3,148 results on '"Rothamsted Research"'
Search Results
2. Chronic Cardiovascular and Gut-bacteria Effects of Phenolic Rich Oats in Adults With Above Average Blood Pressure
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PepsiCo, Inc., Rothamsted Research, Biotechnology and Biological Sciences Research Council, and Jeremy Paul Edward Spencer, Professor
- Published
- 2016
3. Broadbalk Wheat Experiment plan and cropping since 2018
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,long term experiments ,fertilizer ,arable farming ,cropping system - Abstract
Experiment plan for the Broadbalk Wheat Experiment, showing fertilizer and manure treatments, crop rotations and the Broadbalk wilderness. Details of fertilizer and cropping since 2018.
- Published
- 2021
- Full Text
- View/download PDF
4. Broadbalk Wheat Experiment plan and cropping 1968-2017
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,fungi ,long term experiments ,food and beverages ,arable farming ,fertilizer ,cropping system - Abstract
Experiment plan for the Broadbalk Wheat Experiment, showing fertilizer and and manure treatments, crop rotations and the Broadbalk Wilderness (not to scale). Details of fertilizer and manure treatments and cropping 1968-2017., _**Page 1:** Cover page _**Pages 2-3:** Plan and fertilizer treatments 1968-2017 _**Pages 4-5:** Cropping details 1968-2017, Standardised experimental plan, not to scale, Dervied from Rothamsted Research (2006) Guide to the Classical and other Long-term experiments, datasets and sample archive. Rothamsted Research, Lawes Agricultural Trust, Harpenden, UK. None None
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- 2021
- Full Text
- View/download PDF
5. Broadbalk plan 1926-1967
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,long term experiments ,farmyard manure ,fertilizer - Abstract
Experiment plan for the Broadbalk wheat experiment, 1926-1967, with details of fertilizer and manure treatments, **Page 1:** Cover page -**Pages 2-3:** Broadbalk experiment plan 1926-1967, showing plot layout and treatment codes, with full details of fertilizer and manure treatments applied., Standardised experimental plan (not to scale), Derived from Johnston and Garner (1969) and Rothamsted Experiments Station (1970), Details of the Classical and Long-term field experiments up to 1967. None None
- Published
- 2021
- Full Text
- View/download PDF
6. Park Grass experiment plan and treatments since 1965, updated 2018
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Rothamsted Research
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Rothamsted Research ,experimental design ,liming ,long term experiments ,Park grass long-term experiment ,permanent grassland ,farmyard manure ,fertilizer - Abstract
Standardised experiment plan for the Park Grass experiment since 1965, updated 2018, with details of lime, fertilizer and manure treatments (not to scale). Minor corrections October 2021.
- Published
- 2021
- Full Text
- View/download PDF
7. Broadbalk Fertilizer and Manure Treatments 1852-2021
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,long term experiments ,farmyard manure ,fertilizer ,phosphorous ,nitrogen - Abstract
Description of Broadbalk Wheat Experiment fertilizer and organic manure treatments, 1852-2021. Annual treatments per hectare. Updated June 2021., Updated version of Macdonald et al, 2018. Also derived from Johnston and Garner, 1969. None None
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- 2021
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- View/download PDF
8. Broadbalk plan 1996-2017
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,fungi ,long term experiments ,food and beverages ,arable farming ,cropping system ,fertilizer - Abstract
Experiment plan for the Broadbalk experiment, showing fertilizer and manure treatments and crop rotations (not to scale), with crop rotations from 1996 and fertilizer treatments from 2001. Also showing the Broadbalk Wilderness., **Page 1:** Cover page -**Pages 2-3:** Broadbalk experiment plan 1996-2017, showing plot layout, rotation and treatment codes, and Broadbalk Wilderness., Standardised experimental plan, not to scale., Derived from Rothamsted Research (2006) Guide to the Classical and other Long-term experiments, datasets and sample archive. Rothamsted Research, Lawes Agricultural Trust, Harpenden, UK. None None
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- 2021
- Full Text
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9. Broadbalk Wheat Experiment cropping 1843-2021
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Electronic Rothamsted Archive, Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,long term experiments - Abstract
Cropping details for the Broadbalk wheat experiment, 1843-2021, with details of cultivars, crops and rotations.
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- 2021
- Full Text
- View/download PDF
10. Broadbalk Wheat Experiment plan and cropping 1926-1967
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Rothamsted Research
- Subjects
Broadbalk long-term experiment ,Rothamsted Research ,experimental design ,wheat ,long term experiments ,farmyard manure ,fertilizer - Abstract
Experiment plan for the Broadbalk Wheat Experiment 1926-1967, with details of fertilizer and manure treatments (not to scale). Also cropping details 1926-1967, showing wheat cultivars, wheat/fallow rotations and the different sections. Updated June 2021 with addition of cropping details., **Page 1:** Cover page -**Pages 2-3:** Broadbalk Wheat Experiment plan 1926-1967, showing plot layout and treatments codes, with full details of fertilizer and manure treatments applied. -**Pages 4-5:** Broadbalk Wheat Experiment cropping details 1926-1967, showing wheat cultivars, wheat/fallow rotations and the different sections., Standardised experimental plan (not to scale), Dervived from Johnston and Garner (1969) and Rothamsted Experimental Station (1970), Details of the Classical and Long-term field experiments up to 1967. None None
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- 2021
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11. Woburn long-term liming experiments lime and fertilizer treatments 1962-1996
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Glendining, Margaret and Rothamsted Research
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Rothamsted Research ,liming ,long term experiments ,fertilizer ,arable farming - Abstract
Details of the lime applications, fertilizer treatments and basal fertilizer applied to the Long-term Liming Experiment at Woburn 1962-1996., The Long-term Liming Experiments studied the effects of soil pH, P and other fertilizer treatments on the yields of a sequence of arable crops at two sites, Rothamsted and Woburn, with contrasting soil types., 1) Lime application dates and amounts applied, 1962-1996 2) Fertilizer treatments (P, K, Mg, Mn and S) application amounts, dates and forms, 1962-1996. 3) Basal fertilizer (N, K and Mg) application amounts and forms, 1962-1996., Prepared from experimental plans and Rothamsted Research annual Yields Books. None None
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- 2020
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12. Sustainability Assessment of 175 years of wheat cultivation in the United Kingdom using the AgBalance™ Model LCM 2019 -Poznan (Poland)
- Author
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Gelder, Richard Van, Saling, Peter, Ulrich, Kerstin, Schulze, Sebastian, Granados, Patricia, Goulding, Keith, Perryman, Sarah, Rothamsted Research, Frank, Markus, Basf Se, and Rehl, Torsten
- Published
- 2019
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13. Broadbalk Fertiliser and Manure Treatments 1852-2021
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Rothamsted Research
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Broadbalk long-term experiment ,Rothamsted Research ,wheat ,farmyard manure ,fertilizer ,phosphorous ,nitrogen - Abstract
Description of Broadbalk fertiliser and organic manure treatments, 1852-2021. Annual treatments per hectare., Updated from Macdonald et al, 2018. None None
- Published
- 2018
- Full Text
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14. Guide to the Classical and other Long-term Experiments, Datasets and Sample Archive
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Rothamsted Research
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broadbalk winter wheat ,woburn ,lawes agricultural trust ,agdell ,meteorological data ,saxmundham ,rothamsted ,park grass ,environmental change network ,broadbalk and geescroft wildernesses ,Broadbalk long-term experiment ,woburn ley-arable experiment ,market garden experiment ,hoosfield wheat and fallow ,rothamsted classical experiments ,rothamsted insect survey ,Park grass long-term experiment ,hoosfield spring Barley ,exhaustion land ,Long term experiments ,rothamsted sample archive ,long-term experiments ,garden clover ,barnfield ,highfield ley-arable experiment ,fosters ley-arable experiment ,Hoosfield spring barley long-term experiment - Abstract
The guide to the Rothamsted Classical and other Long-term Experiments, Datasets and Sample Archive. Originally published 2006, updated and reprinted 2012., Introduction ................................................................................................................5 The Classical Experiments - Broadbalk Winter Wheat ..................................................................................8 - Broadbalk and Geescroft Wildernesses ........................................................19 - Park Grass......................................................................................................20 - Hoosfield Spring Barley ..................................................................................31 - Exhaustion Land ............................................................................................35 - Hoosfield Wheat and Fallow ..........................................................................36 - Garden Clover ................................................................................................37 - Barnfield..........................................................................................................38 - Agdell..............................................................................................................39 Other Long-term Experiments - At Rothamsted ................................................................................................40 - At Woburn ......................................................................................................41 - At Saxmundham ............................................................................................43 Meteorological data..................................................................................................44 Long-term Experiments as a Resource ..................................................................45 Sample Archive........................................................................................................46 The Rothamsted Insect Survey ..............................................................................48 Environmental Change Network ..............................................................................51 Electronic Rothamsted Archive................................................................................51 Map of Rothamsted Farm ........................................................................................26
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- 2018
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15. Woburn Experimental Farm Soil and Field Maps
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Watts, Chris, Glendining, Margaret, Castells-Brooke, Nathalie, and Rothamsted Research
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soil organic carbon ,soil fertility ,liming ,long term experiments ,crop yield ,arable farming - Abstract
A collection of maps and plans for the Woburn Experimental Station., Woburn Experimental Farm Soil Texture - Woburn Experimental Farm Soil Series - Complete Legend to Soil Series Revised 2017 - Woburn Farm Field Map - Woburn Farm OS map, including Stackyard
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- 2017
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16. Exhaustion Land Experiment overview figure
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Rothamsted Research
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potatoes ,rainfall patterns ,ecological succession ,precipitation - Abstract
Figure illustrating the main treatment phases for the Exhaustion Land Long-term experiment
- Published
- 2016
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17. Exhaustion Land plan & fertilizer treatments Phase IV 2000-06
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Rothamsted Research
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potatoes ,rainfall patterns ,ecological succession ,precipitation ,cropping system - Abstract
Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV 2000-2006 and showing "P Test" and "K Test" plots.
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- 2016
- Full Text
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18. Exhaustion Land plan & fertilizer treatments Phase V 2007- present
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Rothamsted Research
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soil pH ,climate change ,potatoes ,rainfall patterns ,ecological succession ,precipitation ,cropping system - Abstract
Plan of the Exhaustion Land Experiment illustrating plots and treatments for Phase V 2007
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- 2016
- Full Text
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19. Experimental layout and total nutrients applied, Phase I
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Rothamsted Research
- Subjects
soil pH ,climate change ,potatoes ,rainfall patterns ,ecological succession ,precipitation - Abstract
Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase I (1856-1901).
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- 2016
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20. Exhaustion Land plan & fertilizer treatments Phase IV 1986-92 P build-up
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Rothamsted Research
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soil pH ,potatoes ,precipitation ,cropping system ,Hoosfield spring barley long-term experiment - Abstract
Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV P Build up 1986-1992.
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- 2016
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21. Exhaustion Land Annual P and K inputs 1986 onwards
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Rothamsted Research
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potatoes ,rainfall patterns ,ecological succession ,precipitation - Abstract
Annual P and K Inputs for the Exhaustion land long-term experiment from 1986-2016
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- 2016
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22. Exhaustion Land plan & fertilizer treatments Phase IV 1993-99
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Rothamsted Research
- Subjects
potatoes ,rainfall patterns ,ecological succession ,precipitation ,cropping system - Abstract
Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV 1993-1999 and showing "P Test" and "K Test" plots.
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- 2016
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23. Hoosfield spring barley experiment plans 1968-2000
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Rothamsted Research
- Subjects
Rothamsted Research ,experimental design ,long term experiments ,barley ,farmyard manure ,fertilizer ,Hoosfield spring barley long-term experiment - Abstract
Standardised experiment plans for the Hoosfield spring barley experiment, 1968-2000, with details of fertilizer and manure treatments (not to scale). Includes rotation of potatoes, beans and barley (1968-1978) and silicate treatments (1979-2000)., Derived from plans published in the Rothamsted Guides to the Classical and Field Experiments, 1977 and 1991. None None
- Published
- 2015
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24. Hoosfield spring barley experiment plan 1852-1967
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Rothamsted Research
- Subjects
Rothamsted Research ,experimental design ,long term experiments ,barley ,farmyard manure ,fertilizer ,Hoosfield spring barley long-term experiment - Abstract
Standardised experiment plan for the Hoosfield spring barley experiment, 1852-1967, with details of fertilizer and manure treatments (not to scale)., Derived from Rothamsted Experimental Station (1970): Details of the Classical and Long-term Experiments up to 1967, pp18-21. None None
- Published
- 2012
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25. Park Grass experiment plan and fertilizer treatments 1903-1964
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Rothamsted Research
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Rothamsted Research ,experimental design ,liming ,long term experiments ,Park grass long-term experiment ,permanent grassland ,farmyard manure ,fertilizer - Abstract
Standardised experiment plan for the Park Grass experiment 1903-1964, with details of lime, fertilizer and manure treatments (not to scale).
- Published
- 2010
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- View/download PDF
26. Park Grass experiment plan and treatments 1856-1902
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Rothamsted Research
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Rothamsted Research ,experimental design ,liming ,long term experiments ,Park grass long-term experiment ,permanent grassland ,farmyard manure ,fertilizer - Abstract
Standardised experiment plan for the Park Grass experiment 1856-1902, with details of lime, fertilizer and manure treatments (not to scale).
- Published
- 2010
- Full Text
- View/download PDF
27. Hoosfield spring barley experiment plan 2001 onwards
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Rothamsted Research
- Subjects
Rothamsted Research ,experimental design ,long term experiments ,barley ,farmyard manure ,fertilizer ,Hoosfield spring barley long-term experiment - Abstract
Standardised experiment plan for the Hoosfield spring barley experiment, 2001 onwards (not to scale), with details of fertilizer and manure treatments applied since 1968., Dervied from Rothamsted Guide to the Classical and other Long-term experiments, 2006. None None
- Published
- 2009
- Full Text
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28. Neotropical maize genotypes with different levels of benzoxazinoids affect fall armyworm development
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Mirian F. F. Michereff, Izabela N. Nascimento, Gisele T. Santana, André L. F. Sarria, Miguel Borges, Raúl A. Laumann, David M. Withall, John C. Caulfield, Michael A. Birkett, Maria Carolina Blassioli‐Moraes, MIRIAN F. F. MICHEREFF, IZABELA N. NASCIMENTO, Universidade Federal da Paraíba, GISELE T. SANTANA, Universidade de Brasília, ANDRÉ L. F. SARRIA, Rothamsted Research, Harpenden, UK, MIGUEL BORGES, Cenargen, RAUL ALBERTO LAUMANN, Cenargen, DAVID M. WITHALL, Rothamsted Research, Harpenden, UK, JOHN C. CAULFIELD, Rothamsted Research, Harpenden, UK, MICHAEL A. BIRKETT, Rothamsted Research, Harpenden, UK, and MARIA CAROLINA BLASSIOLI MORAES, Cenargen.
- Subjects
Direct defence ,Benzoxazinoids ,Physiology ,Insect Science ,Maize genotypes ,Fall armyworm ,Ecology, Evolution, Behavior and Systematics - Abstract
Plants are equipped with various defensive attributes against herbivores, including volatile and nonvolatile compounds. In maize plants, benzoxazinoids mediate resistance against some herbivores, with the most abundant being (2R)-2-β-D-glucopyranosyloxy-4-hydroxy-7-methoxy-2H-1,4-benzoxazin3(4H)-one (DIMBOA-Glc), and its corresponding aglucone 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA). Both compounds have been shown to interfere in the larval development of generalist herbivores but are less effective on specialist, that is, grass-feeding, herbivores. Using a Brazilian population of Spodoptera frugiperda, we investigated (i) the level of constitutive benzoxazinoids in Neotropical maize genotypes, that is, Zapalote Chico, Mirt 2A, Sintético Spodoptera, L3, BRS 4103 and BRS 1040 (ii) the effect of S. frugiperda herbivory on benzoxazinoid levels in these genotypes and (iii) the impact of the genotypes on the development of S. frugiperda larvae. The results showed that the six maize genotypes produce different levels of benzoxazinoids, with Mirt 2A and BRS 1040 producing constitutively higher levels of HDMBOA-Glc and DIMBOA-Glc respectively compared to the other genotypes. When feeding on BRS 1040 and Mirt 2A, S. frugiperda larvae took an additional week to pupate, but this effect does not affect larval survival, what was the same and high on all the genotypes (>70%). Furthermore, production of DIMBOA-Glc and HDMBOA-Glc in these genotypes was suppressed, suggesting that S. frugiperda larvae can alter maize defence plant responses. In summary, our results demonstrate that Neotropical maize genotypes produce varying levels of benzoxazinoids, genotypes respond differently to S.frugiperda herbivory and S. frugiperda is able to cope with secondary metabolite-based defence in Neotropical maize. Made available in DSpace on 2022-05-16T13:13:18Z (GMT). No. of bitstreams: 1 Physiological-Entomology-2022-Michereff-Neotropical-maize-genotypes-with-different-levels-of-benzoxazinoids-affect.pdf: 962114 bytes, checksum: cbbcdb1f0711b41ceaa6476cd8972046 (MD5) Previous issue date: 2022 Na publicação - Maria Carolina Blassioli-Moraes.
- Published
- 2022
29. Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization
- Author
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Antônio Marcos Coelho, Sylvia Morais de Sousa, Andrew L. Neal, Mariana Lourenço Campolino, Ubiraci Gomes de Paula Lana, David Hughes, Timothy I. McLaren, Eliane Aparecida Gomes, ANDREW L. NEAL, Rothamsted Research, TIMOTHY MCLAREN, Swiss Federal Institute of Technology, MARIANA LOURENÇO CAMPOLINO, Universidade Federal de Sao João del-Rei, DAVID HUGHES, Rothamsted Research, ANTONIO MARCOS COELHO, CNPMS, UBIRACI GOMES DE PAULA LANA, CNPMS, ELIANE APARECIDA GOMES, CNPMS, and SYLVIA MORAIS DE SOUSA TINOCO, CNPMS.
- Subjects
0106 biological sciences ,0301 basic medicine ,Sorgo ,chemistry.chemical_element ,engineering.material ,Biology ,01 natural sciences ,Applied Microbiology and Biotechnology ,Microbiology ,Soil ,03 medical and health sciences ,Milho ,Botany ,Sorghum ,Phylogeny ,Soil Microbiology ,Rhizosphere ,Ecology ,Ecotype ,Fitase ,Phosphorus ,Genetic transfer ,food and beverages ,Cerrado ,Phosphoric Monoester Hydrolases ,Maize ,Fosfatase ,Phylogenetic diversity ,030104 developmental biology ,Phosphorite ,chemistry ,Fertilization ,engineering ,Phytase ,Microbiome ,Metagenomics ,Fertilizer ,Metagenômica ,Brazil ,Microbioma ,010606 plant biology & botany - Abstract
Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere. Made available in DSpace on 2021-04-22T12:33:54Z (GMT). No. of bitstreams: 1 Crop-type.pdf: 3986814 bytes, checksum: 821c0c429ef4059018e435040228ca78 (MD5) Previous issue date: 2021
- Published
- 2021
30. Wheat dwarfing influences selection of the rhizosphere microbiome
- Author
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Penny R. Hirsch, Itamar Soares de Melo, Tim H. Mauchline, Maike Rossmann, Vanessa Nessner Kavamura, Rebekah J. Robinson, David Hughes, Ian M. Clark, Rodrigo Mendes, VANESSA NESSNER KAVAMURA, Rothamsted Research, REBEKAH J ROBINSON, Royal Horticultural Society, DAVID HUGHES, Rothamsted Research, IAN M CLARK, Rothamsted Research, MIKE ROSSMANN, ITAMAR SOARES DE MELO, CNPMA, PENNY R HIRSCH, Rothamsted Research, RODRIGO MENDES, CNPMA, and TIM, Rothamsted Research.
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:Medicine ,Plant Roots ,7. Clean energy ,01 natural sciences ,Plant breeding ,RNA, Ribosomal, 16S ,Cultivar ,lcsh:Science ,Triticum ,2. Zero hunger ,Rhizosphere ,Multidisciplinary ,biology ,Microbiota ,food and beverages ,Agriculture ,Organ Size ,Dwarfing ,Microbiologia do Solo ,VARIEDADES VEGETAIS ,Ribosomal RNA ,Wheat ,Proteobacteria ,Soil microbiology ,musculoskeletal diseases ,congenital, hereditary, and neonatal diseases and abnormalities ,endocrine system ,Dwarf cultivars ,Trigo ,Melhoramento Genético Vegetal ,Rizosfera ,Microbiology ,Article ,Actinobacteria ,03 medical and health sciences ,lcsh:R ,fungi ,15. Life on land ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Agronomy ,lcsh:Q ,Microbiome ,010606 plant biology & botany ,Acidobacteria - Abstract
The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere. Made available in DSpace on 2020-07-16T11:12:44Z (GMT). No. of bitstreams: 1 Melo-wheat-dwarfing-2020.pdf: 1489035 bytes, checksum: e5b313aaa742787e5b663c2fcf4f7eb0 (MD5) Previous issue date: 2020
- Published
- 2020
31. Alley cropping agroforestry systems: Reservoirs for weeds or refugia for plant diversity?
- Author
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Delphine Meziere, Guillaume Fried, Sébastien Boinot, Pierre-Eric Lauri, Jonathan Storkey, Helen Metcalfe, Karim Barkaoui, Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), Unité entomologie et plantes invasives, Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Rothamsted Research, and The doctoral research of SB is financially supported by La Fondation de France. This research was also part of the project BAG’AGES (Bassin Adour-Garonne : quelles performances des pratiques AGroécologiquES?) supported by Agence de l’Eau Adour-Garonne. SB would like to thank the French National Institute for Agricultural Research (INRA) for funding his three-months stay at Rothamsted Research, UK. JS and HM are funded by the research programme NE/N018125/1 LTS-M ASSIST.
- Subjects
0106 biological sciences ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,F40 - Écologie végétale ,spillover ,F08 - Systèmes et modes de culture ,Biology ,010603 evolutionary biology ,01 natural sciences ,Culture intercalaire ,under story vegetation strip ,functional trait ,2. Zero hunger ,Plante d'ombrage ,Ecology ,Intensive farming ,business.industry ,Agroforestry ,temperate region ,04 agricultural and veterinary sciences ,Vegetation ,15. Life on land ,Weed control ,Tillage ,semi-natural habitat ,Agriculture ,hemerophobic species ,040103 agronomy & agriculture ,Organic farming ,0401 agriculture, forestry, and fisheries ,Animal Science and Zoology ,Biodiversité ,business ,Weed ,Agronomy and Crop Science ,Cropping - Abstract
International audience; Alley cropping agroforestry is a land use practice in which arable crops are grown between tree rows. In such agroforestry systems, non-crop herbaceous vegetation develops on the tree rows, resulting in understory vegetation strips (UVS). UVS are perceived both as reservoirs for weeds and opportunities for biodiversity conservation. The purpose of this study was to assess the contribution of UVS to (i) plant spillover and (ii) plant diversity conservation, depending on their functional structure and the farming system. Vegetation surveys were carried out in May 2017 in South-Western France over 16 winter cereal fields (8 alley cropping agroforestry systems and 8 pure crop controls), half under conventional farming and half under organic farming. Using data on plant functional traits related to dispersal strategies and response to agricultural disturbances, we explained the mechanisms involved in plant spillover between habitats. The study revealed that very few species were able to disperse far into crop alleys, except perennial species producing rhizomes and stolons whose spread has been favored by tillage. The presence of UVS in agroforestry fields did not increase weed-crop ratio (i.e. weed coverage / weed and crop coverage) in adjacent crop alleys. On the other hand, UVS harbored richer and more abundant floras (with high proportions of species rarely found in arable habitats) compared to crop alleys and pure crop controls, especially under conventional farming. The functional approach provided insights for weed management in alley cropping agroforestry systems in order to optimize plant diversity conservation without increasing weed-crop ratio. This study showed the relevance of using the functional approach to understand the mechanisms behind plant spillover in cropping systems that integrate semi-natural habitats.
- Published
- 2019
32. Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat
- Author
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Penny R. Hirsch, Ian M. Clark, Tim H. Mauchline, Rodrigo Mendes, Rifat Hayat, David Hughes, Rebekah J. Robinson, Vanessa Nessner Kavamura, Maike Rossmann, VANESSA NESSNER KAVAMURA, Rothamsted Research, REBEKAH J ROBINSON, Plant Pathology Laboratory, RHS, RIFAT HAYAT, Pir Mehr Ali Shah Arid Agriculture University, IAN MICHAEL CLARK, Rothamsted Research, DAVID HUGHES, Rothamsted Research, MAIKE ROSSMANN, PENNY R HIRSCH, Rothamsted Research, RODRIGO MENDES, CNPMA, and TIM H MAUCHLINE, Rothamsted Research.
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Microbiology (medical) ,Land management ,lcsh:QR1-502 ,microbiome ,embryo ,Trigo ,Biology ,Rizosfera ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,wheat ,Microbiome ,Microbial inoculant ,030304 developmental biology ,Original Research ,2. Zero hunger ,0303 health sciences ,Rhizosphere ,Seed ,Land use ,030306 microbiology ,business.industry ,Root microbiome ,Community structure ,food and beverages ,15. Life on land ,Semente ,Biotechnology ,Microbial population biology ,Embryo ,endosphere ,Wheat ,Seeds ,Manejo do Solo ,População Microbiana ,Endosphere ,business ,rhizosphere ,seed - Abstract
Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the rhizosphere, particular operational taxonomic units (OTUs) in the culture-dependent fraction were absent from the culture-independent fraction, indicating that deeper sequence analysis is required for this approach to be exhaustive. We also found that the microbial seed load defined the endosphere, but not rhizosphere, community structure for plants grown in soil which was not wheat adapted. Together, these findings increase our understanding of the importance of land management and microbial seed load in shaping the root microbiome of wheat and this knowledge will facilitate the exploitation of plant?microbe interactions for the development of novel microbial inoculants. Made available in DSpace on 2019-11-28T18:09:03Z (GMT). No. of bitstreams: 1 MendesLandManagement2019.pdf: 1523874 bytes, checksum: b77a63cae9c39bf2c86f6b11f4925e17 (MD5) Previous issue date: 2019
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- 2019
33. Fortification of Human Milk for Preterm Infants: Update and Recommendations of the European Milk Bank Association (EMBA) Working Group on Human Milk Fortification
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Sertac Arslanoglu, Clair-Yves Boquien, Caroline King, Delphine Lamireau, Paola Tonetto, Debbie Barnett, Enrico Bertino, Antoni Gaya, Corinna Gebauer, Anne Grovslien, Guido E. Moro, Gillian Weaver, Aleksandra Maria Wesolowska, Jean-Charles Picaud, Istanbul Medeniyet University, Partenaires INRAE, Physiopathologie des Adaptations Nutritionnelles (PhAN), Université de Nantes (UN)-Institut National de la Recherche Agronomique (INRA), Imperial College Healthcare NHS Trust, CHU Bordeaux [Bordeaux], Neonatal Unit, Karolinska Institutet [Stockholm], Royal Hospital for Sick Children, Fundació Banc Sang i Teixits de les Illes Balears, Abteilung Neonatologie Klinik und Poliklinik für Kinder und Jugendliche, Oslo University Hospital [Oslo], Associazione Italiana delle Banche del Latte Umano Donato, BBSRC Rothamsted Research, University of Warsaw (UW), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Institut National de la Recherche Agronomique (INRA)-Université de Nantes (UN), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), ProdInra, Migration, and Arslanoglu, Sertac
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Adjustable fortification ,Growth ,Human milk ,Individualized fortification ,Nutrition ,Prematurity ,Protein ,Post discharge ,growth ,Fortification ,Médecine humaine et pathologie ,Review ,030204 cardiovascular system & hematology ,Health benefits ,Breast milk ,Health outcomes ,Pediatrics ,03 medical and health sciences ,0302 clinical medicine ,030225 pediatrics ,Intensive care ,Environmental health ,medicine ,Food and Nutrition ,adjustable fortification ,human milk ,individualized fortification ,nutrition ,prematurity ,protein ,[SDV.MHEP] Life Sciences [q-bio]/Human health and pathology ,business.industry ,lcsh:RJ1-570 ,lcsh:Pediatrics ,medicine.disease ,3. Good health ,[SDV.AEN] Life Sciences [q-bio]/Food and Nutrition ,Low birth weight ,Bronchopulmonary dysplasia ,Alimentation et Nutrition ,Pediatrics, Perinatology and Child Health ,Human health and pathology ,medicine.symptom ,business ,[SDV.AEN]Life Sciences [q-bio]/Food and Nutrition ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
Evidence indicates that human milk (HM) is the best form of nutrition uniquely suited not only to term but also to preterm infants conferring health benefits in both the short and long-term. However, HM does not provide sufficient nutrition for the very low birth weight (VLBW) infant when fed at the usual feeding volumes leading to slow growth with the risk of neurocognitive impairment and other poor health outcomes such as retinopathy and bronchopulmonary dysplasia. HM should be supplemented (fortified) with the nutrients in short supply, particularly with protein, calcium, and phosphate to meet the high requirements of this group of babies. In this paper the European Milk Bank Association (EMBA) Working Group on HM Fortification discusses the existing evidence in this field, gives an overview of different fortification approaches and definitions, outlines the gaps in knowledge and gives recommendations for practice and suggestions for future research. EMBA recognizes that Standard Fortification, which is currently the most utilized regimen in neonatal intensive care units, still falls short in supplying sufficient protein for some VLBWinfants. EMBA encourages the use of Individualized Fortification to optimize nutrient intake. Adjustable Fortification and Targeted Fortification are 2 methods of individualized fortification. The quality and source of human milk fortifiers constitute another important topic. There is work looking at human milk derived fortifiers, but it is still too early to draw precise conclusions about their use. The pros and cons are discussed in this Commentary in addition to the evidence around use of fortifiers post discharge., The authors thank the Italian Association of Human Milk Banks (Associazione Italiana Banche del Latte Umano Donato = AIBLUD) for its continuous efforts to promote research in the field of donor human milk and human milk banks, and for the financial support given to the publication of this manuscript.
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- 2019
34. Development of pull and push-pull systems for management of Lesser Mealworm, Alphitobius diaperinus, in poultry houses using alarm and aggregation pheromones
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HASSEMER, M. J., BORGES, M., WITHALL, D. M., PICKETT, J. A., LAUMANN, R. A., BIRKETT, M. A., BLASSIOLI-MORAES, M. C., MARLA J. HASSEMER, UNB, MIGUEL BORGES, Cenargen, DAVID M. WITHALL, ROTHAMSTED RESEARCH, UK, JOHN A. PICKETT, CARDIF UNIVERSITY, UK, RAUL ALBERTO LAUMANN, Cenargen, MICHAEL A. BIRKETT, ROTHAMSTED RESEARCH, UK, and MARIA CAROLINA BLASSIOLI MORAES, Cenargen.
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Attractant and repellent ,fungi ,Repellent ,Aggregation pheromone ,Poultry production ,Pheromone traps ,Attractant - Abstract
BACKGROUND The lesser mealworm, Alphitobius diaperinus (Coleoptera: Tenebrionidae), is the most important insect pest affecting poultry production around the world, with all life stages being susceptible to infection by bacteria, viruses and fungi. Control of A. diaperinus in poultry houses using intensive insecticide application is not effective due to the cryptic behaviour of this pest. Here, we evaluated the potential of recently identified A. diaperinus alarm (1,4‐benzoquinone, 2‐methyl‐1,4‐benzoquinone and 2‐ethyl‐1,4‐benzoquinone) and aggregation [(R)‐limonene, 2‐nonanone, (E)‐ocimene, (S)‐linalool, (R)‐daucene and (E,E)‐α‐farnesene] pheromones as tools for the management of this pest in poultry houses in Brazil. RESULTS Laboratory arena assays with synthetic alarm pheromone confirmed A. diaperinus repellency. In an initial field assay, traps baited with synthetic aggregation pheromone captured significantly more insects than control traps. In further field assays that compared a pull (aggregation pheromone) and a push–pull (simultaneous alarm/aggregation pheromone deployment) system, a higher number of A. diaperinus were captured in aggregation pheromone‐baited traps in the push–pull system. CONCLUSION Our results suggest that alarm and aggregation pheromones can be deployed in poultry houses to trap significant numbers of adult A. diaperinus. Studies are underway to determine the potential for using these components as part of an integrated A. diaperinus management strategy.
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- 2019
35. The contribution of spatial mass effects to plant diversity in arable fields
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Sébastien Boinot, Helen Metcalfe, Jonathan Storkey, Kirsty L. Hassall, Rothamsted Research, BBSRC Rothamsted Research, Partenaires INRAE, Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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)
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0106 biological sciences ,arable fields ,resident weed community ,010603 evolutionary biology ,01 natural sciences ,fidelity score ,transient community ,Abundance (ecology) ,weeds ,Ruderal species ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Research Articles ,2. Zero hunger ,Vegetal Biology ,Ecology ,spatial mass effects ,010604 marine biology & hydrobiology ,Plant community ,15. Life on land ,plant diversity ,conservation headlands ,Geography ,field edge ,Habitat ,agricultural landscape ,Biological dispersal ,Species richness ,Arable land ,Weed ,Biologie végétale ,Research Article - Abstract
In arable fields, plant species richness consistently increases at field edges. This potentially makes the field edge an important habitat for the conservation of the ruderal arable flora (or ‘weeds’) and the invertebrates and birds it supports. Increased diversity and abundance of weeds in crop edges could be owing to either a reduction in agricultural inputs towards the field edge and/or spatial mass effects associated with dispersal from the surrounding landscape.We contend that the diversity of weed species in an arable field is a combination of resident species, that can persist under the intense selection pressure of regular cultivation and agrochemical inputs (typically more ruderal species), and transient species that rely on regular dispersal from neighbouring habitats (characterised by a more ‘competitive’ ecological strategy).We analysed a large dataset of conventionally managed arable fields in the UK to study the effect of the immediate landscape on in‐field plant diversity and abundance and to quantify the contribution of spatial mass effects to plant diversity in arable fields in the context of the ecological strategy of the resulting community.We demonstrated that the decline in diversity with distance into an arable field is highly dependent on the immediate landscape, indicating the important role of spatial mass effects in explaining the increased species richness at field edges in conventionally managed fields.We observed an increase in the proportion of typical arable weeds away from the field edge towards the centre. This increase was dependent on the immediate landscape and was associated with a higher proportion of more competitive species, with a lower fidelity to arable habitats, at the field edge. Synthesis and applications. Conserving the ruderal arable plant community, and the invertebrates and birds that use it as a resource, in conventionally managed arable fields typically relies on the targeted reduction of fertilisers and herbicides in so‐called ‘conservation headlands’. The success of these options will depend on the neighbouring habitat and boundary. They should be placed along margins where the potential for ingress of competitive species, that may become dominant in the absence of herbicides, is limited. This will enhance ecosystem services delivered by the ruderal flora and reduce the risk of competitive species occurring in the crop., Conserving the ruderal arable plant community, and the invertebrates and birds that use it as a resource, in conventionally managed arable fields typically relies on the targeted reduction of fertilisers and herbicides in so‐called ‘conservation headlands’. The success of these options will depend on the neighbouring habitat and boundary. They should be placed along margins where the potential for ingress of competitive species, that may become dominant in the absence of herbicides, is limited. This will enhance ecosystem services delivered by the ruderal flora and reduce the risk of competitive species occurring in the crop.
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- 2019
36. Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici
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Stephen J. Powers, William Marande, Hélène Bergès, Jason J. Rudd, Cristobal Uauy, Wing-Sham Lee, Florence Cambon, Robert King, Andrew L. Phillips, Kostya Kanyuka, Cyrille Saintenac, Thierry Langin, Kim E. Hammond-Kosack, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Rothamsted Research, BBSRC Rothamsted Research, Partenaires INRAE, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Plant Sciences, University of Cambridge [UK] (CAM), Norwich Research Park, Institute Strategic Program from the Biotechnology and Biological Sciences Research Council of the UK (BBSRC) [BB/J/00426x/1, BB/P016855/1], French National Institute for Agricultural Research (INRA), and Biotechnology and Biological Sciences Research Council (BBSRC)
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0106 biological sciences ,0301 basic medicine ,Hypersensitive response ,Quantitative Trait Loci ,Mutagenesis (molecular biology technique) ,Plant disease resistance ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,Septoria ,Ascomycota ,Genetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Gene ,Triticum ,Disease Resistance ,Plant Diseases ,2. Zero hunger ,Cloning ,Wall-Associated Kinase ,biology ,Effector ,food and beverages ,Chromosome Mapping ,biology.organism_classification ,Plants, Genetically Modified ,030104 developmental biology ,Amino Acid Substitution ,Mutagenesis ,Host-Pathogen Interactions ,biology.protein ,Protein Kinases ,010606 plant biology & botany - Abstract
International audience; Deployment of fast-evolving disease-resistance genes is one of the most successful strategies used by plants to fend off pathogens(1,2). In gene-for-gene relationships, most cloned disease-resistance genes encode intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) recognizing pathogen-secreted isolate-specific avirulence (Avr) effectors delivered to the host cytoplasm(3,4). This process often triggers a localized hypersensitive response, which halts further disease development(5). Here we report the map-based cloning of the wheat Stb6 gene and demonstrate that it encodes a conserved wall-associated receptor kinase (WAK)-like protein, which detects the presence of a matching apoplastic effector(6-8) and confers pathogen resistance without a hypersensitive response(9). This report demonstrates gene-for-gene disease resistance controlled by this class of proteins in plants. Moreover, Stb6 is, to our knowledge, the first cloned gene specifying resistance to Zymoseptoria tritici, an important foliar fungal pathogen affecting wheat and causing economically damaging septoria tritici blotch (STB) disease(10-12).
- Published
- 2017
37. GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease
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Roberto C. Togawa, Natália F. Martins, Emmanuel Bresso, Bernard Maigret, Kim E. Hammond-Kosack, Martin Urban, Computational Algorithms for Protein Structures and Interactions (CAPSID), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Embrapa Uva e Vinho (BRAZIL), Rothamsted Research, Universidade Federal do Ceará = Federal University of Ceará (UFC), EMBRAPA, CAPES, CNPq (Brazil), BBSRC (UK), EMBRAPA (Br), LORIA (Fr), Rothamsted Research (UK), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Biotechnology and Biological Sciences Research Council (BBSRC)
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0301 basic medicine ,030103 biophysics ,In silico ,Genomics ,Computational biology ,Biology ,Molecular Dynamics Simulation ,Biochemistry ,Chemical library ,Receptors, G-Protein-Coupled ,Fungal Proteins ,03 medical and health sciences ,Structural bioinformatics ,chemistry.chemical_compound ,Fusarium ,Structural Biology ,Homology modeling ,Molecular Biology ,Plant Diseases ,2. Zero hunger ,Fungal protein ,Virtual screening ,business.industry ,Applied Mathematics ,Research ,food and beverages ,Computer Science Applications ,Biotechnology ,Fusarium graminearum ,030104 developmental biology ,G-protein coupled receptors ,Fusarium head blight ,chemistry ,13. Climate action ,Docking (molecular) ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,business ,Signal Transduction - Abstract
Backgound Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination. Results In this study, GPCRs were predicted in the FG proteome using a manually curated pipeline dedicated to the identification of GPCRs. Based on several successive filters, the most appropriate GPCR candidate target for developing new fungicides was selected. Searching for new compounds blocking this particular target requires the knowledge of its 3D-structure. As no experimental X-Ray structure of the selected protein was available, a 3D model was built by homology modeling. The model quality and stability was checked by 100 ns of molecular dynamics simulations. Two stable conformations representative of the conformational families of the protein were extracted from the 100 ns simulation and were used for an ensemble docking campaign. The model quality and stability was checked by 100 ns of molecular dynamics simulations previously to the virtual screening step. The virtual screening step comprised the exploration of a chemical library with 11,000 compounds that were docked to the GPCR model. Among these compounds, we selected the ten top-ranked nontoxic molecules proposed to be experimentally tested to validate the in silico simulation. Conclusions This study provides an integrated process merging genomics, structural bioinformatics and drug design for proposing innovative solutions to a world wide threat to grain producers and consumers. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1342-9) contains supplementary material, which is available to authorized users.
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- 2016
38. Simulation of winter wheat response to variable sowing dates and densities in a high-yielding environment
- Author
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Dueri, Sibylle, Brown, Hamish, Asseng, Senthold, Ewert, Frank, Webber, Heidi, George, Mike, Craigie, Rob, Guarin, Jose Rafael, Pequeno, Diego N.L., Stella, Tommaso, Ahmed, Mukhtar, Alderman, Phillip D., Basso, Bruno, Berger, Andres G., Mujica, Gennady Bracho, Cammarano, Davide, Chen, Yi, Dumont, Benjamin, Rezaei, Ehsan Eyshi, Fereres, Elias, Ferrise, Roberto, Gaiser, Thomas, Gao, Yujing, Garcia-Vila, Margarita, Gayler, Sebastian, Hochman, Zvi, Hoogenboom, Gerrit, Kersebaum, Kurt C., Nendel, Claas, Olesen, Jørgen E., Padovan, Gloria, Palosuo, Taru, Priesack, Eckart, Pullens, Johannes W.M., Rodríguez, Alfredo, Rötter, Reimund P., Ramos, Margarita Ruiz, Semenov, Mikhail A., Senapati, Nimai, Siebert, Stefan, Srivastava, Amit Kumar, Stöckle, Claudio, Supit, Iwan, Tao, Fulu, Thorburn, Peter, Wang, Enli, Weber, Tobias Karl David, Xiao, Liujun, Zhao, Chuang, Zhao, Jin, Zhao, Zhigan, Zhu, Yan, Martre, Pierre, Rebetzke, Greg, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), The New Zealand Institute for Plant & Food Research Limited [Auckland] (Plant & Food Research), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Brandenburg University of Technology [Cottbus – Senftenberg] (BTU), Foundation for Arable Research (FAR), University of Florida [Gainesville] (UF), Earth Institute at Columbia University, Columbia University [New York], International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Swedish University of Agricultural Sciences (SLU), Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), Oklahoma State University [Stillwater] (OSU), Michigan State University [East Lansing], Michigan State University System, Instituto Nacional de Investigación Agropecuaria (INIA), Georg-August-University = Georg-August-Universität Göttingen, Aarhus University [Aarhus], Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Córdoba = University of Córdoba [Córdoba], Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence (UniFI), Institute of Crop Science and Resource Conservation [Bonn] (INRES), University of Hohenheim, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Global Change Research Centre (CzechGlobe), University of Potsdam = Universität Potsdam, Natural Resources Institute Finland (LUKE), Helmholtz Zentrum München = German Research Center for Environmental Health, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Institute of Biochemical Plant Pathology (BIOP), Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Washington State University (WSU), Wageningen University and Research [Wageningen] (WUR), Zhejiang University, Nanjing Agricultural University (NAU), China Agricultural University (CAU), Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4 and was supported by the French National Research Institute for Agriculture, Food (INRAE) and the International Maize and Wheat Improvement Center (CIMMYT) through the International Wheat Yield Partnership (IWYP, grant IWYP115)., metaprogram Agriculture and forestry in the face of climate change: adaptation and mitigation (CLIMAE) of INRAE, grant-aided support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat [BB/P016855/1] and Achieving Sustainable Agricultural Systems [NE/N018125/1] jointly funded with NERC, DivCSA project funded by the Academy of Finland (decision no. 316215)., National Natural Science Foundation of China (No. 31761143006), financial support from BARISTA project (031B0811A) through ERA-NET SusCrop under EU-FACCE JPI, German Federal Ministry of Education and Research (BMBF) through the BonaRes project ’’I4S’’ (031B0513I), German Federal Ministry of Education and Research (BMBF) through the BonaRes Project 'Soil3' (FKZ 031B0026A), Ministry of Education, Youth and Sports of Czech Republic through SustES—Adaption strategies for sustainable ecosystem services and food security under adverse environmental conditions (CZ.02.1.01/0.0/0.0/16_019/000797), Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2070 – 390732324', German Research Foundation (DFG, Grant Agreement SFB 1253/1 2017), European Project: 618105,EC:FP7:KBBE,FP7-ERANET-2013-RTD,FACCE ERA NET PLUS(2013), Institut National de la Recherche Agronomique (France), International Maize and Wheat Improvement Center, International Wheat Yield Partnership, National Natural Science Foundation of China, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Education, Youth and Sports (Czech Republic), German Research Foundation, Biotechnology and Biological Sciences Research Council (UK), Natural Environment Research Council (UK), and Academy of Finland
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Physiology ,Climate Change ,sowing date ,Plant Science ,CHINA ,Multi-model Ensemble ,New Zealand ,Sowing Date ,Sowing Density ,Tiller Mortality ,Tillering ,Wheat ,Yield Potential ,tillering ,wheat ,USE EFFICIENCY ,sowing density ,Life Science ,Biomass ,ADAPTATION ,PLANT-DENSITY ,Triticum ,METAANALYSIS ,Multi-model ensemble ,WIMEK ,CLIMATE-CHANGE ,tiller mortality ,PRODUCTIVITY ,Temperature ,CROP MODELS ,yield potential ,[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation ,ROTATION ,GROWTH ,Water Systems and Global Change ,Seasons - Abstract
Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of MME to capture crop responses to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season. We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients, and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities, and warmer winter temperatures., This study was a part of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4 and was supported by the French National Research Institute for Agriculture, Food (INRAE) and the International Maize and Wheat Improvement Center (CIMMYT) through the International Wheat Yield Partnership (IWYP, grant IWYP115). SD and PM acknowledge support from the metaprogram Agriculture and forestry in the face of climate change: adaptation and mitigation (CLIMAE) of INRAE. YC and FT acknowledge support from the National Natural Science Foundation of China (No. 31761143006). RPR and GBM acknowledge financial support from BARISTA project (031B0811A) through ERA-NET SusCrop under EU-FACCE JPI. KCK was funded by the German Federal Ministry of Education and Research (BMBF) through the BonaRes project ’’I4S’’ (031B0513I). AS and TG acknowledge funding by the German Federal Ministry of Education and Research (BMBF) through the BonaRes Project “Soil3” (FKZ 031B0026A). KCK and JEO were supported by the Ministry of Education, Youth and Sports of Czech Republic through SustES—Adaption strategies for sustainable ecosystem services and food security under adverse environmental conditions (CZ.02.1.01/0.0/0.0/16_019/000797). FE acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2070 – 390732324”. TKDW was funded by the German Research Foundation (DFG, Grant Agreement SFB 1253/1 2017). MAS and NS at Rothamsted Research received grant-aided support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat [BB/P016855/1] and Achieving Sustainable Agricultural Systems [NE/N018125/1] jointly funded with NERC. TP and FT are supported by the DivCSA project funded by the Academy of Finland (decision no. 316215).
- Published
- 2022
39. Improving crop Yield potential: Underlying biological processes and future prospects
- Author
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Burgess, Alexandra, Masclaux-Daubresse, Céline, Strittmatter, Günter, Weber, Andreas, Taylor, Samuel Harry, Harbinson, Jeremy, Yin, Xinyou, Long, Stephen, Paul, Matthew, Westhoff, Peter, Loreto, Francesco, Ceriotti, Aldo, Saltenis, Vandasue, Pribil, Mathias, Nacry, Philippe, Scharff, Lars, Jensen, Poul Erik, Muller, Bertrand, Cohan, Jean‐pierre, Foulkes, John, Rogowsky, Peter, Debaeke, Philippe, Meyer, Christian, Nelissen, Hilde, Inzé, Dirk, Klein Lankhorst, René, Parry, Martin, Murchie, Erik, Baekelandt, Alexandra, University of Nottingham, UK (UON), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Lancaster Environment Centre, Lancaster University, Wageningen University and Research [Wageningen] (WUR), University College of London [London] (UCL), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Copenhagen = Københavns Universitet (UCPH), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Food Science [Copenhagen] (UCPH FOOD), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), ARVALIS - Institut du végétal [Paris], Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), European Commission 817690, and European Project: 817690,ERC
- Subjects
food supply ,photosynthesis ,[SDV]Life Sciences [q-bio] ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,crop yield ,nutrient remobilisation ,crop improvement ,organ growth - Abstract
International audience; The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant- derived products. In the coming years, plant- based research will be among the major drivers ensuring food security and the expansion of the bio- based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.
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- 2023
40. Modelling the impact of environmental changes on grassland systems with SPACSYS
- Author
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Gianni Bellocchi, Andrew P. Whitmore, Lianhai Wu, Department of Sustainable Soils & Grassland Systems Rothamsted Research, Rothamsted Research, Harpenden, UR 0874 Unité de recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA), Institut National de la Recherche Agronomique (INRA), and MACSUR
- Subjects
geography ,geography.geographical_feature_category ,Agroforestry ,[SDE.MCG]Environmental Sciences/Global Changes ,prairies ,Dynamic simulation model ,Environmental science ,General Medicine ,Ecosystem respiration ,scénarios ,Grassland ,modélisation - Abstract
absent
- Published
- 2015
41. Modulation of lipid biosynthesis by stress in diatoms
- Author
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Annick Morant-Manceau, Virginie Mimouni, Lionel Ulmann, Benoît Schoefs, Johnathan A. Napier, Virginie Pasquet, Olga Sayanova, Rothamsted Research, Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Chemistry, Rothamsted Research-Rothamsted Research, Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques
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0301 basic medicine ,Fixed carbon ,Bioengineering ,Review Article ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Organic molecules ,stress ,03 medical and health sciences ,Stress, Physiological ,Lipid biosynthesis ,Botany ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,ComputingMilieux_MISCELLANEOUS ,Diatoms ,chemistry.chemical_classification ,Abiotic component ,fungi ,Carbon fixation ,Articles ,Lipid Metabolism ,Lipids ,Temperature stress ,Carbon ,Cold Temperature ,nutrition ,030104 developmental biology ,chemistry ,Biofuel ,biofuel ,omega-3 ,General Agricultural and Biological Sciences ,Polyunsaturated fatty acid - Abstract
Diatoms are responsible for up to 40% of the carbon fixation in our oceans. The fixed carbon is moved through carbon metabolism towards the synthesis of organic molecules that are consumed through interlocking foodwebs, and this process is strongly impacted by the abiotic environment. However, it has become evident that diatoms can be used as ‘platform’ organisms for the production of high valuable bio-products such as lipids, pigments and carbohydrates where stress conditions can be used to direct carbon metabolism towards the commercial production of these compounds. In the first section of this review, some aspects of carbon metabolism in diatoms and how it is impacted by environmental factors are briefly described. The second section is focused on the biosynthesis of lipids and in particular omega-3 long-chain polyunsaturated fatty acids and how low temperature stress impacts on the production of these compounds. In a third section, we review the recent advances in bioengineering for lipid production. Finally, we discuss new perspectives for designing strains for the sustainable production of high-value lipids. This article is part of the themed issue ‘The peculiar carbon metabolism in diatoms’.
- Published
- 2017
42. Evidence for increasing global wheat yield potential
- Author
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Jose Rafael Guarin, Pierre Martre, Frank Ewert, Heidi Webber, Sibylle Dueri, Daniel Calderini, Matthew Reynolds, Gemma Molero, Daniel Miralles, Guillermo Garcia, Gustavo Slafer, Francesco Giunta, Diego N L Pequeno, Tommaso Stella, Mukhtar Ahmed, Phillip D Alderman, Bruno Basso, Andres G Berger, Marco Bindi, Gennady Bracho-Mujica, Davide Cammarano, Yi Chen, Benjamin Dumont, Ehsan Eyshi Rezaei, Elias Fereres, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Margarita Garcia-Vila, Sebastian Gayler, Zvi Hochman, Gerrit Hoogenboom, Leslie A Hunt, Kurt C Kersebaum, Claas Nendel, Jørgen E Olesen, Taru Palosuo, Eckart Priesack, Johannes W M Pullens, Alfredo Rodríguez, Reimund P Rötter, Margarita Ruiz Ramos, Mikhail A Semenov, Nimai Senapati, Stefan Siebert, Amit Kumar Srivastava, Claudio Stöckle, Iwan Supit, Fulu Tao, Peter Thorburn, Enli Wang, Tobias Karl David Weber, Liujun Xiao, Zhao Zhang, Chuang Zhao, Jin Zhao, Zhigan Zhao, Yan Zhu, Senthold Asseng, University of Florida [Gainesville] (UF), Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Universidad Austral de Chile, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), KWS Momont SAS, Universitad de Buenos Aires = University of Buenos Aires [Argentina], Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Agronomía [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Universitat de Lleida, Institució Catalana de Recerca i Estudis Avançats (ICREA), Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS), Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), Swedish University of Agricultural Sciences (SLU), Oklahoma State University [Stillwater] (OSU), Michigan State University [East Lansing], Michigan State University System, Instituto Nacional de Investigación Agropecuaria (INIA), Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence (UniFI), Georg-August-University = Georg-August-Universität Göttingen, Purdue University [West Lafayette], Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Córdoba = University of Córdoba [Córdoba], University of Hohenheim, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Guelph, Global Change Research Centre (CzechGlobe), University of Potsdam = Universität Potsdam, Aarhus University [Aarhus], Natural Resources Institute Finland (LUKE), Helmholtz Zentrum München = German Research Center for Environmental Health, Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Washington State University (WSU), Wageningen University and Research [Wageningen] (WUR), Universität Kassel [Kassel], Zhejiang University, Nanjing Agricultural University (NAU), Building artificial Intelligence between trust, Responsibility and Decision (BIRD), Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Beijing Normal University (BNU), China Agricultural University (CAU), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT)., IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048, National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493), Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797), Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1)., International Wheat Yield Partnership, International Maize and Wheat Improvement Center, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Natural Science Foundation of China, Ministry of Education, Youth and Sports (Czech Republic), and Biotechnology and Biological Sciences Research Council (UK)
- Subjects
Crop Population ,Crop Model Ensemble ,Global Food Security Supplementary Material For This Article Is Available Online ,Radiation Use Efficiency ,Wheat Potential Yield ,Yield Increase ,Climate ,Global Food Security ,crop model ensemble ,Grain Number ,global food security Supplementary material for this article is available online ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Photosynthesis ,yield increase ,General Environmental Science ,WIMEK ,radiation use efficiency ,Renewable Energy, Sustainability and the Environment ,Spring Wheat ,Public Health, Environmental and Occupational Health ,Letter ,wheat potential yield ,global food security ,Food Demand ,ddc ,Solar-Radiation ,Water Systems and Global Change ,Biomass Accumulation - Abstract
Wheat is the most widely grown food crop, with 761 Mt produced globally in 2020. To meet the expected grain demand by mid-century, wheat breeding strategies must continue to improve upon yield-advancing physiological traits, regardless of climate change impacts. Here, the best performing doubled haploid (DH) crosses with an increased canopy photosynthesis from wheat field experiments in the literature were extrapolated to the global scale with a multi-model ensemble of process-based wheat crop models to estimate global wheat production. The DH field experiments were also used to determine a quantitative relationship between wheat production and solar radiation to estimate genetic yield potential. The multi-model ensemble projected a global annual wheat production of 1050 ± 145 Mt due to the improved canopy photosynthesis, a 37% increase, without expanding cropping area. Achieving this genetic yield potential would meet the lower estimate of the projected grain demand in 2050, albeit with considerable challenges., This study was a part of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4. The study was supported by the International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT). Experiments carried out in Valdivia (Chile) were funded by IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048. The experimental work conducted at Valdivia by Dr Jaime Herrera (UACh) is appreciated. F T was supported by the National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493). K C K was supported by the Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797). Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1).
- Published
- 2022
43. Shared influence of pathogen and host genetics on a trade-off between latent period and spore production capacity in the wheat pathogen, Puccinia triticina
- Author
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Christian Lannou, Stephen J. Powers, Frank van den Bosch, Femke van den Berg, Bénédicte Pariaud, Oliver Kaltz, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Dept Computat & Syst Biol, Rothamsted Research, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), INRA-BBSRC, Biotechnology and Biological Sciences Research Council (BBSRC) of the United Kingdom, ISPG 'MATHEMATICAL AND COMPUTATIONAL BIOLOGY' of Rothamsted Research, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-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] : UR226
- Subjects
0106 biological sciences ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,LIFE-HISTORY ,genetic correlation ,latent period ,leaf rust ,sporulation capacity ,Triticum aestivum ,wheat ,Rust (fungus) ,01 natural sciences ,Genetic correlation ,03 medical and health sciences ,Genotype ,Genetics ,PARASITE ,Pathogen ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,2. Zero hunger ,Evolutionary Biology ,0303 health sciences ,QUANTITATIVE TRAIT LOCI ,PLANT-PATHOGENS ,biology ,F-SP-TRITICI ,Host (biology) ,Directional selection ,Original Articles ,biology.organism_classification ,EVOLUTION ,Spore ,Wheat ,VIRULENCE ,POPULATIONS ,GENOTYPE-SPECIFIC INTERACTIONS ,Adaptation ,General Agricultural and Biological Sciences ,010606 plant biology & botany - Abstract
Crop pathogens are notorious for their rapid adaptation to their host. We still know little about the evolution of their life cycles and whether there might be trade-offs between fitness components, limiting the evolutionary potential of these pathogens. In this study, we explored a trade-off between spore production capacity and latent period in Puccinia triticina, a fungal pathogen causing leaf rust on wheat. Using a simple multivariate (manova) technique, we showed that the covariance between the two traits is under shared control of host and pathogen, with contributions from host genotype (57%), pathogen genotype (18.4%) and genotype × genotype interactions (12.5%). We also found variation in sign and strength of genetic correlations for the pathogen, when measured on different host varieties. Our results suggest that these important pathogen life-history traits do not freely respond to directional selection and that precise evolutionary trajectories are contingent on the genetic identity of the interacting host and pathogen.
- Published
- 2013
44. LARGE-SCALE CANDIDATE GENE SCAN REVEALS THE ROLE OF CHEMORECEPTOR GENES IN HOST PLANT SPECIALIZATION AND SPECIATION IN THE PEA APHID
- Author
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Smadja, Carole, Canbäck, Björn, Vitalis, Renaud, Gautier, Mathieu, Ferrari, Julia, Zhou, Jing-Jiang, Butlin, Roger, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Lund University, Lund, Sweden-Microbial Ecology Group, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-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), Department of Biology [York], University of York [York, UK], Biological Chemistry and Crop Protection, Rothamsted Research, Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-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] : UR226, Lund University [Lund], University of York, BBSRC Rothamsted Research, Partenaires INRAE, University of Sheffield, European Commission [RU112509], Centre National pour la Recherche Scientifique (CNRS), Agence Nationale de la Recherche programme BLANC 'EMILE' [09-BLAN-0145-01], Biotechnology and Biological Sciences Research Council of the United Kingdom, NERC, and European Commission network Molecular Adaptation in Ecologically Relevant Organisms
- Subjects
ECOLOGICAL SPECIATION ,[SDV]Life Sciences [q-bio] ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,DIVERGENT SELECTION ,food and beverages ,natural selection ,genome scan ,targeted resequencing ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,Gene flow ,genomic islands ,odorant receptor ,NATURAL-SELECTION ,RECEPTOR GENES ,ODORANT-BINDING PROTEINS ,ACYRTHOSIPHON-PISUM ,DROSOPHILA-SECHELLIA ,REPRODUCTIVE ISOLATION ,POPULATION DIFFERENTIATION ,SYMPATRIC SPECIATION ,ComputingMilieux_MISCELLANEOUS - Abstract
Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Understanding the drivers of speciation is critical to interpreting patterns of biodiversity. The identification of the genetic changes underlying adaptation and reproductive isolation is necessary to link barriers to gene flow to the causal origins of divergence. Here, we present a novel approach to the genetics of speciation, which should complement the commonly used approaches of quantitative trait locus mapping and genome-wide scans for selection. We present a large-scale candidate gene approach by means of sequence capture, applied to identifying the genetic changes underlying reproductive isolation in the pea aphid, a model system for the study of ecological speciation. Targeted resequencing enabled us to scale up the candidate gene approach, specifically testing for the role of chemosensory gene families in host plant specialization. Screening for the signature of divergence under selection at 172 candidate and noncandidate loci, we revealed a handful of loci that show high levels of differentiation among host races, which almost all correspond to odorant and gustatory receptor genes. This study offers the first indication that some chemoreceptor genes, often tightly linked together in the genome, could play a key role in local adaptation and reproductive isolation in the pea aphid and potentially other phytophagous insects. Our approach opens a new route toward the functional genomics of ecological speciation.
- Published
- 2012
45. ELOVL2 controls the level of n-6 28:5 and 30:5 fatty acids in testis, a prerequisite for male fertility and spermmaturation in mice
- Author
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Petr Tvrdik, Hervé Guillou, Mario R. Capecchi, Damir Zadravec, Richard P. Haslam, Tsutomu Kobayashi, Johnathan A. Napier, Anders Jacobsson, Wenner Gren Inst, Stockholm University, Howard Hughes Med Inst, University of Utah, Toxicologie Alimentaire (UTA), 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, Harpend, Rothamsted Research, Harpenden, Rothamsted Research, Swedish Research Council, Cancer Foundation, Sven och Dagmar Salens stiftelse, Institut National de la Recherche Agronomique, Formas, Biotechnology and Biological Sciences Research Council, United Kingdom, Toxicologie Alimentaire ( UTA ), 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, Laboratoire de Pharmacologie et Toxicologie, Institut National de la Recherche Agronomique (INRA), Zadravec, Damir, Tvrdik, Petr, Guillou, Hervé, Haslam, Rilchard, Kobayash, Tsutomu, Napier, Johnathan, Capecchi, Mario, Jacobsson, Anders, The Wenner-Gren Institute, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), and International Conference on the Bioscience of Lipids (ICBL). INT.
- Subjects
Male ,fatty acid elongase • omega-6 • spermatogenesis ,[SDV]Life Sciences [q-bio] ,fatty acid elongase ,MOUSE ,Biochemistry ,ACTIVATION ,Mice ,0302 clinical medicine ,Endocrinology ,Testis ,Research Articles ,media_common ,chemistry.chemical_classification ,MACULAR DYSTROPHY ,GENE ,SPERMATOGENESIS ,DELETION ,CELLS ,IDENTIFICATION ,CYTOKINESIS ,METABOLISM ,0303 health sciences ,spermatogenesis ,Fatty Acids, Unsaturated ,Female ,lipids (amino acids, peptides, and proteins) ,Ploidy ,Haploinsufficiency ,Polyunsaturated fatty acid ,medicine.medical_specialty ,omega-6 ,Fatty Acid Elongases ,media_common.quotation_subject ,Fertility ,QD415-436 ,Biology ,03 medical and health sciences ,Dietary Fats, Unsaturated ,Acetyltransferases ,Internal medicine ,medicine ,Animals ,Molecular Biology ,030304 developmental biology ,[ SDV ] Life Sciences [q-bio] ,Organic Chemistry ,Fatty acid ,Cell Biology ,Metabolism ,Sperm ,Sperm Maturation ,chemistry ,Microsome ,Spermatogenesis ,030217 neurology & neurosurgery - Abstract
ELOVL2 is a member of the mammalian microsomal ELOVL fatty acid enzyme family, involved in the elongation of very long-chain fatty acids including PUFAs required for various cellular functions in mammals. Here, we used ELOVL2-ablated (Elovl2(-/-)) mice to show that the PUFAs with 24-30 carbon atoms of the ω-6 family in testis are indispensable for normal sperm formation and fertility in male mice. The lack of Elovl2 was associated with a complete arrest of spermatogenesis, with seminiferous tubules displaying only spermatogonia and primary spermatocytes without further germinal cells. Furthermore, based on acyl-CoA profiling, heterozygous Elovl2(+/-) male mice exhibited haploinsufficiency, with reduced levels of C28:5 and C30:5n-6 PUFAs, which gave rise to impaired formation and function of haploid spermatides. These new insights reveal a novel mechanism involving ELOVL2-derived PUFAs in mammals and previously unrecognized roles for C28 and C30 n-6 PUFAs in male fertility. In accordance with the function suggested for ELOVL2, the Elovl2(-/-) mice show distorted levels of serum C20 and C22 PUFAs from both the n-3 and the n-6 series. However, dietary supplementation with C22:6n-3 could not restore male fertility to Elovl2(+/-) mice, suggesting that the changes in n-6 fatty acid composition seen in the testis of the Elovl2(+/-) mice, cannot be compensated by increased C22:6n-3 content.
- Published
- 2011
46. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
- Author
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Hank Tu, Ioannis Stergiopoulos, Igor V. Grigoriev, Jan P. H. Nap, Alexander H. J. Wittenberg, Kim E. Hammond-Kosack, Judith Bowler, Theo van der Lee, Stefano F.F. Torriani, Bernard Henrissat, Henri van de Geest, Bruno G. G. Donzelli, Natália F. Martins, Andrea Aerts, Pedro M. Coutinho, Rahim Mehrabi, Vincent Lombard, Hans J. Cools, James Bristow, Arnold Kuzniar, Gert H. J. Kema, James K. Hane, Cees Waalwijk, L.H. Zwiers, S.B. Ware, Blondy Canto-Canché, Paramvir S. Dehal, Roeland C. H. J. van Ham, Sarrah Ben M’Barek, Yiannis A. I. Kourmpetis, Pierre J. G. M. de Wit, Andrzej Kilian, Ronald P. de Vries, Chris Maliepaard, Charles F. Crane, Michael Csukai, Burt H. Bluhm, Laura Conde-Ferráez, Ad Wiebenga, Erika Lindquist, Richard P. Oliver, Alisa Ponomarenko, Asaf Salamov, Adilson Kenji Kobayashi, Stephen B. Goodwin, Edda Koopmann, Braham Dhillon, Henk J. Schouten, Jason J. Rudd, John F. Antoniw, Harris Shapiro, Alice C. L. Churchill, Andrew J Foster, Andy M. Bailey, Ate van der Burgt, Jane Grimwood, Jeremy Schmutz, Malik, Harmit S, STEPHEN B. GOODWIN, USDA–AGRICULTURAL RESEARCH SERVICE, SARRAH BEN M’BAREK, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, BRAHAM DHILLON, PURDUE UNIVERSITY, USA, ALEXANDER H. J. WITTENBERG, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, CHARLES F. CRANE, USDA–AGRICULTURAL RESEARCH SERVICE, JAMES K. HANE, MURDOCH UNIVERSITY, PERTH, AUSTRALIA, ANDREW J. FOSTER, IBWF e.V., GERMANY, THEO A. J. VAN DER LEE, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, JANE GRIMWOOD, HUDSONALPHA INSTITUTE OF BIOTECHNOLOGY, USA, ANDREA AERTS, DOE JOINT GENOME INSTITUTE, USA, JOHN ANTONIW, ROTHAMSTED RESEARCH, UNITED KINGDOM, ANDY BAILEY, UNIVERSITY OF BRISTOL, UNITED KINGDOM, BURT BLUHM, UNIVERSITY OF ARKANSAS, USA, JUDITH BOWLER, SYNGENTA, UNITED KINGDOM, JIM BRISTOW, HUDSONALPHA INSTITUTE OF BIOTECHNOLOGY, USA, ATE VAN DER BURGT, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, BLONDY CANTO CANCHE, CENTRO DE INVESTIGACIÓN CIENTÍFICA DE YUCATÁN, MÉXICO, ALICE C. L. CHURCHILL, CORNELL UNIVERSITY, USA, LAURA CONDE FERRÀEZ, CENTRO DE INVESTIGACIÓN CIENTÍFICA DE YUCATÁN, MÉXICO, HANS J. COOLS, ROTHAMSTED RESEARCH, UNITED KINGDOM, PEDRO M. COUTINHO, ARCHITECTURE ET FONCTION DES MACROMOLECULES BIOLOGIQUES, CNRS, FRANCE, MICHAEL CSUKAI, SYNGENTA, UNITED KINGDOM, PARAMVIR DEHAL, DOE JOINT GENOME INSTITUTE, USA, PIERRE DE WIT, WAGENINGEN UNIVERSITY AND RESEARCH CENTRE, THE NETHERLANDS, BRUNO DONZELLI, USDA–AGRICULTURAL RESEARCH SERVICE, HENRI C. VAN DE GEEST, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, ROELAND C. H. J. VAN HAM, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, KIM E. HAMMOND KOSACK, ROTHAMSTED RESEARCH, UNITED KINGDOM, BERNARD HENRISSAT, ARCHITECTURE ET FONCTION DES MACROMOLECULES BIOLOGIQUES, CNRS, FRANCE, ANDRZEJ KILIAN, DIVERSITY ARRAYS TECHNOLOGY PTY LTD, AUSTRALIA, ADILSON KENJI KOBAYASHI, CPAMN, EDDA KOOPMANN, BAYER CROPSCIENCE AG, GERMANY, YIANNIS KOURMPETIS, WAGENINGEN UNIVERSITY AND RESEARCH CENTRE, THE NETHERLANDS, ARNOLD KUZNIAR, WAGENINGEN UNIVERSITY AND RESEARCH CENTRE, THE NETHERLANDS, ERIKA LINDQUIST, DOE JOINT GENOME INSTITUTE, USA, VINCENT LOMBARD, ARCHITECTURE ET FONCTION DES MACROMOLECULES BIOLOGIQUES, CNRS, FRANCE, CHRIS MALIEPAARD, WAGENINGEN UNIVERSITY AND RESEARCH CENTRE, THE NETHERLANDS, NATALIA FLORENCIO MARTINS, CENARGEN, RAHIM MEHRABI, SEED AND PLANT IMPROVEMENT INSTITUTE, IRAN, JAN P. H. NAP, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, ALISA PONOMARENKO, PURDUE UNIVERSITY, USA, JASON J. RUDD, ROTHAMSTED RESEARCH, UNITED KINGDOM, ASAF SALAMOV, DOE JOINT GENOME INSTITUTE, USA, JEREMY SCHMUTZ, HUDSONALPHA INSTITUTE OF BIOTECHNOLOGY, USA, HENK J. SCHOUTEN, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, HARRIS SHAPIRO, DOE JOINT GENOME INSTITUTE, USA, IOANNIS STERGIOPOULOS, WAGENINGEN UNIVERSITY AND RESEARCH CENTRE, THE NETHERLANDS, STEFANO F. F. TORRIANI, SWISS FEDERAL INSTITUTE OF TECHNOLOGY (ETH), SWITZERLAND, HANK TU, DOE JOINT GENOME INSTITUTE, USA, RONALD P. DE VRIES, CBS–KNAW FUNGAL BIODIVERSITY CENTRE, THE NETHERLANDS, CEES WAALWIJK, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, SARAH B. WARE, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS, AD WIEBENGA, CBS–KNAW FUNGAL BIODIVERSITY CENTRE, THE NETHERLANDS, LUTE-HARM ZWIERS, CBS–KNAW FUNGAL BIODIVERSITY CENTRE, THE NETHERLANDS, RICHARD P. OLIVER, CURTIN UNIVERSITY, AUSTRALIA, IGOR V. GRIGORIEV, DOE JOINT GENOME INSTITUTE, USA, and GERT H. J. KEMA, PLANT RESEARCH INTERNATIONAL B.V., WAGENINGEN, THE NETHERLANDS.
- Subjects
Cancer Research ,neurospora ,RRES175 ,Genome ,Graminicola ,Fungus ,PRI Biodiversiteit en Veredeling ,2.2 Factors relating to the physical environment ,Aetiology ,Triticum ,Genetics (clinical) ,Gene Rearrangement ,Genetics ,PBR Kwantitatieve aspecten ,biology ,EPS-2 ,Fungal genetics ,food and beverages ,Agriculture ,Genomics ,organization ,symbiosis ,Fungal ,Infectious Diseases ,annotation ,host ,Mycosphaerella graminicola ,Zero Hunger ,Mycosphaerella ,Chromosomes, Fungal ,Genome, Fungal ,Infection ,Fungo ,Research Article ,Biotechnology ,175_Genetics ,lcsh:QH426-470 ,Bioinformatics ,Synteny ,Chromosomes ,PBR Quantitative aspects of Plant Breeding ,resistance ,BIOS Applied Bioinformatics ,Ascomycota ,expression ,Bioinformatica ,175_Plant sciences ,b-chromosomes ,gene ,Biology ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Plant Diseases ,B chromosome ,Biointeracties and Plant Health ,Bioint Moleculair Phytopathology ,magnaporthe-grisea ,Gene rearrangement ,biology.organism_classification ,175_Fungi ,Laboratorium voor Phytopathologie ,PRI Biodiversity and Breeding ,lcsh:Genetics ,Plant Breeding ,Laboratory of Phytopathology ,PRI Biointeractions en Plantgezondheid ,Pest Control ,Developmental Biology - Abstract
The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors., PLoS Genetics, 7 (6), ISSN:1553-7390, ISSN:1553-7404
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- 2011
47. Modelling rotations: can crop sequences explain arable weed seedbank abundance?
- Author
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Bohan, David, Powers, S J, Champion, G, Haughton, A J, Hawes, C, Squires, G, Cussans, J, Mertens, S K, Biologie et Gestion des Adventices (BGA), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Rothamsted Research, BBSRC Rothamsted Research, Partenaires INRAE, and Scottish Crop Research Institute
- Subjects
seedbank ,sowing season ,herbicide management ,model ,oilseed rape ,herbicide tolerant crops ,crop sequence ,system ,rotation ,diversity ,farm scale evaluations ,invertebrate abundance ,tillage ,population dynamics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,crop type ,management ,biodiversity - Abstract
International audience; We investigated the effects of crop sequences on monocotyledon, dicotyledon and total weed seedbank abundance. Using seedbank data sampled from the conventionally cropped part of the GB farm-scale evaluations of genetically modified, herbicide-tolerant (GMHT) crops, we asked whether it is possible to identify crop sequence effects, to identify their duration and to simplify crop sequences into crop management classes with similar effects on weed seedbanks. This work showed that it is possible to detect historical effects of past crops, sown in sequence, on weed seedbanks for up to 3 years and that crop sequences may be simplified to crop management classes describing the season of sowing, crop type and weed target for herbicide application. Model estimates for the seedbanks were validated against an independent, follow-up seedbank data set. The analysis provided abundance estimates that ranged over 3 and 1.7 orders of magnitude for the monocotyledon and dicotyledon weed seedbanks for different crop sequence. This work yields a methodology for estimating seedbank abundance in current crop sequences, potentially allowing sequences to be identified that better reconcile the competing needs for weed control to maintain crop productivity and the demand for increased farmland biodiversity.
- Published
- 2011
48. Diffuse reflectance spectroscopy for estimating soil properties: A technology for the 21st century
- Author
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Raphael A. Viscarra Rossel, Thorsten Behrens, Eyal Ben‐Dor, Sabine Chabrillat, José Alexandre Melo Demattê, Yufeng Ge, Cecile Gomez, César Guerrero, Yi Peng, Leonardo Ramirez‐Lopez, Zhou Shi, Bo Stenberg, Richard Webster, Leigh Winowiecki, Zefang Shen, School of Earth and Planetary Science [Perth - Curtin university], Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Swiss Competence Center for Soils, Tel Aviv University (TAU), German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ), Leibniz Universität Hannover=Leibniz University Hannover, Universidade de São Paulo = University of São Paulo (USP), University of Nebraska–Lincoln, University of Nebraska System, Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), 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), Institut de Recherche pour le Développement (IRD), Universidad Miguel Hernández [Elche] (UMH), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), BÜCHI Labortechnik AG, Partenaires INRAE, Zhejiang University, Swedish University of Agricultural Sciences (SLU), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Raphael A. Viscarra Rossel received funding from the Australian Government via grant ACSRIV000077.
- Subjects
Model localization ,Reflectance spectroscopy ,Soil constituents ,Spectral libraries ,[SDV]Life Sciences [q-bio] ,Calibration ,Machine learning ,Validation ,Soil Science ,Regression ,SOLOS - Abstract
International audience; Spectroscopic measurements of soil samples are reliable because they are highly repeatable and reproducible. They characterise the samples' mineral-organic composition. Estimates of concentrations of soil constituents are inevitably less precise than estimates obtained conventionally by chemical analysis. But the cost of each spectroscopic estimate is at most one-tenth of the cost of a chemical determination. Spectroscopy is cost-effective when we need many data, despite the costs and errors of calibration. Soil spectroscopists understand the risks of over-fitting models to highly dimensional multivariate spectra and have command of the mathematical and statistical methods to avoid them. Machine learning has fast become an algorithmic alternative to statistical analysis for estimating concentrations of soil constituents from reflectance spectra. As with any modelling, we need judicious implementation of machine learning as it also carries the risk of over-fitting predictions to irrelevant elements of the spectra. To use the methods confidently, we need to validate the outcomes with appropriately sampled, independent data sets. Not all machine learning should be considered 'black boxes'. Their interpretability depends on the algorithm, and some are highly interpretable and explainable. Some are difficult to interpret because of complex transformations or their huge and complicated network of parameters. But there is rapidly advancing research on explainable machine learning, and these methods are finding applications in soil science and spectroscopy. In many parts of the world, soil and environmental scientists recognise the merits of soil spectroscopy. They are building spectral libraries on which they can draw to localise the modelling and derive soil information for new projects within their domains. We hope our article gives readers a more balanced and optimistic perspective of soil spectroscopy and its future. Highlights Spectroscopy is reliable because it is a highly repeatable and reproducible analytical technique. Spectra are calibrated to estimate concentrations of soil properties with known error. Spectroscopy is cost-effective for estimating soil properties. Machine learning is becoming ever more powerful for extracting accurate information from spectra, and methods for interpreting the models exist. Large libraries of soil spectra provide information that can be used locally to aid estimates from new samples.
- Published
- 2022
49. Quantifying and isolating stable soil organic carbon using long-term bare fallow experiments
- Author
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Thomas Kätterer, Paul R. Poulton, Pierre Barré, F. van Oort, Thomas Eglin, Philippe Ciais, Sabine Houot, Claire Chenu, Bent T. Christensen, Vladimir Romanenkov, Philippe Peylin, Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Aarhus University [Aarhus], Environnement et Grandes Cultures (EGC), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Soil Fertility and Plant Nutrition, Swedish University of Agricultural Sciences (SLU), PESSAC LABORATORY, Institut National de la Recherche Agronomique (INRA), ROTHAMSTED RESEARCH, Rothamsted Research, Pryanishnikov All Russian Institute for Agrochemistry VNIIA, Russian Institute for Agrochemistry VNIIA, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ICOS-ATC (ICOS-ATC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Biotechnology and Biological Sciences Research Council (BBSRC)
- Subjects
cycle du carbone ,sol ,010504 meteorology & atmospheric sciences ,BARE FALLOW ,CARBON CYCLE ,LONG-TERM EXPERIMENT ,SOIL CARBON DYNAMICS ,STABLE SOIL CARBON ,SOL STABLE ,SOM ,jachère ,lcsh:Life ,Soil science ,01 natural sciences ,russie ,danemark ,chemistry.chemical_compound ,lcsh:QH540-549.5 ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,2. Zero hunger ,Total organic carbon ,suède ,Soil organic matter ,lcsh:QE1-996.5 ,Simulation modeling ,Soil classification ,Global change ,04 agricultural and veterinary sciences ,Soil carbon ,15. Life on land ,grande bretagne ,lcsh:Geology ,lcsh:QH501-531 ,chemistry ,scandinavie ,13. Climate action ,Carbon dioxide ,Soil water ,[SDE]Environmental Sciences ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Environmental science ,lcsh:Ecology ,europe ,france - Abstract
The stability of soil organic matter (SOM) is a major source of uncertainty in predicting atmospheric CO2 concentration during the 21st century. Isolating the stable soil carbon (C) from other, more labile, C fractions in soil is of prime importance for calibrating soil C simulation models, and gaining insights into the mechanisms that lead to soil C stability. Long-term experiments with continuous bare fallow (vegetation-free) treatments in which the decay of soil C is monitored for decades after all inputs of C have stopped, provide a unique opportunity to assess the quantity of stable soil C. We analyzed data from six bare fallow experiments of long-duration (>30 yrs), covering a range of soil types and climate conditions, and sited at Askov (Denmark), Grignon and Versailles (France), Kursk (Russia), Rothamsted (UK), and Ultuna (Sweden). A conceptual three pool model dividing soil C into a labile pool (turnover time of a several years), an intermediate pool (turnover time of a several decades) and a stable pool (turnover time of a several centuries or more) fits well with the long term C decline observed in the bare fallow soils. The estimate of stable C ranged from 2.7 g C kg−1 at Rothamsted to 6.8 g C kg−1 at Grignon. The uncertainty associated with estimates of the stable pool was large due to the short duration of the fallow treatments relative to the turnover time of stable soil C. At Versailles, where there is least uncertainty associated with the determination of a stable pool, the soil contains predominantly stable C after 80 years of continuous bare fallow. Such a site represents a unique research platform for characterization of the nature of stable SOM and its vulnerability to global change.
- Published
- 2010
50. La protection intégrée dans l'agriculture européenne. Résultats du projet 2007-2010
- Author
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Ricci, Pierre, Barzman, Marc, Labussière, Emilie, Bigler, Franz, Boonekamp, Piet, Denholm, I., Hommels, B., Kiss, J., Kudsk, P., Messean, Antoine, Sarah, J.L., Sattin, M., Troillard, Vincent, Institut National de la Recherche Agronomique (INRA), Délégation à l'Expertise scientifique collective, à la Prospective et aux Etudes (UAR), Agroscope FAL Reckenholz (AGROSCOPE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), ROTHAMSTED RESEARCH, Rothamsted Research, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), SZIE, Partenaires INRAE, Aarhus University [Aarhus], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), CNR - National Research Council of Italy, Institute of Molecular Biology and Pathology, INRA Transfert, UE, and INRA
- Subjects
2. Zero hunger ,scenarios ,protection intégrée ,pesticides ,15. Life on land ,prospective ,protection des cultures ,[SDE.ES]Environmental Sciences/Environmental and Society - Abstract
Le Réseau d'Excellence ENDURE partage les fruits de 4 années de recherche avec les acteurs de la protection es cultures.
- Published
- 2010
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