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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.

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

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

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.

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

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

Cropping details for the Broadbalk wheat experiment, 1843-2021, with details of cultivars, crops and rotations.

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

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

Description of Broadbalk fertiliser and organic manure treatments, 1852-2021. Annual treatments per hectare., Updated from Macdonald et al, 2018. None None

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

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

Figure illustrating the main treatment phases for the Exhaustion Land Long-term experiment

Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV 2000-2006 and showing "P Test" and "K Test" plots.

Plan of the Exhaustion Land Experiment illustrating plots and treatments for Phase V 2007

Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase I (1856-1901).

Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV P Build up 1986-1992.

Annual P and K Inputs for the Exhaustion land long-term experiment from 1986-2016

Plan of the Exhaustion Land Experiment illustrating plots and total inputs for Phase IV 1993-1999 and showing "P Test" and "K Test" plots.

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

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

Standardised experiment plan for the Park Grass experiment 1903-1964, with details of lime, fertilizer and manure treatments (not to scale).

Standardised experiment plan for the Park Grass experiment 1856-1902, with details of lime, fertilizer and manure treatments (not to scale).

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

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.

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

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

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.

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

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.

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.

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.

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).

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.

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).

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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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’.

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).

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.

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.

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.

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

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.

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.

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.

Le Réseau d'Excellence ENDURE partage les fruits de 4 années de recherche avec les acteurs de la protection es cultures.