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International audience; Crop species rely on genetic and phenotypic diversity to adapt to various environments. Genotypes respond differently, resulting in genotype-by-environment interactions (GxE). Recent advances in phenomics and modeling allow for the prediction of GxE for traits related to sustainability and productivity. However, a phenotype-centered framework that effectively navigates the interplay between genetics, physiology, and the environment is needed. Here we present maize data from phenotyping platforms and field experiments and explore strategies to integrate concepts and techniques from ecophysiology, ecology, and math to: (i) define and describe phenotypic space across spatial, temporal, and biological scales; (ii) identify unique phenotypic combinations and constraints; and (iii) identify territories of the phenotypic space representing favorable adaptations for crop improvement. Our findings demonstrate the value of phenotype-focused perspectives for adapting crops to climate change.

We used genotyping-by-sequencing to investigate the evolutionary history of bere, the oldest barley variety still cultivated in Britain and possibly in all of Europe. With a panel of 203 wild and 401 cultivated barley accessions, including 35 samples identified as bere, we obtained filtered datasets comprising up to 1,946,469 single nucleotide polymorphisms (SNPs). The beres formed two genetically-distinct groups, the larger of which included beres from Orkney and the Scottish Western Isles, as well as varieties not identified as bere from the Faroe Islands. This group of beres was distinct from other British barleys, but had a close genetic affiliation with Scandinavian accessions. Although the data were partly compatible with the traditional view that bere was introduced to Scotland by the Vikings during the eighth century AD, the evidence as whole suggested that the bere and Scandinavian barleys are sister groups descended from a more distant common progenitor, possibly dating to the Bronze Age when hulled barleys first become common in northern Europe. More recently, there has been gene flow from these beres into Polish barleys, possibly following export of grain to the Baltic region during periods when Orkney was under Norwegian or Danish rule. A second, smaller group of beres, which included a traditional Welsh variety, was genetically distinct from the main group and probably represents a more recent introduction of barley from central Europe. Our results emphasize the uniqueness of bere barley and its importance as a heritage crop and a potential source of germplasm for breeding programmes.

Concerns regarding high maize yield losses due to increasing occurrences of drought events are growing, and breeders are still looking for molecular markers for drought tolerance. However, the genetic determinism of traits in response to drought is highly complex and identification of causal regions is a tremendous task. Here, we exploit the phenotypic data obtained from four experiments carried out on a phenotyping platform, where a diversity panel of 254 maize hybrids was grown under well-watered and water deficit conditions. To dissociate drought effect from other environmental factors, we performed multi-environment genome-wide association study on steady-state means or drought plasticity indices computed for six ecophysiological traits. We identify 102 steady-state QTLs and 40 plasticity QTLs. Most of them were new compared to those obtained from a previous study on the same dataset. Our results show that plasticity QTLs cover genetic regions not identified by steady-state QTLs. Furthermore, for all traits, except one, plasticity QTLs are specifically involved in the genotype by water availability interaction, for which they explain between 60\% and 100\% of the variance. Altogether, steady-state and plasticity QTLs captured more than 75\% of the genotype by water availability interaction variance, and allowed to find new genetic regions. Overall, our results demonstrate the importance of considering plasticity indices in multiple environments to decipher the genetic architecture of trait response to stress.

International audience; Potassium (K) is an essential element, which is often supplied to horticultural crops via foliar spraying. Some studies have investigated the effect of different foliar-applied K compounds; however, most studies have focussed on crop quality and yield parameters, or were performed with isolated leaf cuticles. The aim of this study was to evaluate the rates of the foliar ion penetration and leaf surface deposition of 130 mM K sprays of compounds with markedly different point of deliquescence (POD) and efflorescence (POE) values, the rates having been previously estimated in climate chamber trials. Shoots of field-grown, commercial olive trees were sprayed with K-nitrate (KNO3), K-sulphate (K2SO4), K-chloride (KCl), K-phosphate (K3PO4), K-carbonate (K2CO3) and K-bicarbonate (KHCO3), and leaf samples were collected after 3 and 24 h. Cation and anion concentrations were determined in the leaf tissues, and in a preliminary leaf water wash for estimating surface-deposited ion concentrations. No significant leaf tissue K increments were recorded between the K sprays. Olive tissue anion concentrations showed different patterns, and a chloride (Cl−) increase was detected 3 h after the foliar KCl supply. On the other hand, the foliar K applications led to leaf nitrate changes regardless of the K source supplied. High amounts of K and accompanying ions were recovered in the washing liquid of the foliar K-supplied leaves. Some foliar K treatments increased the leaf surface concentration of sulphate and chloride, suggesting a potential effect on leaf cell anion extrusion. Hence, despite no evidence of foliar K uptake, an effect of leaf anion concentrations was observed, indicating that foliar nutrient sprays may influence leaf and leaf surface anion balance.

International audience; Monilinia laxa is a fungus that causes brown rot in stone fruit. Immature green fruits in the first stage of fruit development (stage I) are generally susceptible. To investigate the relationship between the physical characteristics of immature fruit and susceptibility to M. laxa, we characterized the progeny, derived from a clone of wild peach (Prunus davidiana) crossed with two commercial nectarines (Prunus persica) varieties, through laboratory infection, transpiration monitoring and stomata counting. Two types of fruit infections were observed - ‘classic’ brown rot and ‘clear spot’ symptoms - which have not previously been described in the literature. The number and density of stomata did not explain the observed variability of infection in the progeny. However, surface conductance was positively correlated with infection level. This study provides experimental evidence partially linking physical fruit characteristics to brown rot infection at the immature fruit stage. The role of delayed cuticle deposition in susceptibility to brown rot of immature fruit is discussed.

Strawberry (Fragaria × ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F1 population derived from parental lines ‘Candonga’ and ‘Senga Sengana’, adapted to distinct Southern and Northern European areas. To account for environmental effects, the F1 and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A), and the chloroplast-located AsA transporter gene FaPHT4;4(7C) might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A) inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A) was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.

International audience; To meet the increasing global demand for food, feed, fibre and other plant- derivedproducts, a steep increase in crop productivity is a scientifically and technicallychallenging imperative. The CropBooster- P project, a response to the H2020call ‘Future proofing our plants’, is developing a roadmap for plant research toimprove crops critical for the future of European agriculture by increasing cropyield, nutritional quality, value for non- food applications and sustainability.However, if we want to efficiently improve crop production in Europe and pri-oritize methods for crop trait improvement in the coming years, we need to takeinto account future socio- economic, technological and global developments, in-cluding numerous policy and socio- economic challenges and constraints. Basedon a wide range of possible global trends and key uncertainties, we developedfour extreme future learning scenarios that depict complementary future devel-opments. Here, we elaborate on how the scenarios could inform and direct fu-ture plant research, and we aim to highlight the crop improvement approachesthat could be the most promising or appropriate within each of these four futureworld scenarios. Moreover, we discuss some key plant technology options thatwould need to be developed further to meet the needs of multiple future learningscenarios, such as improving methods for breeding and genetic engineering. Inaddition, other diverse platforms of food production may offer unrealized poten-tial, such as underutilized terrestrial and aquatic species as alternative sources ofnutrition and biomass production. We demonstrate that although several meth-ods or traits could facilitate a more efficient crop production system in some ofthe scenarios, others may offer great potential in all four of the future learningscenarios. Altogether, this indicates that depending on which future we are head-ing toward, distinct plant research fields should be given priority if we are to meetour food, feed and non- food biomass production needs in the coming decades.

Mixed cropping (MC) is a key strategy to harness agriculture for climate-change. Breeding adapted genotypes can unleash the full potential of MC, both in terms of yield potential and yield stability. To achieve this goal, concepts from both breeding and ecology have to be fused in order to develop a suitable methodology for breeding for MC. In order to advance the field of breeding for MC, we evaluated yield and trait data of pure stands (PS) and mixed stands (MS) of pea (P. sativum L.) and barley (H. vulgare L.) as a legume-cereal model system. Twenty-eight pea and seven barley lines, representing European breeding material, were grown in an incomplete factorial design at two organically managed sites across two years. The general mixing ability (GMA) of pea for total mixture yield was predominant as specific mixing ability (SMA) was absent, facilitating future breeding and seed marketing efforts. The most promising pea cultivar ‘Volt’ resulted in an average total mixture yield increase of 11% (+0.43 t/ha) in MC compared to the average, while the cultivar ’Florida’ led to a yield decrease of − 31% (−1.23 t/ha), highlighting the importance of the choice of the genotype in MS. The analysis of separated MS yields allowed to investigate the underlying mechanistic principles in genotypes’ contribution to MS yields and we revealed the major role of producer (Pr) effects in this context. The correlation between Pr effects and GMA revealed that GMA can be maximized by selecting for high Pr effects. Early vigor, onset of flowering, shoot biomass and stipule length were identified as key traits for indirect selection for high GMA in pea accounting for up to 17% of the identified variation in total mixture yield. PS yields were moderately correlated with mixture yields (r = 0.52, P = 0.013) and can serve as an additional selection criterion. Discrepancies between correlations with PS and MS yields can be exploited to identify unique MS traits that confer niche complementarity in MS. By this method we identified stipule size as such a key trait for increasing GMA of pea. Pea genotype mixtures have a stabilizing effect also in MC systems and exhibited considerably less genotype × year and genotype × location interaction than single genotypes. Our findings close existing knowledge gaps towards breeding for MC and pave the way to develop improved genotypes for diversified cropping systems as a strategy for sustainable intensification and climate change adaptation.

International audience; Tree architecture shows large genotypic variability, but how this affects water-deficit responses is poorly understood. To assess the possibility of reaching ideotypes with adequate combinations of architectural and functional traits in the face of climate change, we combined high-throughput field phenotyping and genome-wide association studies (GWAS) on an apple tree (Malus domestica) core-collection. We used terrestrial light detection and ranging (T-LiDAR) scanning and airborne multispectral and thermal imagery to monitor tree architecture, canopy shape, light interception, vegetation indices and transpiration on 241 apple cultivars submitted to progressive field soil drying. GWAS was performed with single nucleotide polymorphism (SNP)-by-SNP and multi-SNP methods. Large phenotypic and genetic variability was observed for all traits examined within the collection, especially canopy surface temperature in both well-watered and water deficit conditions, suggesting control of water loss was largely genotype-dependent. Robust genomic associations revealed independent genetic control for the architectural and functional traits. Screening associated genomic regions revealed candidate genes involved in relevant pathways for each trait. We show that multiple allelic combinations exist for all studied traits within this collection. This opens promising avenues to jointly optimize tree architecture, light interception and water use in breeding strategies. Genotypes carrying favourable alleles depending on environmental scenarios and production objectives could thus be targeted.

IntroductionDespite its rapid worldwide adoption as an efficient mutagenesis tool, plant genome editing remains a labor-intensive process requiring often several months of in vitro culture to obtain mutant plantlets. To avoid a waste in time and money and to test, in only a few days, the efficiency of molecular constructs or novel Cas9 variants (clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9) prior to stable transformation, rapid analysis tools are helpful.MethodsTo this end, a streamlined maize protoplast system for transient expression of CRISPR/Cas9 tools coupled to NGS (next generation sequencing) analysis and a novel bioinformatics pipeline was established.Results and discussionMutation types found with high frequency in maize leaf protoplasts had a trend to be the ones observed after stable transformation of immature maize embryos. The protoplast system also allowed to conclude that modifications of the sgRNA (single guide RNA) scaffold leave little room for improvement, that relaxed PAM (protospacer adjacent motif) sites increase the choice of target sites for genome editing, albeit with decreased frequency, and that efficient base editing in maize could be achieved for certain but not all target sites. Phenotypic analysis of base edited mutant maize plants demonstrated that the introduction of a stop codon but not the mutation of a serine predicted to be phosphorylated in the bHLH (basic helix loop helix) transcription factor ZmICEa (INDUCER OF CBF EXPRESSIONa) caused abnormal stomata, pale leaves and eventual plant death two months after sowing.

International audience; In the frame of the G2P-SOL project, core collections representative of the worldwide genetic diversity of the four major Solanaceous crops (tomato, pepper, eggplant, potato) were created. These collections were phenotyped and subjected to metabolic profiling. Hundreds of novel metabolites have been identified and quantified, and QTLs have been mapped, both in the core collections and in segregating populations. The genetic architecture of some of these traits will be discussed in detail.

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International audience; Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observe an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. This increase in mobility is lost in the sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Also, DSB sites show particularly high mobility levels and their enhanced mobility requires the HR factor RAD54. Our data suggest that repair mechanisms promote chromatin mobility upon DNA damage, implying a role of this process in the early steps of the DNA damage response.

Pollen-specific phospholipase A-mediated in vivo haploid induction system was functionally well conserved in numerous monocots. However, no functional orthologous gene has been identified in dicots plants. Here, we show that loss-of-function of gynoecium-expressed phospholipase AII (pPLAIIγ) triggers haploid plants in Arabidopsis, at an average rate of 1.46%. Reciprocal crosses demonstrate that haploid plants are triggered from the female side and not from the pollen, and the haploid plants carry the maternal genome.

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Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via down regulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula 9 Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit.We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways ; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.

As in other eukaryotes, the plant genome is functionally organized in two mutually exclusive chromatin fractions, a gene-rich and transcriptionally active euchromatin, and a gene-poor, repeat-rich, and transcriptionally silent heterochromatin. In Drosophila and humans, the molecular mechanisms by which euchromatin is preserved from heterochromatin spreading have been extensively studied, leading to the identification of insulator DNA elements and associated chromatin factors (insulator proteins), which form boundaries between chromatin domains with antagonistic features. In contrast, the identity of factors assuring such a barrier function remains largely elusive in plants. Nevertheless, several genomic elements and associated protein factors have recently been shown to regulate the spreading of chromatin marks across their natural boundaries in plants. In this minireview, we focus on recent findings that describe the spreading of chromatin and propose avenues to improve the understanding of how plant chromatin architecture and transitions between different chromatin domains are defined.

Ensuring balanced distribution of chromosomes in gametes, meiotic recombination is essential for fertility in most sexually reproducing organisms. The repair of the programmed DNA double strand breaks that initiate meiotic recombination requires two DNA strand-exchange proteins, RAD51 and DMC1, to search for and invade an intact DNA molecule on the homologous chromosome. DMC1 is meiosis-specific, while RAD51 is essential for both mitotic and meiotic homologous recombination. DMC1 is the main catalytically active strand-exchange protein during meiosis, while this activity of RAD51 is downregulated. RAD51 is however an essential cofactor in meiosis, supporting the function of DMC1. This work presents a study of the mechanism(s) involved in this and our results point to DMC1 being, at least, a major actor in the meiotic suppression of the RAD51 strand-exchange activity in plants. Ectopic expression of DMC1 in somatic cells renders plants hypersensitive to DNA damage and specifically impairs RAD51-dependent homologous recombination. DNA damage-induced RAD51 focus formation in somatic cells is not however suppressed by ectopic expression of DMC1. Interestingly, DMC1 also forms damage-induced foci in these cells and we further show that the ability of DMC1 to prevent RAD51-mediated recombination is associated with local assembly of DMC1 at DNA breaks. In support of our hypothesis, expression of a dominant negative DMC1 protein in meiosis impairs RAD51-mediated DSB repair. We propose that DMC1 acts to prevent RAD51-mediated recombination in Arabidopsis and that this down-regulation requires local assembly of DMC1 nucleofilaments.Author SummaryEssential for fertility and responsible for a major part of genetic variation in sexually reproducing species, meiotic recombination establishes the physical linkages between homologous chromosomes which ensure their balanced segregation in the production of gametes. These linkages, or chiasmata, result from DNA strand exchange catalyzed by the RAD51 and DMC1 recombinases and their numbers and distribution are tightly regulated. Essential for maintaining chromosomal integrity in mitotic cells, the strand-exchange activity of RAD51 is downregulated in meiosis, where it plays a supporting role to the activity of DMC1. Notwithstanding considerable attention from the genetics community, precisely why this is done and the mechanisms involved are far from being fully understood. We show here in the plant Arabidopsis that DMC1 can downregulate RAD51 strand-exchange activity and propose that this may be a general mechanism for suppression of RAD51-mediated recombination in meiosis.

International audience; Key message Phenomic prediction of wheat grain yield and heading date in different multi-environmental trial scenarios is accurate. Modelling the genotype-by-environment interaction effect using phenomic data is a potentially low-cost complement to genomic prediction. The performance of wheat cultivars in multi-environmental trials (MET) is difficult to predict because of the genotype-by-environment interactions (G x E). Phenomic selection is supposed to be efficient for modelling the G x E effect because it accounts for non-additive effects. Here, phenomic data are near-infrared (NIR) spectra obtained from plant material. While phenomic selection has recently been shown to accurately predict wheat grain yield in single environments, its accuracy needs to be investigated for MET. We used four datasets from two winter wheat breeding programs to test and compare the predictive abilities of phenomic and genomic models for grain yield and heading date in different MET scenarios. We also compared different methods to model the G x E using different covariance matrices based on spectra. On average, phenomic and genomic prediction abilities are similar in all different MET scenarios. Better predictive abilities were obtained when G x E effects were modelled with NIR spectra than without them, and it was better to use all the spectra of all genotypes in all environments for modelling the G x E. To facilitate the implementation of phenomic prediction, we tested MET designs where the NIR spectra were measured only on the genotype-environment combinations phenotyped for the target trait. Missing spectra were predicted with a weighted multivariate ridge regression. Intermediate predictive abilities for grain yield were obtained in a sparse testing scenario and for new genotypes, which shows that phenomic selection is an efficient and practicable prediction method for dealing with G x E.

Pemphigus is a life-threatening auto-immune blistering disease of the skin and mucous membrane that is caused by the production of auto-antibodies (auto-Abs) directed against adhesion proteins: desmoglein 1 and 3. We demonstrated in the "Ritux3" trial, the high efficacy of rituximab, an anti-CD20 recombinant monoclonal antibody, as the first-line treatment for pemphigus. However, 25% of patients relapsed during the six-month period after rituximab treatment. These early relapses were associated with a lower decrease in anti-desmoglein auto-Abs after the initial cycle of rituximab. The N-glycosylation of immunoglobulin-G (IgG) can affect their affinity for Fc receptors and their serum half-life. We hypothesized that the extended half-life of Abs could be related to modifications of IgG N-glycans. The IgG N-glycome from pemphigus patients and its evolution under rituximab treatment were analyzed. Pemphigus patients presented a different IgG N-glycome than healthy donors, with less galactosylated, sialylated N-glycans, as well as a lower level of N-glycans bearing an additional N-acetylglucosamine. IgG N-glycome from patients who achieved clinical remission was not different to the one observed at baseline. Moreover, our study did not identify the N-glycans profile as discriminating between relapsing and non-relapsing patients. We report that pemphigus patients present a specific IgG N-glycome. The changes observed in these patients could be a biomarker of autoimmunity susceptibility rather than a sign of inflammation. ispartof: BIOMEDICINES vol:10 issue:8 ispartof: location:Switzerland status: published

The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence., HB was funded by USDA-NIFA SBIRI and SBIRII. PH and SG were funded by project P18-RT-992 from Junta de Andalucía (Andalusian Regional Government), Spain (Co-funded by FEDER). JC was funded by BBSRC grant BB/P010741/1. MF is supported by the 2Blades Foundation and Grains Research and Development Corporation (project CSP1801-013RTX/9176010). VK is supported by the Ministry of Science and Higher Education of the Russian Federation (grant no. 075-15-2019-1881). GH was supported by funding of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2048/1—project ID 390686111 and grants 426557363 and 458717903, the European Regional Development Fund (Project ID ZS/2018/06/93171), and the Czech Science Foundation (CZ.02.1.01./0.0/0.0/16_019/0000827, SPP 813103381). BK thanks the Government of Norway (QZA-14/0005) for funding the initiative of “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” (https://www.cwrdiversity.org/project/pre-breeding/).

Potassium (K) deficiency has consequences not only on cellular ion balance and transmembrane potential but also on metabolism. In fact, several enzymes are K-dependent including enzymes in catabolism, causing an alteration in glycolysis and respiration. In addition, K deficiency is associated with the induction of specific pathways and accumulation of metabolic biomarkers, such as putrescine. However, such drastic changes are usually observed when K deficiency is established. Here, we carried out a kinetic analysis with metabolomics to elucidate early metabolic events when nutrient conditions change from K-sufficiency to K-deficiency in Arabidopsis rosettes from both wild type and mutants affected in both K absorption and low-K signalling (hak5 akt1 cipk23). Our results show that mutants have a metabolomics pattern similar to K-deficient wild-type, showing a constitutive metabolic response to low K. In addition, shifting to low K conditions induces (i) changes in sugar metabolism and (ii) an accumulation of salicylic acid metabolites before the appearance of biomarkers of K deficiency (putrescine and aconitate), and such an accumulation is more pronounced in mutants. Our results suggest that early events in the response to low K conditions involve salicylic acid metabolism., G.T. thank the Région Pays de la Loire and Angers Loire Métropole for its financial support via the grant Connect Talent Isoseed. We thank Sergio García for his skilful assistance. This work was funded by grant number 20806/PI/18 (to FR) from Fundación Séneca de la Región de Murcia, Spain, grant PID2019-106649RB-I00 from Ministerio de Ciencia e Innovación, Spain (to FR and MN-C). This work was also supported by the Red de Excelencia BIO2016-81957-REDT from Ministerio de Economía, Industria y Competitividad. All grants from Spanish ministries were co-financed by the FEDER Fund. MN-C, is recipient of a Ramón y Cajal Fellowship (RyC-2017-21924) from Ministerio de Economía y Competitividad, Spain

Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is among the most threatening wheat diseases in Europe. Genetic resistance remains one of the main environmentally sustainable strategies to efficiently control STB. However, the molecular and physiological mechanisms underlying resistance are still unknown, limiting the implementation of knowledge-driven management strategies. Among the 22 known major resistance genes (Stb), the recently cloned Stb16q gene encodes a cysteine-rich receptor-like kinase conferring a full broad-spectrum resistance against Z. tritici. Here, we showed that an avirulent Z. tritici inoculated on Stb16q quasi near isogenic lines (NILs) either by infiltration into leaf tissues or by brush inoculation of wounded tissues partially bypasses Stb16q-mediated resistance. To understand this bypass, we monitored the infection of GFP-labeled avirulent and virulent isolates on Stb16q NILs, from germination to pycnidia formation. This quantitative cytological analysis revealed that 95% of the penetration attempts were unsuccessful in the Stb16q incompatible interaction, while almost all succeeded in compatible interactions. Infectious hyphae resulting from the few successful penetration events in the Stb16q incompatible interaction were arrested in the sub-stomatal cavity of the primary-infected stomata. These results indicate that Stb16q-mediated resistance mainly blocks the avirulent isolate during its stomatal penetration into wheat tissue. Analyses of stomatal aperture of the Stb16q NILs during infection revealed that Stb16q triggers a temporary stomatal closure in response to an avirulent isolate. Finally, we showed that infiltrating avirulent isolates into leaves of the Stb6 and Stb9 NILs also partially bypasses resistances, suggesting that arrest during stomatal penetration might be a common major mechanism for Stb-mediated resistances.

International audience; Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies such as molecular marker arrays, genomic selection and genome wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.

Background The ongoing adaptation of plants to their environment is the basis for their survival. In this adaptation, mechanoperception of gravity and local curvature plays a role of prime importance in finely regulating growth and ensuring a dynamic balance preventing buckling. However, the abiotic environment is not the exclusive cause of mechanical stimuli. Biotic interactions between plants and microorganisms also involve physical forces and potentially mechanoperception. Whether pathogens trigger mechanoperception in plants and the impact of mechanotransduction on the regulation of plant defense remains however elusive. Results Here, we found that the perception of pathogen-derived mechanical cues by microtubules potentiates the spatio-temporal implementation of plant immunity to fungus. By combining biomechanics modeling and image analysis of the post-invasion stage, we reveal that fungal colonization releases plant cell wall-born tension locally, causing fluctuations of tensile stress in walls of healthy cells distant from the infection site. In healthy cells, the pathogen-derived mechanical cues guide the reorganization of mechanosensing cortical microtubules (CMT). The anisotropic patterning of CMTs is required for the regulation of immunity-related genes in distal cells. The CMT-mediated mechanotransduction of pathogen-derived cues increases Arabidopsis disease resistance by 40% when challenged with the fungus Sclerotinia sclerotiorum. Conclusions CMT anisotropic patterning triggered by pathogen-derived mechanical cues activates the implementation of early plant defense in cells distant from the infection site. We propose that the mechano-signaling triggered immunity (MTI) complements the molecular signals involved in pattern and effector-triggered immunity.

International audience

International audience

Drought stress can considerably affect maize yields, which is a source of concern for maintaining global food security in the coming years. Identification of quantitative traits loci (QTLs) involved in the genotype x environment interaction (GxE) is a way to increase maize resilience to drought through marker-assisted breeding or candidate gene identification. However, these QTLs generally have low effects, which make them difficult to detect. We hypothesized that computing ratios from phenotypic values measured in two contrasted watering conditions would help in identifying QTLs involved in GxE interaction that would not be detected when considering each condition separately. To test this hypothesis, we used previously published data containing phenotypic measurements for six drought-responsive ecophysiological traits acquired on 254 maize hybrids grown under two watering conditions, well-watered (WW) and water deficit (WD), in four greenhouse experiments (Prado et al., 2018). We conducted a genome wide association study on the trait values obtained in each watering condition as well as on the WD/WW ratios, taking into account an effect of the experiment. A total of 140 QTLs were detected, 102 (73%) were detected in one of the two watering conditions and 38 (27%) were detected only on the ratios. We quantified the contribution of the detected QTLs to the variations of the traits by fitting statistical mixed models including fixed effects of the QTLs and random effects of the genotype, genotype x condition interaction and genotype x experiment interaction. This showed that the QTLs detected in each watering condition mostly contributed the genotype variation (39%-65% of the variance captured depending on the trait) while the QTLs detected only for the ratios mainly contributed to the genotype x condition interaction (69%-100% of the variance captured). Altogether, these results show that ratio-specific QTLs are complementary to the QTLs detected in each condition separately and are worth being considered to explain the GxE interaction.

Reproducibility in organ size and shape is a fundamental trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ morphology. To address this question, we produced a dataset composed of both transcriptomic and morphological information obtained from 27 individual sepals from wild-type plants. Although nearly identical in their genetic background, environment, and developmental stage, these sepals exhibited appreciable variability in both morphology and transcriptome. We identified modules of co-expressed genes in sepals, three of which correlated significantly with morphology, revealing biologically relevant gene regulatory networks. Interestingly, cell-wall related genes were overrepresented in two of these three modules. Additionally, we found that highly variable genes were unexpectedly enriched in cell-wall related processes. We then analyzed sepal morphology from 16 cell-wall mutants and found that the more a gene is expressed in wild-type, the more variable the morphology of the corresponding mutant. Altogether, our work unravels the contribution of cell-wall related genes to the robustness of sepal morphology. More generally, we propose that canalizing traits during development could rely on the modulation of highly expressed genes.

SummaryDespite the essential role of Specialized Metabolites (SMs) in the interaction of plants with the environment, studying the ability of crop seeds to produce these protective compounds has been neglected. Furthermore, seeds produce a myriad of SMs providing an interesting model to investigate their diversity and plasticity. Camelina sativa gained a lot of interest in the past few years as rustic oil seed crop. A characterization of seed SM landscapes in six camelina genotypes grown in the field and harvested during five growing seasons has been undertaken in this work. This allowed a comprehensive annotation of seed SMs combining analyses that cluster SMs based on their chemical structures and co-accumulation patterns. These data showed broad effects of the environment on the stimulation of the seed-specialized metabolome. Among well annotated compounds, flavonols were identified as the metabolic class characterised by high plasticity, revealing significant variable accumulation according to the year and/or the genotype. Lastly, a deeper characterisation of primary metabolites and lipids in two selected genotypes has been performed. We showed that, in addition to flavonols, alkaloids and glucosinolates displayed a higher phenotypic plasticity with respect to most of the primary metabolites, including some sugars and major storage compounds such as fatty acids, proteins and most lipid classes (e.g. DAG, TAG), but similar plasticity compared to free aminoacids and carboxylic acids. This work highlighted major and unexplored effects of the environment on the seed specialized metabolome demonstrating that seeds exhibit a dynamic and plastic metabolism, with an impact on seed quality.Significance statementSeeds produce a myriad of Specialized Metabolites (SMs) with an essential role in the interaction of plants with the environment. We characterized SM landscapes, primary metabolites and lipid composition in the seeds of camelina genotypes grown in the open field in five consecutive growing seasons. Our results showed the predominant effect of the environment on the regulation of the seed - specialized metabolome, with a potential impact on seed quality of camelina that may also occur in other oilseed crops.

International audience; The metabolomic profiling analyses of 11 vitamins' statuses of wheat grain in a subsample of 167 accessions from the INRAE worldwide bread wheat core collection planted in two contrasting environments in France (Le Moulon and Clermont-Ferrand) have been evaluated using a high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS) procedure. This has allowed us to perform a genome-wide association study (GWAS) for these nutritional traits of interest combining the phenotypic data with the genotypic data derived from the TaBW280K SNP chip. Considering both thresholds (P < 0.0003 and R2 ≥ 8%), the GWAS identified between 1 and 22 marker-trait associations (MTAs) for the individual vitamins at the individual locations, and 12 SNP markers were stable and associated with vitamin contents across two environments. Desirable alleles and superior genotypes identified in the current analysis provide novel genetic data that can be used for future research on the genetics of vitamins and their application in wheat breeding.

Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00619-0.

Key messageRose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance.AbstractPowdery mildew, caused byPodosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certainMLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, theseMLOgenes are called susceptibility genes. We carried out a genome-wide identification of theMLOgene family in theRosa chinensisgenome, and screened for allelic variants among 22 accessions from seven differentRosaspecies using re-sequencing and transcriptome data. We identified 19MLOgenes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicotMLOsusceptibility genes. We detected a total of 198 different allelic variants in the set ofRosaspecies and accessions, corresponding to 5–15 different alleles for each of the genes. Some diploidRosaspecies shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the fourRhMLOgenes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them,RhMLO1andRhMLO2, are required for infection byP. pannosaand suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.

International audience; Rhynchosporium is one of the main biotic stresses on barley production worldwide. A set of 312 spring barley accessions was tested in four different locations over 3 years, to identify novel genetic resistances to rhynchosporium and to explore the allelic diversity for resistance genes present in this global germplasm collection. High-density genotypes from exome capture and RNA-seq were used to conduct high-resolution association mapping. Seven quantitative trait loci (QTL) were detected, including one in the Rrs2 region, amongst five containing known resistances. Relatively short physical intervals harbouring these resistances were proposed, providing a platform for the identification of underlying genes and tightly linked genetic markers for use in marker assisted selection. Genes encoding kinases were present in four of the QTL, in addition to Rrs1 and Rrs18, two loci known to contribute to rhynchosporium resistance. The frequencies and distributions of these novel and known QTL were superimposed on the regional origin of the landrace genotypes comprising the genome-wide association studies (GWAS) panel, highlighting the value of genetic resources as a source of diverse genetically controlled resistance to rhynchosporium. The detected QTL along with their linked genetic markers, could be exploited either directly for breeding purposes or for candidate gene identification in future studies.

The metals iron, zinc, manganese, copper, molybdenum, and nickel are essential for the growth and development of virtually all plant species. Although these elements are required at relatively low amounts, natural factors and anthropogenic activities can significantly affect their availability in soils, inducing deficiencies or toxicities in plants. Because essential trace metals can shape root systems and interfere with the uptake and signaling mechanisms of other nutrients, the non-optimal availability of any of them can induce multi-element changes in plants. Interference by one essential trace metal with the acquisition of another metal or a non-metal nutrient can occur prior to or during root uptake. Essential trace metals can also indirectly impact the plant’s ability to capture soil nutrients by targeting distinct root developmental programs and hormone-related processes, consequently inducing largely metal-specific changes in root systems. The presence of metal binding domains in many regulatory proteins also enables essential trace metals to coordinate nutrient uptake by acting at high levels in hierarchical signaling cascades. Here, we summarize the known molecular and cellular mechanisms underlying trace metal-dependent modulation of nutrient acquisition and root development, and highlight the importance of considering multi-element interactions to breed crops better adapted to non-optimal trace metal availabilities.

Participation en visioconférenceAnimation scientifique de type Journal Club. Domaine: biologie (pluridisciplinaire). Organisé par Jean-Luc Morel pour les scientifiques intéressés par la recherche spatiale (CNES).; National audience

International audience; In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.

International audience; No abstract available

Le douglas est une espèce forestière originaire de l'ouest de l'Amérique du Nord, particulièrement appréciée et valorisée pour la qualité de son bois, sa vigueur et sa résistance aux maladies et insectes. Après le pin maritime, c'est l'essence résineuse la plus utilisée dans les reboisements français.Dès le début des années 1960, l'INRA s'est engagé dans un programme d'amélioration génétique du douglas pour, d'une part, créer des variétés adaptées aux reboisements dans les stations forestières productives de basse et moyenne altitude et, d'autre part, mettre en place des vergers à graines pour assurer la production de semences.Ces travaux de recherche ont contribué à générer plusieurs impacts sociétaux : - Economique : plus de 100 000 ha de reboisement ont été réalisés à partir des graines améliorées issues des travaux de l'INRA, ce qui a engendré un supplément de revenu pour le massif français de douglas. - Politique : depuis 2011, la France n'est plus tributaire d'importation pour satisfaire ses besoins en graines de douglas et est même exportatrice en Europe. - Environnemental : Le douglas tend à se substituer à l'épicéa commun qui souffre de dépérissement dans le contexte du changement climatique. Avec un impact minime sur les sols comparativement à d'autres résineux, le douglas est l'espèce forestière métropolitaine la plus performante pour la séquestration du carbone. - Sociaux : le douglas contribue à la compétitivité et la dynamique de la filière forêt-bois dans de nombreuses régions de France. Toutefois, dans certaines régions, la présence de plantations de Douglas suscite des controverses chez les riverains.Cette étude a été conduite selon la méthode Asirpa ex-post., Douglas fir is a forest species native to western North America, particularly appreciated and valued for the quality of its wood, its vigor and its resistance to diseases and insects. After maritime pine, it is the resinous species most used in French reforestation.From the beginning of the 1960s, INRA started a genetic improvement program for Douglas-fir to, on the one hand, create varieties suitable for reforestation in productive low and medium altitude forest stations and, on the other hand, to set up seed orchards to ensure the production of seeds.This research work has helped generate several societal impacts: - Economic: more than 100,000 ha of reforestation was carried out using improved seeds resulting from the work of INRA, which generated additional income for the French Douglas-fir massif. - Policy: since 2011, France is no longer dependent on imports to meet its needs for Douglas-fir seeds and is even an exporter in Europe. - Environmental: Douglas-fir tends to replace common spruce, which suffers from dieback in the context of climate change. With minimal impact on soils compared to other conifers, Douglas-fir is the most efficient metropolitan forest species for carbon sequestration. - Social: Douglas fir contributes to the competitiveness and dynamics of the forest-wood industry in many regions of France. However, in some regions, the presence of Douglas-fir plantations is causing controversy among local residents.

Son périmètre concerne la biologie végétale, l'agronomie, la transformation et la nutrition humaine.

Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.

International audience; Cucumber vein yellowing virus (CVYV) is an emerging virus on cucurbits in the Mediterranean Basin, against which few resistance sources are available, particularly in melon. The melon accession PI 164323 displays complete resistance to isolate CVYV-Esp, and accession HSD 2458 presents a tolerance, i.e. very mild symptoms in spite of virus accumulation in inoculated plants. The resistance is controlled by a dominant allele Cvy-1 1 , while the tolerance is controlled by a recessive allele cvy-2, independent from Cvy-1 1 . Before introducing the resistance or tolerance in commercial cultivars through a long breeding process, it is important to estimate their specificity and durability. Upon inoculation with eight molecularly diverse CVYV isolates, the resistance was found to be isolate-specific since many CVYV isolates induced necrosis on PI 164323, whereas the tolerance presented a broader range. A resistance-breaking isolate inducing severe mosaic on PI 164323 was obtained. This isolate differed from the parental strain by a single amino acid change in the VPg coding region. An infectious CVYV cDNA clone was obtained, and the effect of the mutation in the VPg cistron on resistance to PI 164323 was confirmed by reverse genetics. This represents the first determinant for resistance-breaking in an ipomovirus. Our results indicate that the use of the Cvy-1 1 allele alone will not provide durable resistance to CVYV and that, if used in the field, it should be combined with other control methods such as cultural practices and pyramiding of resistance genes to achieve long-lasting resistance against CVYV.

Starch is by far the major storage compound accumulated by plants and algae, one of the most abundant polysaccharides present on earth and principal source of dietary calories in the human and animal diet. Starch synthesis occurs during the day, using global outputs of photosynthesis and its degradation starts as night falls to sustain energy-demanding cellular functions. Little is known about the regulatory mechanisms governing starch metabolism in microalgae and current knowledge is lim-ited to factors impacting starch accumulation under adverse environmental conditions such as nitro-gen limitation. A link between light perception and starch accumulation has been suggested in the case of higher plants: Mutants devoid of Phytochrome have a reduced CO2 uptake but over-accumulate daytime sucrose and starch while PHOT has been found to mediate starch degradation in guard cells in the light to energize stomatal opening. Light perception and metabolism have not been associated in microalgae. Here we present a detailed PHOT-dependent signalling cascade, linking blue light perception with starch accumulation in the green microalga Chlamydomonas reinhard-tii:Pathway 1: Blue light, via PHOT, represses the bHLH domain-containing transcription factor (TF) GAPr4, an activator of GAP1, (glyceraldehyde-3-phosphate dehydrogenase, involved in glycolysis and in photosynthetic CO2 fixation). Both the PHOT knock-out mutant phot and GAP1 over-expressing lines accumulate high amounts of starch.Pathway 2: Blue light, via PHOT, activates the RWP5 TF (belonging to the RWP-K family of TFs), a re-pressor of starch accumulation in a GAP1-independent manner.Pathway 3: PHOT-dependent phosphorylation of the serine/threonine kinase Blue Starch Kinase 1 (BSK1; orthologue of the Arabidopsis HT1 kinase that controls stomatal movements in response to CO2) mediates GAP1 and starch accumulation levels in a GAPr4-independent manner.Our work advances the current understanding of how light signaling controls metabolism in microal-gae. It also adds one more aspect in the multifaceted role of PHOT so far reported to control gameto-genesis at low nitrogen, expression of genes encoding chlorophyll and carotenoid biosynthesis, the size of the eyespot and photoprotection., L'amidon est non seulement, et de loin, le principal composé de stockage accumulé par les plantes et les algues, mais c’est également l'un des polysaccharides les plus abondants sur terre. De plus, il s’agit de la principale source de calories dans l'alimentation humaine et animale. La synthèse de l'amidon est un des produits finaux de la photosynthèse et sa synthèse se déroule pendant la journée, alors que sa dégradation commence à la tombée de la nuit pour soutenir les fonctions cellulaires exigeantes en énergie. On sait peu de choses sur les mécanismes de régu-lation qui régissent le métabolisme de l'amidon chez les micro-algues et les connaissances ac-tuelles se limitent aux facteurs qui ont un impact sur l'accumulation d'amidon dans des condi-tions environnementales défavorables telles que par exemple la disponibilité en azote. Un lien entre la perception de la lumière et l'accumulation d'amidon a été suggéré dans le cas des plantes supérieures : Les mutants dépourvus de Phytochrome ont une absorption réduite de CO2 tandis qu’ils accumulent de façon anormale du saccharose et de l'amidon pendant la journée. De plus, il a été découvert que PHOT jouait un rôle dans ce processus en servant de médiateur à la dégradation de l'amidon dans les cellules de garde à la lumière pour stimuler l'ouverture des stomates. Toutefois et jusqu’à présent, la perception de la lumière et le métabo-lisme n'ont pas été associés chez les micro-algues. Nous présentons ici une cascade de signali-sation détaillée dépendante de PHOT, reliant la perception de la lumière bleue à l'accumula-tion de l'amidon dans la microalgue verte Chlamydomonas reinhardtii :Voie 1 : La lumière bleue, via PHOT, réprime le facteur de transcription (TF) GAPr4 conte-nant le domaine bHLH, un activateur de GAP1, (glyceraldehyde-3-phosphate déshydrogé-nase, impliqué dans la glycolyse et dans la fixation photosynthétique du CO2). Le mutant PHOT knock-out phot et les lignées surexprimant GAP1 accumulent de grandes quantités d'amidon.Voie 2 : La lumière bleue, via PHOT, active le TF RWP5 (appartenant à la famille des TFs RWP-K), un répresseur de l'accumulation d'amidon d'une manière indépendante de GAP1.Voie 3 : la phosphorylation dépendante de PHOT de la sérine/thréonine kinase Blue Starch Kinase 1 (BSK1 ; orthologue de la kinase HT1 d'Arabidopsis qui contrôle les mouvements stomatiques en réponse au CO2) sert de médiateur entre les niveaux de GAP1 et l’accumulation d'amidon d'une manière indépendante de GAPr4.Notre travail a fait progresser la compréhension actuelle de la façon dont la signalisation lumi-neuse contrôle le métabolisme chez les micro-algues. Il ajoute également une nouvelle fonction aux multiples rôles jouée par PHOT dont le contrôle de la gamétogenèse à faible teneur en azote, l'expression des gènes codant pour la synthèse de la chlorophylle et celle des caroté-noïdes, ainsi que la taille du stigma et la photoprotection.

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.

International audience; The challenges of securing future food security will require deployment of innovative technologies to accelerate crop production. Plant phenotyping methods have advanced significantly, spanning low-cost hand-held devices to large-scale satellite imaging. Field-based phenotyping aims to capture plant response to the environment, generating data that can be used to inform breeding and selection requirements. This in turn requires access to multiple representative locations and capacities for collecting useful information. In this paper we identify the current challenges in access to field phenotyping in multiple locations in Europe based on stakeholder feedback. We present a map of current infrastructure and propose opportunities for greater integration of existing facilities for meeting different user requirements. We also review the currently available technology and data requirements for effective multi-location field phenotyping and provide recommendations for ensuring future access and coordination. Taken together we provide an overview of the current status of European field phenotyping capabilities and provides a roadmap for their future use to support crop improvement. This provides a wider framework for the analysis and planning of field phenotyping activities for crop improvement worldwide.

International audience

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency., This work was partially supported by the project RIS3CAT (COTPA-FRUIT3CAT) financed by the European Regional Development Fund through the FEDER frame of Catalonia 2014-2020 and by the CERCA Program from Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-20150533) and 2020-2023 (CEX2019-000902-S)., With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000902-S)

International audience; Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios.

Cette étude, basée sur une analyse de la bibliographie du domaine, a été réalisée par un groupe de chercheurs de différents départements de recherche d’INRAE appuyé par des documentalistes de la Direction pour la Science Ouverte d’INRAE. Son contenu n’engage que la responsabilité de leurs auteurs.Le groupe a été animé par Carole Caranta et Guy Richard.