Sobocká, Jaroslava. National Agricultural And Food Centre; Fil: Alegre, Julio. Fil: Henriquez, Carlos Roberto. Universidad de Costa Rica; Costa Rica Fil: Mendonça-Santos, Maria de Lourdes. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil Fil: Taboada, Miguel Angel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Suelos; Argentina Fil: Espinosa-Victoria, David. Colegio de Postgraduados; México Fil: AlShankiti, Abdullah. International Center For Biosaline Agriculture; Fil: AlaviPanah, Sayed Kazem. University Of Tehran; Irán Fil: Mustafa Elsheikh, Elsiddig Ahmed El. Khartoum University; Sudán Fil: Hempel, Jon. United States Department of Agriculture; Estados Unidos Fil: Arbestain, Marta Camps. Institute Of Agriculture And Environment; Fil: Nachtergaele, Freddy. Food And Agriculture Organization Of The United Nations; Fil: Vargas, Ronald. Food And Agriculture Organization Of The United Nations
Published: 2015
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31. The EU-FP7 Project: Wheat and barley legacy for breeding improvement

Author: Charmet, Gilles, Kilian, B., Russell, J., Cattivelli, L., Bink, M., Keller, B., Lage, J., Gosman, N., Crepieux, S., Lagendijk, Emmanuelle, Pendu, R., Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Leibniz Institute of Plant Genetics and Crop Plant Research, James Hutton Institute (JHI), Consiglio per la Ricerca e Sperimentazione in Agricoltura, Stichting dienst landbouwkundig onderzoek (DLO), Universität Zürich, KWS-UK, National Institute of Agricultural Botany (NIAB), ARCADIA International, INRA Transfert, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and The James Hutton Institute
Subjects: blé, wheat, [SDV]Life Sciences [q-bio], orge
Abstract: Book of abstracts, p. 144; WHEALBI is granted 5 M€ by EU-FP7 for 5 years starting January, 2014. It involves 18 partners (8 academics, 7 industry /SME) in 9 countries and aims at improving European wheat and barley production in competitive and sustainable cropping systems. Germplasm will be selected and characterised by next-generation-sequencing. Adaptive traits will be evaluated in both transnational field experiments and precision phenotyping platforms. Germplasm will be stored in a bio-repository and associated data in knowledge bases that will represent a valuable legacy to the community. Whole genome association scans will be conducted for several traits, signatures of adaptive selection will be explored, and allele mining of candidate genes will reveal new variation associated with specific phenotypes. Pre-breeding tools will be developed to optimize the efficiency of allele transfer from unadapted germplasm into elite breeding lines. New methodologies will explore how to optimally exploit the large amount of new genotypic and phenotypic data available. Ideotypes with improved yield stability and tolerance to biotic and climatic stresses will be designed and and provide proof of concept of the efficiency of genome and phenome assisted selection. Ideotypes and reference varieties will be evaluated in innovative cropping systems, particularly organic farming and no-till agriculture, and an economic evaluation will be conducted. Results will be disseminated to a broad user community, highlighting the benefits and issues associated with the adoption of sustainable wheat and barley crop production. WHEALBI aims to help the EU remain a major actor in world small grain cereal production while addressing the pressing global priorities of improving food quality and reducing environmental impact.
Published: 2014

32. Clonage des gènes effecteurs de phytophtora capsici pour guider le développement de variétés résistantes de poivrons

Author: Lefebvre, Véronique, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Agropolis Fondation, Association Provençale de Recherche et d'Expérimentation Légumière (APREL), University of Tennessee, The James Hutton Institute, Contrat : 1300-002, and Partenaires : Association Provençale de Recherche et d'Expérimentation Légumière (APREL), University of Tennessee, The James Hutton Institute
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences
Published: 2014

33. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper

Author: Gaëtan Maillot, Emmanuel Szadkowski, Anne Massire, Véronique Brunaud, Guillem Rigaill, Bernard Caromel, Joël Chadœuf, Alexandre Bachellez, Nasradin Touhami, Ingo Hein, Kurt Lamour, Sandrine Balzergue, Véronique Lefebvre, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des Forêts Méditerranéennes (URFM), The James Hutton Institute, University of Tennessee, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agropolis Fondation, SOLEFFECT project from INRAE Plant biology and breeding Division and French Provence-Alpes-Côte d’Azur Region, and Companies Gautier Semences and Rijk Zwaan France.
Subjects: Capsicum annuum, RXLR effector, Capsicum annuum partial plant resistance pathogen adaptation Phytophthora capsici RXLR effector transcriptomics, transcriptomics, partial plant resistance, pathogen adaptation, Phytophthora capsici, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Science
Abstract: Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
Published: 2022
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34. Analyzing lateral root development: how to move forward

Author: A. Glyn Bengough, Ulrich Schurr, Renze Heidstra, Sacha J. Mooney, Hidehiro Fukaki, Philip N. Benfey, Benjamin Péret, Jonathan P. Lynch, John P. Hammond, Lionel X. Dupuy, Ilda Casimiro, Marta Joan Laskowski, Marc Lepetit, Tom Beeckman, Ive De Smet, Phillipe Nacry, Laurent Laplaze, Xavier Draye, Hanma Zhang, Philip J. White, Frank Hochholdinger, Malcolm J. Bennett, Martin R. Broadley, Boris Parizot, Division of Plant and Crop Sciences (DPCS), School of Biosciences-University of Nottingham, UK (UON), The James Hutton Institute, Laboratoire Commun de Microbiologie (LCM), Department of Plant Systems Biology, State University of Ghent, Universidad de Extremadura (UEX), Molecular Genetic, Utrecht University [Utrecht]-Faculty of Science-Department of Biology, Biology Department, Oberlin College, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Biology, Kobe University, Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Division of Agricultural and Environmental Sciences, Department of Horticulture, Pennsylvania State University (Penn State), Penn State System-Penn State System, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institute of Bio- and Geosciences-2: Plant Sciences, Forschungszentrum Jülich GmbH, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University [Durham], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universidad de Extremadura - University of Extremadura (UEX), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Université Catholique de Louvain = Catholic University of Louvain (UCL), Plant Environmental Physiology and Stress Signaling (PEPSS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Nottingham, UK (UON)-School of Biosciences, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Division of Plant and Crop Sciences ( DPCS ), School of Biosciences-Loughborough-University of Nottingham, UK ( UON ), James Hutton Institute ( JHI ), Invergowrie, Laboratoire Commun de Microbiologie ( LCM ), Universidad de Extremadura, Facultad de Ciencias, Laboratoire des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institute of Crop Science and Resource Conservation ( INRES ), Bonn Universität [Bonn], Earth and Life Institute [Louvain-La-Neuve], Université Catholique de Louvain ( UCL ), Laboratoire de Biologie du Développement des Plantes ( LBDP ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre for Plant Integrative Biology [Nothingham] ( CPIB ), University of Nottingham, UK ( UON ), School of Biosciences-University of Nottingham, UK ( UON ), PennState University [Pennsylvania] ( PSU ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Forschungszentrum Jülich, IBG-2: Plant Sciences, Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), and Duke university [Durham]
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Root (linguistics), Process (engineering), growth, MESH : Plant Roots, Plant Developmental Biology, MESH: Plant Roots, plant, Plant Science, Agricultural engineering, system architecture, Biology, Plant Roots, 01 natural sciences, ray computed-tomography, 03 medical and health sciences, traits, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nutrient-uptake, phosphorus, MESH: Models, Theoretical, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Vegetal Biology, MESH : Models, Theoretical, Ecology, business.industry, Lateral root, green-revolution, Biology and Life Sciences, Cell Biology, Models, Theoretical, 15. Life on land, Variety (cybernetics), arabidopsis, Agriculture, Sustainability, Commentary, Systems architecture, business, auxin, Biologie végétale, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.
Published: 2012
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35. Unusual Features of Pomoviral RNA Movement

Author: Eugene I. Savenkov, Lesley Torrance, Graham H. Cowan, Nina I. Lukhovitskaya, Kathryn M. Wright, François Crutzen, Claude Bragard, Cell and Molecular Sciences, Invergowrie, Dundee, DD2 5DA , Scotland / UK - The James Hutton Institute, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland / UK - Cell and Molecular Sciences, UCL - SST/ELI/ELIM - Applied Microbiology, Uppsala BioCentre, Swedish University of Agricultural Sciences, Uppsala, Sweden - Department of Plant Biology and Forest Genetics, University of St Andrews. School of Biology, and University of St Andrews. Biomedical Sciences Research Complex
Subjects: Microbiology (medical), Nucleolus, Mini Review, lcsh:QR1-502, Pomovirus, Microbiology, lcsh:Microbiology, microtubules, Microtubule, medicine, nucleolus, Gene, Ribonucleoprotein, BSBV, Genetics, QR355, TGB, biology, Movement (music), nucleus, RNA, biology.organism_classification, BVQ, medicine.anatomical_structure, pomovirus, Nucleus, QR355 Virology, PMTV
Abstract: This work is partially supported by the Scottish Government’s Rural and Environment Science and Analytical Services (RESAS) Division Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of the capsid protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2, and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement. Publisher PDF
Published: 2011

36. Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number

Author: Benoit Darrier, Isabelle Colas, Hélène Rimbert, Frédéric Choulet, Jeanne Bazile, Aurélien Sortais, Eric Jenczewski, Pierre Sourdille, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Syngenta France, Cell and Molecular Sciences, The James Hutton Institute, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MR/K015869/1, FP7/2007–2013 (no.222883), ERC Shuffle (Project ID: 669182), and BBSRC BB/T008636/1
Subjects: Ecology, synapsis, [SDV]Life Sciences [q-bio], Plant Science, recombination, chiasmata, cytogenetics, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, wheat, deletion bin, 3D-SIM, meiosis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Understanding meiotic crossover (CO) variation in crops like bread wheat (Triticum aestivum L.) is necessary as COs are essential to create new, original and powerful combinations of genes for traits of agronomical interest. We cytogenetically characterized a set of wheat aneuploid lines missing part or all of chromosome 3B to identify the most influential regions for chiasma formation located on this chromosome. We showed that deletion of the short arm did not change the total number of chiasmata genome-wide, whereas this latter was reduced by ~35% while deleting the long arm. Contrary to what was hypothesized in a previous study, deletion of the long arm does not disturb the initiation of the synaptonemal complex (SC) in early meiotic stages. However, progression of the SC is abnormal, and we never observed its completion when the long arm is deleted. By studying six different deletion lines (missing different parts of the long arm), we revealed that at least two genes located in both the proximal (C-3BL2-0.22) and distal (3BL7-0.63-1.00) deletion bins are involved in the control of chiasmata, each deletion reducing the number of chiasmata by ~15%. We combined sequence analyses of deletion bins with RNA-Seq data derived from meiotic tissues and identified a set of genes for which at least the homoeologous copy on chromosome 3B is expressed and which are involved in DNA processing. Among these genes, eight (CAP-E1/E2, DUO1, MLH1, MPK4, MUS81, RTEL1, SYN4, ZIP4) are known to be involved in the recombination pathway.
Published: 2022
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37. Towards smart and sustainable development of modern berry cultivars in Europe

Author: Elisa Senger, Sonia Osorio, Klaus Olbricht, Paul Shaw, Béatrice Denoyes, Jahn Davik, Stefano Predieri, Saila Karhu, Sebastian Raubach, Nico Lippi, Monika Höfer, Helen Cockerton, Christophe Pradal, Ebru Kafkas, Suzanne Litthauer, Iraida Amaya, Björn Usadel, Bruno Mezzetti, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Hansabred [Dresden], The James Hutton Institute, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Institute for BioEconomy [Sesto Fiorentino] (IBE | CNR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Natural Resources Institute Finland (LUKE), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), National Institute of Agricultural Botany (NIAB), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Cukurova University, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Università Politecnica delle Marche [Ancona] (UNIVPM), and The authors acknowledge support from the European Union’s Horizon 2020 research and innovation program (grant agreement ID: 101000747)
Subjects: consumer preference, [SDV]Life Sciences [q-bio], métadonnées, plant genetic resources, Plant Science, Fragaria, F30 - Génétique et amélioration des plantes, génomique, Ressource génétique végétale, image analysis, Genetics, genomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Humans, amélioration génétique, QK, BreedingValue project, trait/genotype association, Cell Biology, Sustainable Development, metabolomics, Amélioration des plantes, Petits fruits, Propriété organoleptique, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Valeur génétique, Plant Breeding, ddc:580, berry breeding, Fruit, Rubus, Vaccinium, Génotype, Genome-Wide Association Study
Abstract: International audience; Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies such as molecular marker arrays, genomic selection and genome wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
Published: 2022
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38. Genome-Wide Association Study for Resistance to Rhynchosporium in a Diverse Collection of Spring Barley Germplasm

Author: Jean-Noël Thauvin, Joanne Russell, Dominique Vequaud, Mark Looseley, Micha Bayer, Pierre-Marie Le Roux, Pierre Pin, Robbie Waugh, Anna Avrova, The James Hutton Institute, Division of Plant Sciences, College of Life Sciences, Scottish Crop Research Institute, Invergowrie, University of Dundee, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Secobra Recherches, Partenaires INRAE, Agriculture and Horticulture Development Board (AHDB), and Scottish Government: Rural and Environment Science and Analytical Services (RESAS)
Subjects: landraces, QTL, [SDV]Life Sciences [q-bio], [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, food and beverages, barley, SNP, resistance, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, rhynchosporium, genetic markers, GWAS, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science
Abstract: International audience; Rhynchosporium is one of the main biotic stresses on barley production worldwide. A set of 312 spring barley accessions was tested in four different locations over 3 years, to identify novel genetic resistances to rhynchosporium and to explore the allelic diversity for resistance genes present in this global germplasm collection. High-density genotypes from exome capture and RNA-seq were used to conduct high-resolution association mapping. Seven quantitative trait loci (QTL) were detected, including one in the Rrs2 region, amongst five containing known resistances. Relatively short physical intervals harbouring these resistances were proposed, providing a platform for the identification of underlying genes and tightly linked genetic markers for use in marker assisted selection. Genes encoding kinases were present in four of the QTL, in addition to Rrs1 and Rrs18, two loci known to contribute to rhynchosporium resistance. The frequencies and distributions of these novel and known QTL were superimposed on the regional origin of the landrace genotypes comprising the genome-wide association studies (GWAS) panel, highlighting the value of genetic resources as a source of diverse genetically controlled resistance to rhynchosporium. The detected QTL along with their linked genetic markers, could be exploited either directly for breeding purposes or for candidate gene identification in future studies.
Published: 2022
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39. LOTVS: A global collection of permanent vegetation plots

Author: Marta Gaia Sperandii, Francesco de Bello, Enrique Valencia, Lars Götzenberger, Manuele Bazzichetto, Thomas Galland, Anna E‐Vojtkó, Luisa Conti, Peter B. Adler, Hannah Buckley, Jiří Danihelka, Nicola J. Day, Jürgen Dengler, David J. Eldridge, Marc Estiarte, Ricardo García‐González, Eric Garnier, Daniel Gómez‐García, Lauren Hallett, Susan Harrison, Tomas Herben, Ricardo Ibáñez, Anke Jentsch, Norbert Juergens, Miklós Kertész, Duncan M. Kimuyu, Katja Klumpp, Mike Le Duc, Frédérique Louault, Rob H. Marrs, Gábor Ónodi, Robin J. Pakeman, Meelis Pärtel, Begoña Peco, Josep Peñuelas, Marta Rueda, Wolfgang Schmidt, Ute Schmiedel, Martin Schuetz, Hana Skalova, Petr Šmilauer, Marie Šmilauerová, Christian Smit, Ming‐Hua Song, Martin Stock, James Val, Vigdis Vandvik, Karsten Wesche, Susan K. Wiser, Ben A. Woodcock, Truman P. Young, Fei‐Hai Yu, Amelia A. Wolf, Martin Zobel, Jan Lepš, Centro de Investigaciones sobre Desertificacion (CIDE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad Rey Juan Carlos [Madrid] (URJC), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), UNIVERSITY OF SOUTH BOHEMIA CESKE BUDEJOVICE CZE, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Czech University of Life Sciences Prague (CZU), Utah State University (USU), Auckland University of Technology (AUT), Masaryk University [Brno] (MUNI), Victoria University of Wellington, Zürich University of Applied Sciences (ZHAW), University of New South Wales [Kensington], CREAF - Centre for Ecological Research and Applied Forestries, Instituto Pirenaico de Ecologìa = Pyrenean Institute of Ecology [Zaragoza] (IPE - CSIC), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), University of Oregon, Eugene, OR 97403, United States, University of California (UC), Department of Zoology, Charles University in Prague, Faculty of Science, Viniicna 7, 128 43 Praha 2, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), University of Hamburg, Hungarian Academy of Sciences (MTA), University of Liverpool, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The James Hutton Institute, University of Tartu, Autonomous University of Madrid, Faculty of Sciences, Department of Ecology, 28049 Madrid, Spain, Universidad de Sevilla / University of Sevilla, Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Georg-August-University = Georg-August-Universität Göttingen, Hamburg University of Applied Sciences [Hamburg], Swiss Federal Institute for Forest, Snow and Landscape Research WSL, University of South Bohemia, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Chinese Academy of Agricultural Sciences (CAAS), Wadden Sea National Park of Schleswig-Holstein, University of Bergen (UiB), Senckenberg Museum of Natural History Görlitz, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Manaaki Whenua – Landcare Research [Lincoln], Center for Ecology and Hydrology, Taizhou University, University of Texas-Pan, Smit group, Royal Society of New Zealand, Czech Science Foundation, Academy of Sciences of the Czech Republic, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Institut National de la Recherche Agronomique (France), Federal Ministry of Education and Research (Germany), Oberfranken Stiftung, Agence Nationale de la Recherche (France), Scottish Government's Rural and Environment Science and Analytical Services, Estonian Research Council, European Commission, Fundación Ramón Areces, Generalitat de Catalunya, European Research Council, Dresden University of Technology, Ministry of Business, Innovation, and Employment (New Zealand), Natural Environment Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Comunidad de Madrid, Universidad Rey Juan Carlos, National Science Foundation (US), South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses [University of South Bohemia] (CENAKVA), Faculty of Fisheries and Protection of Waters [University of South Bohemia], University of South Bohemia -University of South Bohemia, Desertification Research Centre (CIDE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universitat de València (UV), University of Bayreuth, German Centre for Integrative Biodiversity Research (iDiv), University of New South Wales [Sydney] (UNSW), Centre for Ecological Research and Forestry Applications (CREAF), Unit CREAF-CSIC-UABB, Global Ecology Unit (CREAF-CSIC-UAB), Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD), Department of Mathematics, University of Oregon [Eugene], University of Oregon [Eugene], Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Charles University [Prague] (CU), Distributed Events Analysis Research Group (MTA SZTAKI Hungarian Academy of Sciences), Mpala Research Centre, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Clermont Auvergne (UCA), Institute of Computer Science [University of Tartu, Estonie], Centre de Recerca Ecològica i Aplicacions Forestals - Centre for Ecological Research and Forestry Applications, Partenaires INRAE, University of Chinese Academy of Sciences [Beijing] (UCAS), Lake Ecosystems Group [Lancaster, U.K.] (Centre for Ecology & Hydrology), Lancaster Environment Centre [Lancaster, U.K.], Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China, Department of Electrical and Computer Engineering - University of Texas (ECE), University of Texas at Austin [Austin], ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), Sperandii, M. G., de Bello, F., Valencia, E., Gotzenberger, L., Bazzichetto, M., Galland, T., E-Vojtko, A., Conti, L., Adler, P. B., Buckley, H., Danihelka, J., Day, N. J., Dengler, J., Eldridge, D. J., Estiarte, M., Garcia-Gonzalez, R., Garnier, E., Gomez-Garcia, D., Hallett, L., Harrison, S., Herben, T., Ibanez, R., Jentsch, A., Juergens, N., Kertesz, M., Kimuyu, D. M., Klumpp, K., Le Duc, M., Louault, F., Marrs, R. H., Onodi, G., Pakeman, R. J., Partel, M., Peco, B., Penuelas, J., Rueda, M., Schmidt, W., Schmiedel, U., Schuetz, M., Skalova, H., Smilauer, P., Smilauerova, M., Smit, C., Song, M. -H., Stock, M., Val, J., Vandvik, V., Wesche, K., Wiser, S. K., Woodcock, B. A., Young, T. P., Yu, F. -H., Wolf, A. A., Zobel, M., and Leps, J.
Subjects: Plant communities, temporal analysis, Plant community, Plant Science, ecological succession, Permanent plot, ecoinformatic, plant communitie, Ecology and Environment, ecoinformatics, vegetation, Ecological succession, Ecoinformatics, Global scale, 577: Ökologie, time-serie, Vegetation, ecosystem stability, Ecology, time-series, Temporal analysis, permanent plot, plant diversity, plant communities, temporal analysi, 580: Pflanzen (Botanik), Plant diversity, global scale, Ecosystem stability, Permanent plots, Time-series, permanent plots, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of plant species in permanent plots. With 79 data sets from five continents and 7,789 vegetation time-series monitored for at least 6 years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology., The authors acknowledge institutional support as follows. Nicola J. Day: Te Apārangi Royal Society of New Zealand (Rutherford Postdoctoral Fellowship). Jiří Danihelka: Czech Science Foundation (project no. 19-28491X) and Czech Academy of Sciences (project no. RVO 67985939). Francesco de Bello: Spanish Plan Nacional de I+D+i (project PGC2018-099027-B-I00). Eric Garnier: La Fage INRA experimental station. Tomáš Herben: GAČR grant 20-02901S. Anke Jentsch: German Federal Ministry of Education and Research (grant 031B0516C - SUSALPS) and Oberfrankenstiftung (grant OFS FP00237). Norbert Juergens: German Federal Ministry of Education and Research (grant 01LG1201N - SASSCAL ABC). Frédérique Louault and Katja Klumpp: AnaEE-France (ANR-11-INBS-0001). Robin J. Pakeman: Strategic Research Programme of the Scottish Government's Rural and Environment Science and Analytical Services Division. Meelis Pärtel: Estonian Research Council (PRG609) and European Regional Development Fund (Centre of Excellence EcolChange). Josep Peñuelas: Spanish Government (grant PID2019-110521GB-I00), Fundación Ramon Areces (grant ELEMENTAL-CLIMATE), Catalan Government (grant SGR 2017-1005), and European Research Council (Synergy grant ERC-SyG-2013-610028, IMBALANCE-P). Ute Schmiedel: German Federal Ministry of Education and Research (Promotion numbers 01LC0024, 01LC0024A, 01LC0624A2, 01LG1201A, 01LG1201N). Hana Skálová: GAČR grant 20-02901S. Karsten Wesche: International Institute Zittau, Technische Universität Dresden. Susan K. Wiser: New Zealand Ministry for Business, Innovation and Employment’s Strategic Science Investment Fund. Ben A. Woodcock: NERC and BBSRC (NE/N018125/1 LTS-M ASSIST - Achieving Sustainable Agricultural Systems). Enrique Valencia: Program for attracting and retaining talent of Comunidad de Madrid (no. 2017-T2/AMB-5406) and Community of Madrid and Rey Juan Carlos University (Young Researchers R&D Project. Ref. M2165 – INTRANESTI). Truman P. Young: National Science Foundation (LTREB DEB 19-31224).
Published: 2022
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40. Potash fertilizer promotes incipient salinization in groundwater irrigated semi-arid agriculture

Author: Buvaneshwari, S., Riotte, Jean, Sekhar, M., Sharma, A. K., Helliwell, R., Kumar, M. S. M., Braun, Jean-Jacques, Ruiz, Laurent, Indian Institute of Science [Bangalore] (IISc Bangalore), Indo-French Cell for Water Sciences (IFCWS), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Littoral, Environnement, Télédétection, Géomatique UMR 6554 (LETG), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN), The James Hutton Institute, Sol Agro et hydrosystème Spatialisation (SAS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Littoral, Environnement, Télédétection, Géomatique (LETG - Rennes), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN)-Université de Caen Normandie (UNICAEN), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-16-CE03-0006,ATCHA,Accompagner l'adaptation de l'agriculture irriguée au changement climatique(2016)
Subjects: Environmental impact, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Environmental chemistry, [SDE]Environmental Sciences, lcsh:R, lcsh:Medicine, lcsh:Q, Hydrology, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, lcsh:Science, Article
Abstract: International audience; Incipient groundwater salinization has been identified in many arid and semi-arid regions where groundwater is increasingly used for irrigation, but the dominant processes at stake in such context are yet uncertain. Groundwater solutes originates from various sources such as atmospheric inputs, rock dissolution and fertilizer residues, and their concentration is controlled by hydrological processes, in particular evapotranspiration. Here, we propose a deconvolution method to identify the sources and processes governing the groundwater Chloride concentration in agricultural catchments, using the relative variations of Sodium and chloride and using a neighbouring pristine catchment as a reference for the release rate of Na by weathering. We applied the deconvolution method to the case of the Kabini Critical Zone Observatory, South India, where groundwater was sampled in 188 farm tubewells in the semi-arid catchment of Berambadi and in 5 piezometers in the pristine catchment of Mule Hole. In Berambadi, groundwater composition displayed a large spatial variability with Cl contents spanning 3 orders of magnitude. The results showed that the concentration factor due to evapotranspiration was on average about 3 times more than in the natural system, with higher values in the valley bottoms with deep Vertisols. Linked with this process, large concentration of Chloride originating from rain was found only in these areas. At the catchment scale, about 60 percent of the Chloride found in groundwater originates from fertilizer inputs. These results show that Potassium fertilization as KCl is an important source of groundwater salinization in semi-arid context, and stress that identifying dominant drivers is crucial for designing efficient mitigation policies.
Published: 2020
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41. Examining Phenotypic Traits Contributing to the Spread in Northern European Potato Crops of EU_41_A2, a New Clonal Lineage of Phytophthora infestans

Author: Håvard Eikemo, Romain Mabon, Pauline Dewaegeneire, Guillaume Saubeau, David E. L. Cooke, Britt Puidet, M. Guibert, Frédérique Aurousseau, Alison K. Lees, Isaac Kwesi Abuley, Catherine Chatot, Liina Soonvald, Jens Grønbech Hansen, Didier Andrivon, Melen Leclerc, Roselyne Corbière, Vinh Hong Le, Riinu Kiiker, Estonian University of Life Sciences (EMU), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Fédération Nationale des Producteurs de Plants de Pomme de Terre (FN3PT), Comité Nord Plants de Pommes de Terre, Florimond Desprez, Germicopa, The James Hutton Institute, Aarhus University [Aarhus], 8T150054PKTK, Ministry of Rural Affairs of Estonia, IUT36-2, Eesti Teadusagentuur, European Regional Development Fund, INRAE, The French Office for Biodiversity, MST-667-00174, Miljø- og Fødevareministeriet, 259826, The Research Council of Norway, Scottish Government’s Rural and Environment Science and Analytical Services Division, and Coordinated Integrated Pest Management in Europe
Subjects: late blight, sexual reproduction, phenotype, Lineage (evolution), Plant Science, Population biology, Phenotypic trait, Biology, clonal lineage, biology.organism_classification, oomycetes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Sexual reproduction, Evolutionary biology, Western europe, Genotype, Phytophthora infestans, fungal pathogens, Chemical control, Agronomy and Crop Science, Solanum tuberosum
Abstract: International audience; Until recently, genotypes of Phytophthora infestans were regionally distributed in Europe, with populations in western Europe being dominated by clonal lineages and those in northern Europe being genetically diverse because of frequent sexual reproduction. However, since 2013 a new clonal lineage (EU_41_A2) has successfully established itself and expanded in the sexually recombining P. infestans populations of northern Europe. The objective of this study was to study phenotypic traits of the new clonal lineage of P. infestans, which may explain its successful establishment and expansion within sexually recombining populations. Fungicide sensitivity, aggressiveness, and virulence profiles of isolates of EU_41_A2 were analyzed and compared with those of the local sexual populations from Denmark, Norway, and Estonia. None of the phenotypic data obtained from the isolates collected from Denmark, Estonia, and Norway independently explained the invasive success of EU_41_A2 within sexual Nordic populations. Therefore, we hypothesize that the expansion of this new genotype could result from a combination of fitness traits and more favorable environmental conditions that have emerged in response to climate change.
Published: 2022
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42. Ovine fetal testis stage-specific sensitivity to environmental chemical mixtures

Author: Richard G Lea, Beatrice Mandon-Pépin, Benoit Loup, Elodie Poumerol, Luc Jouneau, Biola F Egbowon, Adelle Bowden, Corinne Cotinot, Laura Purdie, Zulin Zhang, Paul A Fowler, Kevin D Sinclair, University of Nottingham, UK (UON), Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), École nationale vétérinaire - Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The James Hutton Institute, University of Aberdeen, and European Project: 212885,EC:FP7:ENV,FP7-ENV-2007-1,REEF(2008)
Subjects: Male, Embryology, Sheep, Sewage, Obstetrics and Gynecology, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Cell Biology, Fetus, Endocrinology, Reproductive Medicine, Pregnancy, Testis, environmental chemical mixtures, Animals, Humans, stage-specific sensitivity, Female, Testosterone, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Sheep, Domestic
Abstract: International audience; Exposure of the fetal testis to numerous individual environmental chemicals (ECs) is frequently associated with dysregulated development, leading to impaired adult reproductive competence. However, ‘real-life’ exposure involves complex mixtures of ECs. Here we test the consequences, for the male fetus, of exposing pregnant ewes to EC mixtures derived from pastures treated with biosolids fertiliser (processed human sewage). Fetal testes from continuously exposed ewes were either unaffected at day 80 or exhibited a reduced area of testis immunostained for CYP17A1 protein at day 140. Fetal testes from day 140 pregnant ewes that were exposed transiently for 80-day periods during early (0–80 days), mid (30–110 days), or late (60–140 days) pregnancy had fewer Sertoli cells and reduced testicular area stained for CYP17A1. Male fetuses from ewes exposed during late pregnancy also exhibited reduced fetal body, adrenal and testis mass, anogenital distance, and lowered testosterone; collectively indicative of an anti-androgenic effect. Exposure limited to early gestation induced more testis transcriptome changes than observed for continuously exposed day 140 fetuses. These data suggest that a short period of EC exposure does not allow sufficient time for the testis to adapt. Consequently, testicular transcriptomic changes induced during the first 80 days of gestation may equate with phenotypic effects observed at day 140. In contrast, relatively fewer changes in the testis transcriptome in fetuses exposed continuously to ECs throughout gestation are associated with less severe consequences. Unless corrected by or during puberty, these differential effects would predictably have adverse outcomes for adult testicular function and fertility.
Published: 2022
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43. Potassium Use Efficiency of Plants

Author: Ivica Djalovic, Philippe Hinsinger, Philip J. White, Michael J. Bell, Zed Rengel, The James Hutton Institute, University of Queensland [Brisbane], Institute of Field and Vegetable Crops [Novi Sad], Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), The University of Western Australia (UWA), Murrell T.S., Mikkelsen R.L., Sulewski G., Norton R., Thompson M.L., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Potassium uptake, Potassium, Root function, chemistry.chemical_element, Context (language use), Root system, Biology, engineering.material, Photosynthesis, Intraspecific variation, Root exudates, 01 natural sciences, Crop, 03 medical and health sciences, Yield (wine), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 2. Zero hunger, Potassium remobilization, 0303 health sciences, Rhizosphere, 15. Life on land, Agronomy, chemistry, Interspecific variation, engineering, Fertilizer, 010606 plant biology & botany
Abstract: There are many terms used to define aspects of potassium (K) use efficiency of plants. The terms used most frequently in an agricultural context are (1) agronomic K use efficiency (KUE), which is defined as yield per unit K available to a crop and is numerically equal to the product of (2) the K uptake efficiency (KUpE) of the crop, which is defined as crop K content per unit K available and (3) its K utilization efficiency (KUtE), which is defined as yield per unit crop K content. There is considerable genetic variation between and within plant species in KUE, KUpE, and KUtE. Root systems of genotypes with greatest KUpE often have an ability (1) to exploit the soil volume effectively, (2) to manipulate the rhizosphere to release nonexchangeable K from soil, and (3) to take up K at low rhizosphere K concentrations. Genotypes with greatest KUtE have the ability (1) to redistribute K from older to younger tissues to maintain growth and photosynthesis and (2) to reduce vacuolar K concentration, while maintaining an appropriate K concentration in metabolically active subcellular compartments, either by anatomical adaptation or by greater substitution of K with other solutes in the vacuole. Genetic variation in traits related to KUpE and KUtE might be exploited in breeding crop genotypes that require less K fertilizer. This could reduce fertilizer costs, protect the environment, and slow the exhaustion of nonrenewable resources.
Published: 2021
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44. Rhizosphere Processes and Root Traits Determining the Acquisition of Soil Potassium

Author: John L. Kovar, Philip J. White, Philippe Hinsinger, Michael J. Bell, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Queensland [Brisbane], USDA-ARS : Agricultural Research Service, The James Hutton Institute, King Saud University [Riyadh] (KSU), Murrell T.S., Mikkelsen R.L., Sulewski G., Norton R., Thompson M.L., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Mobility Root hair, Root length, Bioavailability, Potassium, chemistry.chemical_element, Root hair, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, Acidification, Diffusion, Depletion, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Organic matter, Dissolution, Subsoil, 2. Zero hunger, chemistry.chemical_classification, Rhizosphere, Chemistry, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, Agronomy, Rooting depth, Soil water, 040103 agronomy & agriculture, Exudation, 0401 agriculture, forestry, and fisheries, Clay minerals, 010606 plant biology & botany
Abstract: Plants acquire K+ ions from the soil solution, and this small and dynamic pool needs to be quickly replenished via desorption of surface-adsorbed K from clay minerals and organic matter, by release of interlayer K from micaceous clay minerals and micas, or structural K from feldspars. Because of these chemical interactions with soil solid phases, solution K+ concentration is kept low and its mobility is restricted. In response, plants have evolved efficient strategies of root foraging. Root traits related to root system architecture (root angle and branching), root length and growth, together with root hairs and mycorrhiza-related traits help to determine the capacity of plants to cope with the poor mobility of soil K. Rooting depth is also important, given the potentially significant contribution of subsoil K in many soils. Root-induced depletion of K+ shifts the exchange equilibria, enhancing desorption of K, as well as the release of nonexchangeable, interlayer K from minerals in the rhizosphere. Both these pools can be bioavailable if plant roots can take up significant amounts of K at low concentrations in the soil solution (in the micromolar range). In addition, roots can significantly acidify their environment or release large amounts of organic compounds (exudates). These two processes ultimately promote the dissolution of micas and feldspars in the rhizosphere, contributing to the mining strategy evolved by plants. There are thus several root or rhizosphere-related traits (morphological, physiological, or biochemical) that determine the acquisition of K by crop species and genotypes.
Published: 2021
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45. Unravelling homeostasis effects of phosphorus and zinc nutrition by leaf photochemistry and metabolic adjustment in cotton plants

Author: Ricardo Antunes Azevedo, Philip J. White, Paula Pongrac, Flávio Henrique Silveira Rabêlo, André Rodrigues dos Reis, Elcio Ferreira Santos, José Lavres, Universidade de São Paulo (USP), University of Ljubljana, Jožef Stefan Institute, Universidade Estadual Paulista (UNESP), The James Hutton Institute, King Saud University, and Huazhong Agricultural University
Subjects: 0106 biological sciences, Antioxidant, Science, medicine.medical_treatment, Plant physiology, chemistry.chemical_element, Zinc, Photochemistry, Photosynthesis, 01 natural sciences, Article, Nutrient, Carbonic anhydrase, medicine, Multidisciplinary, biology, Phosphorus, Acid phosphatase, 04 agricultural and veterinary sciences, Metabolism, chemistry, Plant stress responses, 040103 agronomy & agriculture, biology.protein, Medicine, 0401 agriculture, forestry, and fisheries, Plant sciences, 010606 plant biology & botany
Abstract: Made available in DSpace on 2022-04-28T19:41:19Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Javna Agencija za Raziskovalno Dejavnost RS Rural and Environment Science and Analytical Services Division Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Phosphorus (P) and zinc (Zn) uptake and its physiological use in plants are interconnected and are tightly controlled. However, there is still conflicting information about the interactions of these two nutrients, thus a better understanding of nutritional homeostasis is needed. The objective of this work was to evaluate responses of photosynthesis parameters, P-Zn nutritional homeostasis and antioxidant metabolism to variation in the P × Zn supply of cotton (Gossypium hirsutum L.). Plants were grown in pots and watered with nutrient solution containing combinations of P and Zn supply. An excess of either P or Zn limited plant growth, reduced photosynthesis-related parameters, and antioxidant scavenging enzymes. Phosphorus uptake favoured photochemical dissipation of energy decreasing oxidative stress, notably on Zn-well-nourished plants. On the other hand, excessive P uptake reduces Zn-shoot concentration and decreasing carbonic anhydrase activity. Adequate Zn supply facilitated adaptation responses to P deficiency, upregulating acid phosphatase activity, whereas Zn and P excess were alleviated by increasing P and Zn supply, respectively. Collectively, the results showed that inter ionic effects of P and Zn uptake affected light use and CO2 assimilation rate on photosynthesis, activation of antioxidant metabolism, acid phosphatase and carbonic anhydrase activities, and plant growth-related responses to different extents. Center for Nuclear Energy in Agriculture University of São Paulo Biotechnical Faculty University of Ljubljana, Jamnikarjeva 111 Jožef Stefan Institute, Jamova 39 São Paulo State University College of Agriculture Luiz de Queiroz University of São Paulo Ecological Science Group The James Hutton Institute Distinguished Scientist Fellowship Program King Saud University College of Resources and Environment Huazhong Agricultural University São Paulo State University CAPES: 309380/2017-0 CNPq: 310572/2017-7
Published: 2021

46. Arachis hypogaea L. from Acid Soils of Nanyang (China) Is Frequently Associated with Bradyrhizobium guangdongense and Occasionally with Bradyrhizobium ottawaense or Three Bradyrhizobium Genospecies

Author: Shuo Li, Brigitte Brunel, Wenfeng Chen, Jiangchun Song, Euan K. James, Junjie Zhang, Mitchell Andrews, En Tao Wang, Shanshan Peng, Zhengzhou University of Light Industry, Collaborative Innovation Center for Food Production and Safety of Henan Province, Partenaires INRAE, Nan Yang Academy of Sciences, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Inst Politecn Nacl, CICATA, Queretaro 76090, Mexico, Instituto Politecnico Nacional [Mexico] (IPN), The James Hutton Institute, State Key Laboratory for Agrobiotechnology, China Agricultural University (CAU), University of Lincoln, and Project for Extramural Scientists of State Key Laboratory of Agrobiotechnology2021SKLAB6-8
Subjects: DNA, Bacterial, MLSA, Arachis, Genospecies, Soil Science, Rhizobia, Bradyrhizobium ottawaense, Bradyrhizobium, 03 medical and health sciences, Soil, Symbiosis, RNA, Ribosomal, 16S, Botany, IAA production, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Lespedeza cuneata, Ecology, biology, Phylogenetic tree, food and beverages, Soil classification, Fabaceae, 04 agricultural and veterinary sciences, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, 15. Life on land, biology.organism_classification, 16S ribosomal RNA, Peanut, [SDE]Environmental Sciences, 040103 agronomy & agriculture, bacteria, 0401 agriculture, forestry, and fisheries, Root Nodules, Plant, Rhizobium
Abstract: International audience; Henan Province is a major area of peanut production in China but the rhizobia nodulating the crop in this region have not been described. A collection of 217 strains of peanut rhizobia was obtained from six field sites across four soil types in Henan Province, North China, by using peanut as a trap host under glasshouse conditions. The 217 strains separated into 8 distinct types on PCR-RFLP analysis of their IGS sequences. Phylogenetic analysis of the 16S rRNA, recA, atpD, and glnII genes of 11 representative strains of the 8 IGS types identified Bradyrhizobium guangdongense, B. ottawaense and three novel Bradyrhizobium genospecies. Bradyrhizobium guangdongense was dominant, accounting for 75.0% of the total isolates across the field sites while B. ottawaense covered 5.1% and the three novel Bradyrhizobium genospecies 4.1 to 8.8% of the total. The symbiosis-related nodA and nifH gene sequences were not congruent with the core genes on phylogenetic analysis and separated into three groups, two of which were similar to sequences of Bradyrhizobium spp. isolated from peanut in south-east China and the third identical to that of B. yuanmingense isolated from Lespedeza cuneata in northern China. A canonical correlation analysis between the distribution of IGS genotypes and soil physicochemical characteristics and climatic factors indicated that the occurrence of IGS types/species was mainly associated with soil pH and available phosphorus.
Published: 2021
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47. Achieving Food System Resilience Requires Challenging Dominant Land Property Regimes

Author: Coline Perrin, Adrien Baysse-Lainé, Annie McKee, Adam Calo, Steven R. McGreevy, Annette Aurélie Desmarais, Mai Kobayashi, Sarah Ruth Sippel, Pierre Gasselin, Naomi Beingessner, Kirsteen Shields, André Magnan, The James Hutton Institute, Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Institute for Humanity and Nature (RIHN), Institute of Cultural Anthropology, University of Leipzig [Leipzig, Allemagne], University of Manitoba [Winnipeg], University of Edinburgh, Pacte, Laboratoire de sciences sociales (PACTE), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Sciences Po Grenoble - Institut d'études politiques de Grenoble (IEPG ), Université Grenoble Alpes (UGA), University of Regina (UR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: agroecology, food system transformation, food sovereignty, agroecology, resilience, property regimes, land tenure, land reform, media_common.quotation_subject, 0211 other engineering and technologies, 0507 social and economic geography, land tenure, 02 engineering and technology, Entitlement, Horticulture, Management, Monitoring, Policy and Law, Food processing and manufacture, land reform, [SHS.DROIT]Humanities and Social Sciences/Law, Political science, ddc:630, TX341-641, Agricultural productivity, Land tenure, resilience, media_common, 2. Zero hunger, Global and Planetary Change, [SHS.SOCIO]Humanities and Social Sciences/Sociology, Ecology, Nutrition. Foods and food supply, 05 social sciences, 021107 urban & regional planning, [SHS.GEO]Humanities and Social Sciences/Geography, 15. Life on land, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, TP368-456, Political ecology, food sovereignty, property regimes, [SHS.SCIPO]Humanities and Social Sciences/Political science, Food sovereignty, 13. Climate action, Political economy, Food systems, Psychological resilience, food system transformation, 050703 geography, Agronomy and Crop Science, Land reform, Food Science
Abstract: International audience; Although evidence continues to indicate an urgent need to transition food systems away from industrialized monocultures and toward agroecological production, there is little sign of significant policy commitment toward food system transformation in global North geographies. The authors, a consortium of researchers studying the land-food nexus in global North geographies, argue that a key lock-in explaining the lack of reform arises from how most food system interventions work through dominant logics of property to achieve their goals of agroecological production. Doing so fails to recognize how land tenure systems, codified by law and performed by society, construct agricultural land use outcomes. In this perspective, the authors argue that achieving food system “resilience” requires urgent attention to the underlying property norms that drive land access regimes, especially where norms of property appear hegemonic. This paper first reviews research from political ecology, critical property law, and human geography to show how entrenched property relations in the global North frustrate the advancement of alternative models like food sovereignty and agroecology, and work to mediate acceptable forms of “sustainable agriculture.” Drawing on emerging cases of land tenure reform from the authors' collective experience working in Scotland, France, Australia, Canada, and Japan, we next observe how contesting dominant logics of property creates space to forge deep and equitable food system transformation. Equally, these cases demonstrate how powerful actors in the food system attempt to leverage legal and cultural norms of property to legitimize their control over the resources that drive agricultural production. Our formulation suggests that visions for food system “resilience” must embrace the reform of property relations as much as it does diversified farming practices. This work calls for a joint cultural and legal reimagination of our relation to land in places where property functions as an epistemic and apex entitlement.
Published: 2021
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48. Unravelling Plant Responses to Stress—The Importance of Targeted and Untargeted Metabolomics

Author: Alex Williams, Pierre Pétriacq, Luis A. J. Mur, Murray Grant, James William Allwood, Nicole M. van Dam, Henriette Uthe, The James Hutton Institute, University of Manchester [Manchester], University of Sheffield [Sheffield], Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Aberystwyth University, University of Warwick [Coventry], Biologie du fruit et pathologie (BFP), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, abiotic stress, Endocrinology, Diabetes and Metabolism, Systems biology, [SDV]Life Sciences [q-bio], Population, Review, Biology, Microbiology, 01 natural sciences, Biochemistry, untargeted, 03 medical and health sciences, Metabolomics, biotic stress, Metabolome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Molecular Biology, SB, 030304 developmental biology, stress resistance, 2. Zero hunger, Abiotic component, targeted, 0303 health sciences, education.field_of_study, QL, business.industry, Abiotic stress, plant pathology, fungi, food and beverages, plant–insect interactions, systems biology, 15. Life on land, Biotic stress, plant-insect interactions, QP, metabolomics, QR1-502, Biotechnology, Unravelling metabolomics, Untargeted metabolomics, 13. Climate action, breeding, business, 010606 plant biology & botany
Abstract: International audience; Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant-insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant-insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.
Published: 2021
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49. Is forest regeneration good for biodiversity? Exploring the social dimensions of an apparently ecological debate

Author: Antonia Eastwood, Annie McKee, Raphaël Mathevet, Sam Staddon, Esteve Corbera, Cécile Barnaud, Alison J. Hester, Kirsty Blackstock, Anke Fischer, Joana Reyes, Clémence Moreau, Clélia Sirami, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Université d'Edimbourg, The James Hutton Institute, Universitat Autònoma de Barcelona (UAB), Institució Catalana de Recerca i Estudis Avançats (ICREA), Centre National de la Recherche Scientifique (CNRS), Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), AgreenSkills + fellowship programme - EU's Seventh Framework Programme : FP7-609398 (PCOFUND-GA-2010-267196), INRA Metaprogram Ecoserv, Scottish Government's Strategic Research Programme 2016-2021, and 'Maria de Maeztu' Programme for Units of Excellence of the Spanish Ministry of Science and Innovation : CEX2019-000940-M
Subjects: Environmental justice, Underpinning, 010504 meteorology & atmospheric sciences, Ecology, Discourse analysis, [SDV]Life Sciences [q-bio], Geography, Planning and Development, 15. Life on land, 010501 environmental sciences, Management, Monitoring, Policy and Law, Political ecology, 01 natural sciences, Conceptual framework, Environmental governance, 13. Climate action, Political science, Power, Rewilding, Situated, Comparative study, Protected area, 0105 earth and related environmental sciences
Abstract: International audience; Forest regeneration is a major land-use change in European uplands, and whether or not this is a desirable change for biodiversity is disputed. While this debate seems to be largely situated in the field of natural sciences, this paper aims to also examine its social dimensions. To do so, we adopt a comparative discourse analysis with four cases of protected areas in France, Spain, and Scotland. We draw on a conceptual framework highlighting both the ecological and social factors underpinning the construction of environmental discourses. It notably emphasises the role of interests, ideas and institutions, and the power dynamics underpinning discourse-coalitions. We show how diverging discourses emerged, gained ground, coalesced and competed differently in different contexts, explaining the adoption of seemingly opposite discourses by protected area authorities. These findings reaffirm the need to conceive environmental governance as an on-going deliberative process in order to achieve environmental justice.
Published: 2021
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50. Welcome new Editors!

Author: Dominique Arrouays, Lorna Dawson, Alfred E. Hartemink, University of Wisconsin-Madison, and The James Hutton Institute
Subjects: 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Soil Science, 04 agricultural and veterinary sciences, 010501 environmental sciences, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: International audience
Published: 2021
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