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Simple Summary Our climate is changing and the world population is growing to an estimated 10 billion people by 2050. This may cause serious problems in global food supply, protection of the environment and safeguarding Earth’s biodiversity. To face these challenges, agriculture will have to adapt and a key element in this will be the development of “future-proof” crops. These crops will not only have to be high-yielding, but also should be able to withstand future climate conditions and will have to make very efficient use of scarce resources such as water, phosphorus and minerals. Future crops should not only sustainably give access to sufficient, nutritious, and diverse food to a worldwide growing population, but also support the circular bio-based economy and contribute to a lower atmospheric CO2 concentration to counteract global warming. Future-proofing our crops is an urgent issue and a challenging goal that only can be realized by large-scale, international research cooperation. We call for international action and propose a pan-European research and innovation initiative, the CropBooster Program, to mobilize the European plant research community and all interested actors in agri-food research and innovation to face the challenge. Abstract The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge.

Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest., Measurement(s) genome • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing assay • sequence assembly process • sequence annotation Sample Characteristic - Organism Meloidogyne enterolobii Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12410363

As an essential nutrient required for plant growth and development, sulfur (S) deficiency in productive systems limits yield and quality. This special issue hosts a collection of original research articles, mainly based on contributions from the 11th International Plant Sulfur Workshop held on 16−20 September 2018 in Conegliano, Italy, focusing on the following topics: (1) The germinative and post-germinative behaviour of Brassica napus seeds when severe S limitation is applied to the parent plants; (2) the independence of S deficiency from the mRNA degradation initiation enzyme PARN in Arabidopsis; (3) the glucosinolate distribution in the aerial parts of sel1-10, a disruption mutant of the sulfate transporter SULTR1;2, in mature Arabidopsis thaliana plants; (4) the accumulation of S-methylcysteine as its γ-glutamyl dipeptide in Phaseolus vulgaris; and (5) the role of ferric iron chelation-strategy components in the leaves and roots of maize, have provided new insights into the effect of S availability on plant functionality. Moreover, the role of S deficiency in root system functionality has been highlighted, focusing on (6) the contribution of root hair development to sulfate uptake in Arabidopsis, and (7) the modulation of lateral root development by the CLE-CLAVATA1 signaling pathway under S deficiency. The role of S in plants grown under drought conditions has been investigated in more detail focusing (8) on the relationship between S-induced stomata closure and the canonical ABA signal transduction machinery. Furthermore, (9) the assessment of S deficiency under field conditions by single measurements of sulfur, chloride, and phosphorus in mature leaves, (10) the effect of fertilizers enriched with elemental S on durum wheat yield, and (11,12) the impact of elemental S on the rhizospheric bacteria of durum wheat contributed to enhance the scientific knowledge on S nutrition under field conditions.

International audience; The necessity to adapt to climate change is even stronger for grapevine than for other crops, because grape berry composition—a key determinant of fruit and wine quality, typicity and market value— highly depends on “terroir” (complete natural environment), on vintage (annual climate variability), and on their interactions. In the same time, there is a strong demand to reduce the use of pesticides. Thus, the equation that breeders and grape growers must solve has three entries that cannot be dissociated: adaptation to climate change, reduction of pesticides, and maintenance of wine typicity. Although vineyard management may cope to some extent to the short–medium-term effects of climate change, genetic improvement is necessary to provide long-term sustainable solutions to these problems. Most vineyards over the world are planted using vines that harbor two grafted plants’ genomes. Although this makes the range of interactions (scion-atmosphere, rootstock-soil, scion-rootstock) more complex, it also opens up wider possibilities for the genetic improvement of either or both the grafted genotypes. Positive aspects related to grapevine breeding are as follows: (a) a wide genetic diversity of rootstocks and scions that has not been thoroughly explored yet; (b) progress in sequencing technologies that allows high-throughput sequencing of entire genomes, faster mapping of targeted traits and easier determination of genetic relationships; (c) progress in new breeding technologies that potentially permit precise modifications on resident genes; (d) automation of phenotyping that allows faster and more complete monitoring of many traits on relatively large plant populations; (e) functional characterization of an increasing number of genes involved in the control of development, berry metabolism, disease resistance, and adaptation to environment. Difficulties involve: (a) the perennial nature and the large size of the plant that makes field testing long and demanding in manpower; (b) the low efficiency of transformation, regeneration and small size of breeding populations; (c) the complexity of the adaptive traits and the need to define more clearly future ideotypes; (d) the lack of shared and integrative platforms allowing a complete appraisal of the genotype-phenotype-environmental links; (e) legal, market and consumer acceptance of new genotypes. The present chapter provides an overview of suitable strategies and challenges linked to the adaptation of viticulture to a changing environment.

UMR BFP - Equipe Métabolisme; International audience; We analyzed a comprehensive set of contaminants in MON810 and NK603 genetically modified (GM) maize, and their non-GM counterparts, used in a rat feeding study (the GMO90 + project). Both the maize grains and the manufactured pellets were characterized. Only minor differences in contaminant levels between GM and corresponding non-GM harvests were evidenced. Fumonisin and deoxynivalenol mycotoxins were the pollutants present in the highest amounts, with concentrations that were however largely below acceptance reference values. Our data reporting slightly higher levels of fumonisin in MON810 compared to its non-GM counterpart corroborate the lower susceptibility of insect resistant Bt maize to fumonisin-producing fungi. Traces of glyphosate (0.016 mg/kg) were evidenced in grains from NK603 treated crops. Regarding the pellets, analysis of more than 650 potentially toxic substances revealed low amounts of various mycotoxins, pesticides and heavy metals. Concentrations of contaminants quantified in the pellets were however far below the maximum level of residues values set by regulatory agencies, and no substantial differences in contaminants between GM and non-GM pellets were observed. Moreover, when comparing the contamination status of grains and pellets, we demonstrate yet again that characterizing the grains is actually not sufficient to foresee the quality of the produced pellets.

Root-knot nematodes (genusMeloidogyne) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes againstMeloidogynespecies. However, some species such asM. enterolobiiare not controlled by the resistance genes deployed in the most important crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Like the other most damaging Meloidogyne species (e.g.M. incognita,M. arenariaandM. javanica),M. enterolobiireproduces by obligatory mitotic parthenogenesis. Genomic singularities such as a duplicated genome structure and a relatively high proportion of transposable elements have previously been described in the above mentioned mitotic parthenogenetic Meloidogyne.To gain a better understanding of the genomic and evolutionary background we sequenced the genome ofM. enterolobiiusing high coverage short and long read technologies. The information contained in the long reads helped produce a highly contiguous genome assembly ofM. enterolobii, thus enabling us to perform high quality annotations of coding and non-coding genes, and transposable elements.The genome assembly and annotation reveals a genome structure similar to the ones described in the other mitotic parthenogenetic Meloidogyne, described as recent hybrids. Most of the genome is present in 3 different copies that show high divergence. Because most of the genes belong to these duplicated regions only few gene losses took place, which suggest a recent polyploidization. The most likely hypothesis to reconcile high divergence between genome copies despite few gene losses and translocations is also a recent hybrid origin. Consistent with this hypothesis, we found an abundance of transposable elements at least as high as the one observed in the mitotic parthenogenetic nematodesM. incognitaandM. javanica.

This is the accepted manuscript of the paper "Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar", published as final paper in "Global Change Biology Bioenergy Volume 11, Issue 1, 08 February 2019, Pages 118–151 https://doi.org/10.1111/gcbb.12566”. Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namelyPanicum virgatum(switchgrass), species of the generaMiscanthus(miscanthus),Salix(willow) andPopulus(poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

International audience; Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene tetA(P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene tetA(P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.

The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent–offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to ‘Savagnin Blanc’, providing evidence for 900 years of uninterrupted vegetative propagation., This project was funded by the Danish Council for Independent Research (10–081390) and the Danish National Research Foundation (DNRF94). L.B. and R.B. were supported by the French National Agency of Research (VINICULTURE project—ANR-16-CE27–0013).

Marcais, Benoit/0000-0002-8107-644X; Jung, Thomas/0000-0003-2034-0718; Jung, Marilia Horta/0000-0003-2219-8647; Corcobado, Tamara/0000-0001-5762-4728; Lyubenova, Aneta/0000-0001-7414-1808; Pastircak, Martin/0000-0001-5118-9518; Pastircakova, Katarina/0000-0003-0371-428X; Fort, Tomas/0000-0002-4186-0918; Oskay, Funda/0000-0002-8918-5595; Oliva, Jonas/0000-0003-2418-2542; FORT, Tania/0000-0001-6998-5985; Kiss, Levente/0000-0002-4785-4308; Iturritxa, Eugenia/0000-0002-6390-5873; Aday Kaya, Ayse Gulden/0000-0002-5631-6026; Nave, Corina/0000-0003-2290-8282 WOS:000452564900005 The spatial distribution and niche differentiation of three closely related species (Erysiphe alphitoides, Erysiphe quercicola and Erysiphe hypophylla) causing oak powdery mildew was studied at scales ranging from the European continent, where they are invasive, to a single leaf. While E. alphitoides was dominant at all scales, E. quercicola and E. hypophylla had restricted geographic, stand and leaf distributions. The large-scale distributions were likely explained by climatic factors and species environmental tolerances, with E. quercicola being more frequent in warmer climates and E. hypophylla in colder climates. The extensive sampling and molecular analyses revealed the cryptic invasion of E. quercicola in nine countries from which it had not previously been recorded. The presence of the three species was also strongly affected by host factors, such as oak species and developmental stage. Segregation patterns between Erysiphe species were observed at the leaf scale, between and within leaf surfaces, suggesting competitive effects. (C) 2018 Elsevier Ltd and British Mycological Society. All rights reserved. Conseil Regional d'AquitaineRegion Nouvelle-Aquitaine [20030304002FA, 20040305003FA]; European Union FEDEREuropean Commission [2003227]; Investissements d'AvenirFrench National Research Agency (ANR) [ANR-10-EQPX-16-01]; European BiodivERsA project "RESIPATH: Responses of European Forests and Society to Invasive Pathogens"; Portuguese Science and Technology FoundationPortuguese Foundation for Science and Technology [BIODIVERSA/0002/2012, ANR-13-EBID-0005-01]; ANR (France)French National Research Agency (ANR) [ANR-13-BSV7-0011]; Japan Society for the Promotion of ScienceMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science [16K07613, 16F16097]; Slovak Research and Development AgencySlovak Research and Development Agency [APVV-15 0210] We thank Adrien Bolay, Caroline Gordon, Banga Grigaliunaite, Gabriela Juhasova, Vasyl Heluta, Seyed Akbar Khodaparast, Eleni Topalidou, Gy-ongyver Nagy, and all other collectors, for providing samples. Part of the analyses were performed at the Genome Transcriptome Facility of Bordeaux (grants from the Conseil Regional d'Aquitaine no 20030304002FA and 20040305003FA, from the European Union FEDER no 2003227 and from Investissements d'Avenir ANR-10-EQPX-16-01). Funding was obtained through the European BiodivERsA project "RESIPATH: Responses of European Forests and Society to Invasive Pathogens" co-financed by national funds (ANR-13-EBID-0005-01 for France, Portuguese Science and Technology Foundation Ref. BIODIVERSA/0002/2012). Other grants came from the ANR (France) Funfit project (ANR-13-BSV7-0011), the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (Nos. 16K07613 and16F16097), and the Slovak Research and Development Agency under the contract No. APVV-15 0210.

The GRACE (GMO Risk Assessment and Communication of Evidence; www.grace-fp7.eu) project was funded by the European Commission within the 7th Framework Programme. A key objective of GRACE was to conduct 90-day animal feeding trials, animal studies with an extended time frame as well as analytical, in vitro and in silico studies on genetically modified (GM) maize in order to comparatively evaluate their use in GM plant risk assessment. In the present study, the results of a 1-year feeding trial with a GM maize MON810 variety, its near-isogenic non-GM comparator and an additional conventional maize variety are presented. The feeding trials were performed by taking into account the guidance for such studies published by the EFSA Scientific Committee in 2011 and the OECD Test Guideline 452. The results obtained show that the MON810 maize at a level of up to 33 % in the diet did not induce adverse effects in male and female Wistar Han RCC rats after a chronic exposure. Electronic supplementary material The online version of this article (doi:10.1007/s00204-016-1798-4) contains supplementary material, which is available to authorized users.

International audience; Genebanks and other ex situ collections have a significant role in the conservation, management and use of crop genetic diversity, including that of crop wild relatives. Efficient management and use depends on insight into the patterning and distribution of genetic diversity as well as obtaining baseline information on phenotypic characters and traits. Wild carrot (Daucus carota L.) is the closest wild relative of cultivated carrot (Daucus carota L. subsp. sativus (Hoffm.) Arcang.), and is a potential source of useful traits for crop improvement. There are over 900 accessions of D. carota described as wild in European genebanks, however associated phenotypic and genotypic characterization data are sparse. The influence of environment on phenotype is also not well understood in this taxon, meaning that it is difficult to ascertain how data collected at different locations can be compiled and collated. We present initial results of CarrotDiverse, a collaborative project in which wild D. carota accessions are undergoing detailed phenotypic and morphological characterization in parallel at three sites of varying latitude across Europe located in Portugal, France and Sweden. This will allow us to understand which traits are affected by environmental variables. Basic phenotypic information is being collected on a further 150 accessions. Furthermore, resistance screening to Alternaria species and polyacetylene profiling will be included in the evaluation. A Genotyping by Sequencing approach will be used to generate knowledge about genetic background and trait associations. The project will result in a significant data set which will facilitate the use of crop wild relatives in carrot breeding and improvement.

The genetically modified maize event MON810 expresses a Bacillus thuringiensis-derived gene, which encodes the insecticidal protein Cry1Ab to control some lepidopteran insect pests such as the European corn borer. It has been claimed that the immune system may be affected following the oral/intragastric administration of the MON810 maize in various different animal species. In the frame of the EU-funded project GRACE, two 90-day feeding trials, the so-called studies D and E, were performed to analyze the humoral and cellular immune responses of male and female Wistar Han RCC rats fed the MON810 maize. A MON810 maize variety of Monsanto was used in the study D and a MON810 maize variety of Pioneer Hi-Bred was used in the study E. The total as well as the maize protein- and Cry1Ab-serum-specific IgG, IgM, IgA and IgE levels, the proliferative activity of the lymphocytes, the phagocytic activity of the granulocytes and monocytes, the respiratory burst of the phagocytes, a phenotypic analysis of spleen, thymus and lymph node cells as well as the in vitro production of cytokines by spleen cells were analyzed. No specific Cry1Ab immune response was observed in MON810 rats, and anti-maize protein antibody responses were similar in MON810 and control rats. Single parameters were sporadically altered in rats fed the MON810 maize when compared to control rats, but these alterations are considered to be of no immunotoxicological significance. Electronic supplementary material The online version of this article (10.1007/s00204-018-2230-z) contains supplementary material, which is available to authorized users.

International audience; Minor crops include mostly vegetables, fruits, nursery stock and ornamentals. These crops account for an EU production value of over (sic) 60 billion per year, representing more than 20% of the value of EU's total agricultural production. The sustainable production of such crops, from an economic point of view, is vital for both human health and European economies. For minor crops, this sustainability can only be realized by the continued availability of crop protection solutions for pest control. The number of minor crops in Europe without viable solutions for plant protection has increased in recent years. This is mainly due to the lack of pesticides in certain crops, as a number of previously authorized pesticides has not been re-authorized due to a stricter regulation. Also the introduction of tropical or sub-tropical crops and their pests into Europe has contributed to the problem of minor crops without any crop protection solutions as pesticides used elsewhere to protect these crops are not allowed in Europe. The limited range of pesticides available to farmers has increased the risk of resistance development since, in absence of a sufficient number of pesticides with various modes of action, farmers apply repetitively only a narrow spectrum of molecules. The direct economic impact due to the absence of viable plant protection solutions for minor crops has been estimated over a billion Euros per year, impacting 9 million hectares throughout Europe. In light of this, here we discuss the current state of the art of minor crops in Europe and elucidate ongoing efforts to address such problems through Integrated Pest Management (IPM). The information reported is expected to provide relevance of minor crops in Europe and encourage the development and implementation of effective IPM solutions.

Aims: To detect and identify the cultivable microorganisms putatively associated with esca disease in representative Lebanese vineyards.Methods and results: Two field surveys were conducted in Lebanon in 2005 and 2007 to study the fungal community associated with grapevine wood lesions. A total of 68 vines showing typical esca symptoms were randomly sampled in 17 vineyards and cross sections were obtained of cordons and trunks. The shape and type of inner necrosis and discoloration were examined and isolations were made from the symptomatic wood. Isolation results showed that inner necrosis and isolated fungi were similar to those previously found elsewhere, namely in Central Europe or Mediterranean countries. Additionally, three methods for numerical evaluation of micro-organisms found were compared.Conclusion: Most fungal pathogens generally associated with grapevine trunk diseases were detected, of which the basidiomycete Fomitiporia mediterranea and species of the ascomycete family Botryosphaeriaceae were the most frequently encountered. Additionally, a large diversity of other wood colonizing micro-organisms was detected. The putative role of some of the obtained micro-organisms in the process of wood degradation related to esca disease is discussed.Significance and impact of the study: This isolation study is presently the most completed that was carried out with grapevine wood samples collected in Lebanon. Besides, it is the first to provide isolation results based on a classification of inner necrosis in five categories and to compare three criteria for numerical evaluation. This study also tends to further highlight that Botryosphaeriaceae species are common wood inhabiting fungi that should be associated with esca.

Conservation of grapevine genetic resources is an important and long lasting task. Here, partners of the InWiGrape Activity of the European Cooperative Programme for Plant Genetic Resources have proposed a set of descriptors that will assist in identification, conservation and study of genetic resources of Vitis vinifera L. subsp. sylvestris. A distribution map of Vitis vinifera L. subsp. sylvestris populations in Europe was produced, with on-line access through the European Vitis Database. The several different aspects of conservation of Vitis vinifera L. subsp. sylvestris including bibliographical references, identification in the wild, in situ and ex situ conservation have been discussed. The descriptors and the map will assist different stakeholders, working on biodiversity and ecosystems in more effective conservation of wild grapevine genetic resources., VITIS - Journal of Grapevine Research, Vol 56 No 3 (2017): Vitis

UMR BFP - Equipe Virologie; International audience; Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease. A collection of 241 symptomatic leaf samples from susceptible, rym4 and rym5 varieties was gathered from 117 sites. The viruses present in all samples were identified by specific RT-PCR assays and, for selected samples, by double-stranded RNA next-generation sequencing (NGS). The results show that BaYMV-2 is responsible for the symptoms observed in varieties carrying the resistance gene rym4. In susceptible varieties, both BaYMV-1 and BaYMV-2 were detected, together with BaMMV. Phylogenetic analyses indicate that the rym4 resistance-breaking ability independently evolved in multiple genetic backgrounds. Parallel analyses revealed a similar scenario of multiple independent emergence events in BaMMV for rym5 resistance-breaking, likely involving multiple amino acid positions in the viral-linked genome protein. NGS analyses and classical techniques provided highly convergent results, highlighting and validating the power of NGS approaches for diagnostics and viral population characterization.

Noninversion tillage with tine- or disc-based cultivations prior to crop establishment is the most common way of reducing tillage for arable cropping systems with small grain cereals, oilseed rape, and maize in Europe. However, new regulations on pesticide use might hinder further expansion of reduced-tillage systems. European agriculture is asked to become less dependent on pesticides and promote crop protection programs based on integrated pest management (IPM) principles. Conventional noninversion tillage systems rely entirely on the availability of glyphosate products, and herbicide consumption is mostly higher compared to plow-based cropping systems. Annual grass weeds and catchweed bedstraw often constitute the principal weed problems in noninversion tillage systems, and crop rotations concurrently have very high proportions of winter cereals. There is a need to redesign cropping systems to allow for more diversification of the crop rotations to combat these weed problems with less herbicide input. Cover crops, stubble management strategies, and tactics that strengthen crop growth relative to weed growth are also seen as important components in future IPM systems, but their impact in noninversion tillage systems needs validation. Direct mechanical weed control methods based on rotating weeding devices such as rotary hoes could become useful in reduced-tillage systems where more crop residues and less workable soils are more prevalent, but further development is needed for effective application. Owing to the frequent use of glyphosate in reduced-tillage systems, perennial weeds are not particularly problematic. However, results from organic cropping systems clearly reveal that desisting from glyphosate use inevitably leads to more problems with perennials, which need to be addressed in future research. Non-inversion tillage with tine or disc based cultivations prior to crop establishment is the most common way of reducing tillage for arable cropping systems with small grain cereals, oilseed rape and maize in Europe. However, new regulations on pesticide use may hinder further expansion of reduced tillage systems. European agriculture is asked to become less dependent on pesticides and promote crop protection programmes based on integrated pest management (IPM) principles. Conventional non-inversion tillage systems rely entirely on the availability of glyphosate products, and herbicide consumption is mostly higher as compared to plough-based cropping systems. Annual grass weeds and catchweed bedstraw often constitute the principal weed problems in non-inversion tillage systems and crop rotations concurrently have very high proportions of winter cereals. There is a need to redesign cropping systems to allow for more diversification of the crop rotations to combat these weed problems with less herbicide input. Cover crops, stubble management strategies and tactics that strengthen crop growth relative to weed growth are also seen as important components in future IPM systems but their impact in non-inversion tillage systems needs validation. Direct mechanical weed control methods based on rotating weeding devices such as rotary hoes may become useful in reduced tillage systems where more crop residues and less workable soils are more prevalent but further development is needed for effective application. Owing to the frequent use of glyphosate in reduced tillage systems, perennial weeds are not particularly problematic. However, results from organic cropping systems clearly reveal that desisting from glyphosate use inevitably leads to more problems with perennials, which need to be addressed in future research.

Equipe Virologie; International audience; Endornaviruses are unusual plant-, fungus- and oomycete-infecting viruses with a large, ca 14- to 17-kb linear double-stranded RNA (dsRNA) genome and a persistent lifestyle. The complete genome sequence of an endornavirus from the barley (Hordeum vulgare) Nerz variety was determined from paired Illumina MySeq reads derived from purified dsRNAs. The genome is 14,243 nt long, with 5' and 3' non-coding regions of 207 and 47 nt, respectively. It encodes a single large protein of 4663 amino acids that carries conserved motifs for a methyltransferase, a helicase and an RNA-dependent RNA polymerase. The sequence of Hordeum vulgare endornavirus (HvEV) carries all the hallmarks of a typical member of the genus Endornavirus, with the exception of an UDP-glycosyltransferase motif observed in many, but not all, endornaviral genomes.

Whether modern agriculture without conventional pesticides will be possible or not is a matter of debate. The debate is meaningful within the context of rising health and environmental awareness on one hand, and the global challenge of feeding a steadily growing human population on the other. Conventional pesticide use has come under pressure in many countries, and some European Union (EU) Member States have adopted policies for risk reduction following Directive 2009/128/EC, the sustainable use of pesticides. Highly diverse crop production systems across Europe, having varied geographic and climatic conditions, increase the complexity of European crop protection. The economic competitiveness of European agriculture is challenged by the current legislation, which banned the use of many previously authorized pesticides that are still available and applied in other parts of the world. This challenge could place EU agricultural production at a disadvantage, so EU farmers are seeking help from the research community to foster and support integrated pest management (IPM). Ensuring stable crop yields and quality while reducing the reliance on pesticides is a challenge facing the farming community is today. Considering this, we focus on several diverse situations in European agriculture in general and in European crop protection in particular. We emphasize that the marked biophysical and socio-economic differences across Europe have led to a situation where a meaningful reduction in pesticide use can hardly be achieved. Nevertheless, improvements and/or adoption of the knowledge and technologies of IPM can still achieve large gains in pesticide reduction. In this overview, the current pest problems and their integrated management are discussed in the context of specific geographic regions of Europe, with a particular emphasis on reduced pesticide use. We conclude that there are opportunities for reduction in many parts of Europe without significant losses in crop yields.

International audience; Bacterial quorum sensing (QS) mechanisms play a crucial role in the proper performance and ecological fitness of bacterial populations. Many key physiological processes are regulated in a QS-dependent manner by auto-inducers, like the N-acyl homoserine lactones (AHLs) in numerous Gram-negative bacteria. In addition, also the interaction between bacteria and eukaryotic hosts can be regulated by AHLs. Those mechanisms gained much attention, because of the positive effects of different AHL molecules on plants. This positive impact ranges from growth promotion to induced resistance and is quite contrasting to the rather negative effects observed in the interactions between bacterial AHL molecules and animals. Only very recently, we began to understand the molecular mechanisms underpinning plant responses to AHL molecules. In this review, we gathered the latest information in this research field. The first part gives an overview of the bacterial aspects of quorum sensing. Later we focus on the impact of AHLs on plant growth and AHL-priming, as one of the most understood phenomena in respect to the inter-kingdom interactions based on AHL-quorum sensing molecules. Finally, we discuss the potential benefits of the understanding of bacteria-plant interaction for the future agricultural applications.

The Rosaceae Conserved Orthologous Set (RosCOS) provides a gene-based genome-wide set of markers that have been used in comparative analyses of peach (Prunus persica), apple (Malus × domestica), and strawberry (Fragaria spp.). In order to extend the use of these RosCOS to sweet cherry (Prunus avium L.), we identified markers that are polymorphic in breeding germplasm. Ninety-five percent (595/627) of previously designed RosCOS primer pairs amplified a product in six sweet cherry cultivars predicted to represent the range of genetic diversity in breeding germplasm. A total of 45% (282/627) RosCOS were polymorphic among the six cultivars, and allele number ranged from 2 to 6, with a genome-wide mean of 2.35. A subset of 92 genome-wide single nucleotide polymorphisms (SNPs) corresponding to 76 RosCOS was analyzed in 36 founder accessions and progeny. The expected and observed heterozygosity suggested that 83% of the RosCOS were in Hardy–Weinberg equilibrium, implying that most RosCOS behave as neutral markers. Principal coordinate analysis (PCO) identified one wild accession and two Spanish landraces that clustered differently from the other accessions. The relatively high number of unique alleles found in the three differentially clustered selections suggested that their use as parents has potential to increase the genetic diversity in future US-bred cultivars. Of the 92 RosCOS SNPs, 81 SNPs that represented 68 genome-wide RosCOS segregated in four mapping populations. These RosCOS were mapped in four F1 populations, thereby greatly improving the genetic linkage map of sweet cherry.

International audience; Grapevines (Vitis vinifera L.) form the basis of viticulture, and are susceptible to diseases such as downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator). Therefore, successful viticulture programs require the use of pesticides. Breeding for resistance is the only eco-friendly solution. Marker-assisted selection is currently widely used for grapevine breeding. Consequently, traits of interest must be tagged with molecular markers linked to quantitative trait loci (QTL). We herein present our findings regarding genetic mapping and QTL analysis of resistance to downy and powdery mildew diseases in the progenies of the GF.GA-47-42 ('Bacchus' x 'Seyval') x 'Villard blanc' cross. Simple sequence repeats and single nucleotide polymorphisms of 151 individuals were analyzed. A map consisting of 543 loci was screened for QTL analyses based on phenotypic variations observed in plants grown in the field or under controlled conditions. A major QTL for downy mildew resistance was detected on chromosome 18. For powdery mildew resistance, a QTL was identified on chromosome 15. This QTL was replaced by a novel QTL on chromosome 18 in 2003 (abnormally high temperatures) and 2004. Subsequently, both QTLs functioned together. Additionally, variations in the timing of the onset of veraison, which is a crucial step during grape ripening, were studied to identify genomic regions affecting this trait. A major QTL was detected on linkage group 16, which was supplemented by a minor QTL on linkage group 18. This study provides useful information regarding novel QTL-linked markers relevant for the breeding of disease-resistant grapevines adapted to current climatic conditions.

International audience; Research on innovative Integrated Pest Management (IPM) tools is done on station and on-farm in the PURE project. The idea is that IPM tools are tested under well-defined conditions in experimental orchards. Subsequently, they are tested in commercial orchards as part of a total IPM system where drawbacks and bottlenecks become clear. In subsequent on-station experiments the drawbacks or bottlenecks are solved and adjusted IPM tools are again tested in commercial orchards. We call this the "design - assessment - adjustment cycle". It is meant, together with co-innovation techniques, to promote uptake of innovative IPM tools by commercial farmers. For apple, new innovations are the use of exclusion netting against codling moth (Cydia pomonella), and the use of an antagonist against conidia of Venturia inaequalis. For pear, the overwintering inoculum of brown spot of pear (Stemphylium vesicarium) is reduced by antagonists and natural fertilisers, and the control of pear sucker (Cacopsylla pyricola) is promoted by natural enemies. For both apple and pear an innovative canopy adapted sprayer is used to reduce emissions and to further reduce pesticide use. Efficacy of these innovative IPM tools and IPM systems is assessed by the newly developed software for environmental effects: SYNOPS, for economic effects: PREMISE, and for overall sustainability, including economic, social and environmental aspects: DEXiPM-pomefruit. Results show that the overall sustainability of the conventional system is already high. Nevertheless, innovative IPM tools provided an improvement of environmental quality with an efficient control of diseases or pests. The cost for running the innovative IPM systems was often higher than the conventional system.

Information about disease management in winter wheat (Triticum aestiva) in eight European countries was collated and analysed by scientists and extension workers within the European Network for the Durable Exploitation of Crop Protection Strategies (ENDURE). This included information about specific disease thresholds, decision support systems, host varieties, disease prevalence and pathogen virulence. Major differences in disease prevalence and economic importance were observed. Septoria tritici blotch (Mycosphaerella graminicola) was recognized as the most yield reducing disease in countries with intensive wheat production, but also rust diseases (Puccinia striiformis and Puccinia triticina), powdery mildew (Blumeria graminis) and Fusarium head blight (Fusarium spp.) were seen as serious disease problems. Examples of current integrated pest management (IPM) strategies in different countries have been reported. Disease management and fungicide use patterns showed major differences, with an average input equivalent to 2.3 full dose rates (TFI) in the UK and a TFI of 0.6 in Denmark. These differences are most likely due to a combination of different cropping systems, climatic differences, disease prevalence, and socio-economic factors. The web based information platform www.eurowheat.org was used for dissemination of information and results including information on control thresholds, cultural practices which can influence disease attack, fungicide efficacy, fungicide resistance, and pathogen virulence, which are all elements supporting IPM for disease control in wheat. The platform is open to all users. The target groups of Euro Wheat information are researchers, advisors, breeders, and similar partners dealing with disease management in wheat. Information about disease management in winter wheat (Triticum aestiva) in eight European countries was collated and analysed by scientists and extension workers within a European Network for Durable Exploitation (ENDURE). This included information about specific disease thresholds, decision support systems, host varieties, disease prevalence and pathogen virulence. Major differences in disease prevalence and economic importance were observed. Septoria tritici blotch (Mycosphaerella graminicola) was recognized as the most yield reducing disease in countries with intensive wheat production, but also rust diseases (Puccinia striiformis and Puccinia triticina), powdery mildew (Blumeria graminis) and Fusarium head blight (Fusarium spp.) were seen as serious disease problems. Examples of current IPM strategies in different countries have been reported. Disease management and fungicide use patterns showed major differences, with an average input equivalent to 2.3 full dose rates (TFI) in the UK and a TFI of 0.6 in Denmark. These differences are most likely due to a combination of different cropping systems, climatic differences, disease prevalence and socio-economic factors. The web based information platformwww.EuroWheat.org was used for dissemination of information and results including information on control thresholds, cultural practices which can influence disease attack, fungicide efficacy, fungicide resistance and pathogen virulence, which are all elements supporting IPM for disease control in wheat. The platform is open to all users. The target groups of EuroWheat information are researchers, advisors, breeders and similar partners dealing with disease management in wheat.

Times are changing for pest management in Europe. Stronger societal demands and pesticide resistance pressure farmers to reduce their reliance on pesticides more than ever before. Reconciling human health and environmental goals with production is a challenge for farmers as well as for all crop-protection stakeholders. Expectations that research and extension will quickly provide solutions are high everywhere. Although a few European countries have acquired experience with pesticide action plans or implementation of integrated pest management (IPM) guidelines on a national scale, many others are starting from a more modest base. Stakeholders in Europe are looking beyond their national borders to create synergies and share experiences and know-how. Representatives of the European Commission and Parliament, governments, research, extension, farmers, industry, and civil society are engaged in dynamic interactions. A Europe-wide structure (an ERA-Net) able to coordinate national calls for research and extension proposals on IPM is planned for 2014. Since 2007, the 10-country network ENDURE has pooled expertise among its 15 research, education, and extension member institutions. It has conducted joint reviews and original studies on IPM, organized summer schools, set up an internet-based platform on wheat cultivars and pathogens, and continues to support workshops, newsletters, and an information center with 1,600 entries for advisers. After earlier successes on insect pest management in North America or with resource-poor farmers in developing countries, Europe is set to become a source of renewed inspiration for IPM applied to conventional agriculture in industrialized countries and broadened to encompass all pest categories.

Chapitre 2; International audience; The biological characteristics of a crop together with the way it is managed in the field determine the rate at which genetic material moves by seed and pollen between crops, crop-derived weeds (volunteers), feral plants, and wild relatives. The EU FP6 project, SIGMEA, collated and compared data on the transmission of genetic material in relation to coexistence thresholds for three contrasting species in Europe. The conclusions are: 1) Coexistence will be feasible for maize, because transmission is mostly by pollen flow, which decreases rapidly with distance. 2) Coexistence will also be feasible for sugar beet because, while volunteer beet may be abundant, most crop beet is harvested when vegetative so will not exchange genes during the year of harvest. 3) Coexistence will be difficult or even impossible for oilseed rape, because persistent seed is a major route of transmission. Field management may alleviate the problems of gene transmission in oilseed rape, but will be insufficient to counter the influence of this species' biology.

Strawberry domestication has resulted in a reduction of both morphological and genetic diversity with modern cultivars. Therefore, it seems to be important keeping all the variability available today in order to limit the decrease of the genetic basis of small berries genetic resources and enriched genetic pool for future breeding. One of the tools for preservation genetic resources is maintaining collections that represent all spectrum of variability. Creation of centralized, well characterized and harmonized European strawberry collection was the aim of European project “Small berries genetic resources” (GENBERRY) co-funded by DG AGRI. However, success of maintaining sufficiently large and representative collection depends on many factors, among other sanitary status of the accessions. Methods preventing the breakage of collections caused by pests and diseases, including management growing system to maintain sanitary status of strawberry collections in open field, greenhouse and in vitro conditions were collected and developed by different partners of GENBERRY project.

International audience; Crop protection in general and apple crop protection in particular often rely on pesticides, although several alternative pest management measures are available. In this context European agricultural policy requires the implementation of Integrated Pest Management (IPM) by 2014. Within IPM, more than one strategy can be practiced but selecting the most sustainable strategy is difficult because it requires simultaneous assessment of multiple environmental and economic aspects or attributes. Here, we introduce the SustainOS methodology for sustainability assessment of orchard systems, and we evaluate its usefulness in a case study involving four crop protection strategies in apple orchards of five European regions. SustainOS is an iterative, multi-attribute approach for defining and rating the sustainability of crop protection strategies in comparative studies. It consists of a transparent system-description tool including context, target, and crop protection parameters. The parameters are used as input data for life cycle assessment, environmental risk assessment, and full-cost calculations. The various results from these quantitative assessments are used to generate a multi-attribute rating with respect to ecological and economic sustainability. We demonstrate how the quantitative results can be translated into rating classes. By applying the SustainOS methodology, we show that the ecological sustainability for all five regions can potentially be improved by implementing alternative crop protection measures currently available. We also report that, by increasing yield, yield stability, and fruit quality, implementation of IPM can improve the economic situation of apple growers. Because of its transparency, SustainOS facilitated the collaborative development and comparison of crop protection strategies for sustainable orchard systems by an international network of agronomists, economists, and environmental scientists.

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 genetic structure and diversity information is critical for genetic association studies. In the octoploid cultivated strawberry (Fragaria×ananassa), genetic analyses were focussed on diversity, whereas genetic structure has been poorly explored. This study investigated the genetic structure in a genetic resources collection representing a wide range of the octoploid strawberry cultivars released mainly by North America and western and southern Europe, at different breeding periods and with various pedigrees. The relationship between varieties was examined using 23 microsatellite (simple sequence repeat, SSR) markers. Eight SSR markers were diploid, useful for cultivar discrimination with polymorphic information content (PIC) values between 0.29 and 0.74. Bayesian analyses of genetic structure identified four subpopulations. Three of them, American and modern northern European cultivars (AMNECs), American and modern southern European cultivars (AMSECs) and old European cultivars (OECs), reflected the European breeding history of the cultivated octoploid strawberry. The fourth subpopulation, ‘Intermediate’ group cultivars (IGCs), comprised various origins including OECs that were introgressed with wild species such as Fragaria chiloensis or Fragaria moschata. The OEC group gathered cultivars dating before 1960s, forming the most homogenous and stable subpopulation. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on modified Nei and Li distance confirmed the separation of the AMSEC, AMNEC and OEC groups. In addition, significant differences were observed among the four subpopulations (AMNEC, AMSEC, OEC, IGC), with high variability within groups and between AMSEC and IGC. Our work underlined that the structure within the studied collection was mainly explained by the pedigree and the year of release than the geographical origin of cultivars. In addition, the important loss of diversity observed in the modern European cultivars and a trend towards using mainly American cultivars for breeding programmes led to the progressive abandonment of old European germplasm, which was revealed as a relative distinct and rich group. This European material should be protected and maintained, because it represents a potential source of original traits for broadening the genetic base of cultivated strawberry. In addition, diploid markers we identified can be used without ambiguity in phylogenetic and diversity studies, because they are genome-specific. This study is the first step for further association studies in strawberry.

International audience; Winter wheat is the most important cereal crop in Europe and wheat diseases are commonly seen to have a major impact on yields, quality of grain and fungicide requirements. EuroWheat collates data and information on wheat disease management from several countries aiming at analysing and displaying this information in a European context. It is expected to provide significant added value on a European scale by bringing together existing information from national programmes and ensuring that these data are in a format, which can be readily understood trans-nationally. The information is targeted to support local advisers, breeders and other partners dealing with disease management in wheat. The content of the platform can support IPM (Integrated Plant Protection Management) in a broad sense. The platform is open to all users. Only features, which are still under development, are behind login.

With 2 figures and 4 tables Abstract At the field scale, the co-existence of different farming production systems requires strategies to prevent gene flow between adjacent crops. Oilseed rape produces pollen dispersed by wind and insects and the risks of pollen mediated gene flow are significant for this crop. Cleistogamy, the trait of non-opening flowers, could be used to reduce pollen flow. Cleistogamous oilseed rape genotypes were obtained by INRA in France and were bred in order to improve the stability of this trait. In this paper, we examine the reliability of the cleistogamous trait for two inbred lines. The flower opening level was measured at different dates during the flowering period in six field experiments (three sites × 2 years). The results showed that some flowers were partially opened with rates varying from 0.5% to 33% principally depending on genotypes, trials (site and year) and recording dates. Given that other studies have shown that cleistogamy could reduce pollen dispersal, we consider that, even when partially unstable, cleistogamy could be beneficially used in combination with other means in a containment strategy.

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; Genetic parameters for apple (Malus x domestica) fruit external traits (fruit size, ground colour, proportion of over colour and attractiveness) and sensory traits (firmness, crispness, texture, juiciness, flavour, sugar, acidity and global taste) were estimated using 2,207 pedigreed genotypes from breeding programmes in six European countries. Data were scored for 3 years and four periods during storage. Analyses were performed with a restricted maximum likelihood method using VCE 5.1.2 software. Heritability estimates ranged from medium to high for instrumental traits. Genetic correlations between firmness and sugar were medium and low between firmness and acidity. Sensory traits showed low to high heritability, acidity and flavour being, respectively, the most and the less heritable. Global taste was strongly correlated with texture, juiciness, and flavour and relatively less correlated with crispness and acidity. Sensory sugar and acidity showed highly negative correlations whereas their instrumental measurements showed low and increasing positive correlations from harvest to 4 months post-harvest. Sugar exhibited a higher sensory/instrumental divergence. Conversely, instrumental and sensory firmness were highly correlated. Fruit external characteristics had medium heritability. Fruit attractiveness had highest and lowest correlations with fruit size and ground colour, respectively. Best linear unbiased predictors of breeding values were computed for all genotypes with the software PEST. The results were analysed with regard to the dynamic and the reliability of genetic parameters according to the scoring dates. Original issues of the study and the importance of the obtained results for efficient designs of further apple fruit quality breeding programmes were discussed