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1. GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome

Author

Morgane Ardisson, Johanna Girodolle, Stéphane De Mita, Pierre Roumet, and Vincent Ranwez

Subjects
Complex genome, Domestication, Durum wheat, FAIR principles, Genotyping, Target enrichment capture, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads. Existing workflows predominantly cater to phylogenetic inference, leaving a gap in user-friendly tools for genotyping analysis based on capture methods. In response to these challenges, we have developed GeCKO (Genotyping Complexity Knocked-Out). To assess the effectiveness of combining target enrichment capture with GeCKO, we conducted a case study on durum wheat domestication history, involving sequencing, processing, and analyzing variants in four relevant durum wheat groups. Results GeCKO encompasses four distinct workflows, each designed for specific steps of genomic data processing: (i) read demultiplexing and trimming for data cleaning, (ii) read mapping to align sequences to a reference genome, (iii) variant calling to identify genetic variants, and (iv) variant filtering. Each workflow in GeCKO can be easily configured and is executable across diverse computational environments. The workflows generate comprehensive HTML reports including key summary statistics and illustrative graphs, ensuring traceable, reproducible results and facilitating straightforward quality assessment. A specific innovation within GeCKO is its 'targeted remapping' feature, specifically designed for efficient treatment of targeted enrichment capture data. This process consists of extracting reads mapped to the targeted regions, constructing a smaller sub-reference genome, and remapping the reads to this sub-reference, thereby enhancing the efficiency of subsequent steps. Conclusions The case study results showed the expected intra-group diversity and inter-group differentiation levels, confirming the method's effectiveness for genotyping and analyzing genetic diversity in species with complex genomes. GeCKO streamlined the data processing, significantly improving computational performance and efficiency. The targeted remapping enabled straightforward SNP calling in durum wheat, a task otherwise complicated by the species' large genome size. This illustrates its potential applications in various biological research contexts.

Published
2024
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2. Interest of phenomic prediction as an alternative to genomic prediction in grapevine

Author

Charlotte Brault, Juliette Lazerges, Agnès Doligez, Miguel Thomas, Martin Ecarnot, Pierre Roumet, Yves Bertrand, Gilles Berger, Thierry Pons, Pierre François, Loïc Le Cunff, Patrice This, and Vincent Segura

Subjects
Phenomic prediction, Genomic prediction, Plant breeding, Spectroscopy, Phenomics, Grapevine, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum provides information on the biochemical composition within a tissue, itself being under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been mainly applied in several annual crop species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits, related to berry composition, phenology, morphological and vigour. A major novelty of this study was to collect spectra and phenotypes several years apart from each other. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. Results For the first time, we showed that the similarity between spectra and genomic relationship matrices was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Applying a mixed model on spectra data increased phenomic predictive ability, while using spectra collected on wood or leaves from one year or another had less impact. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, a significant positive correlation was found across traits between predictive ability of genomic and phenomic predictions. Conclusion NIRS is a new low-cost alternative to genotyping for predicting complex traits in perennial species such as grapevine. Having spectra and phenotypes from different years allowed us to exclude genotype-by-environment interactions and confirms that phenomic prediction can rely only on genetics.

Published
2022
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3. Unsupervised analysis of NIRS spectra to assess complex plant traits: leaf senescence as a use case

Author

Héloïse Villesseche, Martin Ecarnot, Elsa Ballini, Ryad Bendoula, Nathalie Gorretta, and Pierre Roumet

Subjects
NIR, Leaf senescence, Unsupervised model, Wheat, Temporal kinetic, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background As a rapid and non-destructive method, Near Infrared Spectroscopy is classically proposed to assess plant traits in many scientific fields, to observe enlarged genotype panels and to document the temporal kinetic of some biological processes. Most often, supervised models are used. The signal is calibrated thanks to reference measurements, and dedicated models are generated to predict biological traits. An alternative unsupervised approach considers the whole spectra information in order to point out various matrix changes. Although more generic, and faster to implement, as it does not require a reference data set, this latter approach is rarely used to document biological processes, and does requires more information of the process. Methods In our work, an unsupervised model was used to document the flag leaf senescence of durum wheat (Triticum turgidum durum). Leaf spectra changes were observed using Moving Window Principal Component Analysis (MWPCA). The dates related to earlier and later spectra changes were compared to two key points on the senescence time course: senescence onset (T0) and the end of the leaf span (T1) derived from a supervised strategy. Results For almost all leaves and whatever the signal pre-treatments and window size considered, the MWPCA found significant spectral changes. The latter was highly correlated with T1 (0.59 ≤ r ≤ 0.86) whereas the correlations between the first significant spectrum changes and T0 were lower (0.09 ≤ r ≤ 0.56). These different relationships are discussed below since they define the potential as well as the limitations of MWPCA to model biological processes. Conclusion Overall, our study demonstrates that the information contained in the spectra can be used when applying an unsupervised method, here the MWPCA, to characterize a complex biological phenomenon such leaf senescence. It also means that using whole spectra may be relevant in agriculture and plant biology.

Published
2022
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4. Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits

Author

Michel Colombo, Pierre Roumet, Christophe Salon, Christian Jeudy, Mickael Lamboeuf, Stéphane Lafarge, Anne-Valérie Dumas, Pierre Dubreuil, Wa Ngo, Brice Derepas, Katia Beauchêne, Vincent Allard, Jacques Le Gouis, and Renaud Rincent

Subjects
bread wheat, durum wheat, root, association mapping, QTL, breeding, Plant culture, SB1-1110
Abstract

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.

Published
2022
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5. Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

Author

Aymé Spor, Agathe Roucou, Arnaud Mounier, David Bru, Marie-Christine Breuil, Florian Fort, Denis Vile, Pierre Roumet, Laurent Philippot, and Cyrille Violle

Subjects
Medicine, Science
Abstract

Abstract Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations.

Published
2020
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6. Preferential helping to relatives: A potential mechanism responsible for lower yield of crop variety mixtures?

Author

Hélène Fréville, Pierre Roumet, Nicolas Olivier Rode, Aline Rocher, Muriel Latreille, Marie‐Hélène Muller, and Jacques David

Subjects
agriculture, durum wheat, indirect genetic effect, kin recognition, kin selection, phenotypic plasticity, Evolution, QH359-425
Abstract

Abstract Variety mixtures, the cultivation of different genotypes within a field, have been proposed as a way to increase within‐crop diversity, allowing the development of more sustainable agricultural systems with reduced environmental costs. Although mixtures have often been shown to over‐yield the average of component varieties in pure stands, decreased yields in mixtures have also been documented. Kin selection may explain such pattern, whenever plants direct helping behaviors preferentially toward relatives and thus experience stronger competition when grown with less related neighbors, lowering seed production of mixtures. Using varieties of durum wheat originating from traditional Moroccan agrosystems, we designed a greenhouse experiment to address whether plants reduced competition for light by limiting stem elongation when growing with kin and whether such phenotypic response resulted in higher yield of kin groups. Seeds were sown in groups of siblings and nonkin, each group containing a focal plant surrounded by four neighbors. At the group level, mean plant height and yield did not depend upon relatedness among competing plants. At the individual level, plant height was not affected by genetic relatedness to neighbors, after accounting for direct genetic effects that might induce among‐genotype differences in the ability to capture resources that do not depend on relatedness. Moreover, in contrast to our predictions, shorter plants had lower inclusive fitness. Phenotypic plasticity in height was very limited in response to neighbor genotypes. This suggests that human selection in crops may have attenuated shade‐avoidance responses to competition for light. Future research on preferential helping to relatives in crops might thus target social traits that drive competition for other resources than light. Overall, our study illustrates the relevance of tackling agricultural issues from an evolutionary standpoint and calls for extending such approaches to a larger set of crop species.

Published
2019
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7. Diversité agro-morphologique et gestion variétale par les agriculteurs du blé dur (Triticum turgidum ssp. durum) dans le Pré-Rif marocain

Author

lamyae CHENTOUFI, Ali SAHRI, Mustapha ARBAOUI, Ahmed BIROUK, Pierre ROUMET, and Marie-Hélène MULLER

Subjects
General Works
Abstract

Durum wheat is a strategic crop in Morocco. Characterization and evaluation of cultivated varieties in different traditional agroecosystems allows safeguard and rehabilitation of this genetic heritage and its use in breeding programs. In this context, a collection of 59 traditional populations of durum wheat from the Pre-Rif region was studied using nine agro-morphological traits. Phenotypic diversity was determined by the Shannon-Weaver diversity index (H’) at different levels (totality of sample, by type of wheat and varietal names). Estimated H’ showed a wide genetic variability for different traits with a mean of H’=0.78. The results of the multiple correspondence analysis and hierarchical clustering showed a clear distinction between modern and traditional varieties. In traditional varieties, agro-morphological traits do not differentiate between varieties. The results of this work revealed the great phenotypic and nominative diversity of durum wheat varieties as well as the existence of homonyms and synonyms in the names given by farmers.

Published
2014

8. Impact du relief et des circuits semenciers locaux sur la diversité agro-morphologique du blé dur (Triticum turgidum ssp. durum) dans la vallée d’Er Rich – Imilchil (Maroc)

Author

Ali SAHRI, Lamyae CHENTOUFI, Mustapha ARBAOUI, Marie-Helene MULLER, Pierre ROUMET, and Loubna BELQADI

Subjects
General Works
Abstract

Phenotypic diversity of 101 durum wheat landrace populations collected from the oasis of the Oriental Atlas Mountains (Morocco) was studied. Nine characters (morphological and agronomic) were measured on the 3030 lines (30 lines per population). The frequencies of each phenotypic class were used for the estimate and the analysis of diversity, by considering the geographical zones of origin and the gradients of altitude. The Shannon-Weaver diversity index (H’) showed a wide variability for all considered traits. This index varies from one area to another and from one altitudinal class to another. The mean H’ recorded for all areas was 0.62, indicating the presence of a high degree of polymorphism among the studied durum wheat landrace populations. The results of the multiple component analysis and the hierarchical clustering showed that the geographical proximity and altitude play a main function in the discrimination and the structure of the studied durum wheat populations. The information gathered from this study could be used in conventional breeding programs and in situ conservation of the diversity.

Published
2014

9. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

Author

Yan Holtz, Morgane Ardisson, Vincent Ranwez, Alban Besnard, Philippe Leroy, Gérard Poux, Pierre Roumet, Véronique Viader, Sylvain Santoni, and Jacques David

Subjects
Medicine, Science
Abstract

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

Published
2016
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10. Impact du relief et des circuits semenciers locaux sur la diversité agro-morphologique du blé dur (Triticum turgidum ssp. durum) dans la vallée d'Er Rich à Imilchil (Maroc)

Author

Ali SAHRI, Lamyae CHENTOUFI, Mustapha ARBAOUI, Marie-Helene MULLER, pierre ROUMET, Loubna BELQADI, and Ahmed BIROUK

Subjects
General Works
Abstract

La diversité phénotypique de 101 populations locales de blé dur issues des oasis de montagnes de l’Atlas oriental (Maroc) a été étudiée. Neuf caractères (morphologiques et agronomiques) ont été mesurés sur les 3030 lignées (30 lignées par population). Les fréquences de chaque classe phénotypique ont été utilisées pour l’estimation et l’analyse de la diversité, en considérant les zones géographiques d’origine et les gradients d’altitude. L’indice de diversité de Shannon-Weaver (H’) a montré une forte variabilité pour l’ensemble des caractères considérés. Cet indice varie d’une zone à une autre et d’une classe d’altitude à une autre. Le H’ moyen obtenu pour l’ensemble des zones est de 0,62, indiquant la présence d’un degré élevé de polymorphisme au sein des populations locales de blé dur collectées. Les résultats de l’analyse en composantes multiples ainsi que de la classification hiérarchique ont montré que la proximité géographique et l’altitude jouent un rôle majeur dans la discrimination ainsi que sur la structuration des populations de blé dur étudiées. Les informations recueillies à partir de ces résultats peuvent être exploitées dans des programmes de sélection conventionnels et de conservation in situ de la diversité. Mots clés: Populations locales, diversité phénotypique, structuration, conservation in situ, blé dur (Triticum turgidum ssp. durum).

Published
2014

11. Domestication provides durum wheat with protection from locust herbivory

Author

Marie‐Pierre Chapuis, Nicolas Leménager, Cyril Piou, Pierre Roumet, Héloïse Marche, Julia Centanni, Christophe Estienne, Martin Ecarnot, François Vasseur, Cyrille Violle, Elena Kazakou, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, This work was supported by the DINER project, publicly funded by the Labex CEMEB and funds from the French Agricultural Research Centre for International Development (CIRAD). CV was supported by the European Research Council (ERC) Starting Grant Project StG-2014-639706-CONSTRAINTS. We thank the CEFE (Centre d'Ecologie Fonctionnelle et Evolutive) and the CBGP (Centre de Biologie pour la Gestion des Populations) for providing us access to the LabEx CeMEB plateform 'terrain d'expérience CEFE,' 43°38′20.2′′N 3°51′51.0′′E, and the SEPA plateform, respectively., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)

Subjects
Ecology, leaf, nutritional ecology, plant toughness, [SDV]Life Sciences [q-bio], domestication syndrome, Locusta migratoria, functional ecology, Triticum turgidum, cereal crop, pest insects, plant nitrogen content, feeding selection, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

International audience; Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.

Published
2023
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13. La fusariose des épis des céréales à paille : synthèse de 10 années de recherche pour une meilleure gestion intégrée de la maladie

Author

Romain Valade, Béatrice Orlando, Claude Maumené, Valerie Laval, Anne-Sophie Walker, Renaud Ioos, Anne-Laure Boutigny, Valerie Cadot, Marie Foulongne-Oriol, Florence Forget, Vessela Atanasova-Penichon, Cyrille Saintenac, Ludovic Bonhomme, Thierry Langin, Frédéric Serre, Delphine Taillieu, Pierre Roumet, ARVALIS - Institut du végétal [Paris], ARVALIS - Institut du Végétal [Boigneville], BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mycologie (USC INRAE LSV-mycologie), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de santé des végétaux (LSV Angers), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Groupe d'Etude et de contrôle des Variétés Et des Semences (GEVES), Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Expérimentale PHénotypage Au Champ des Céréales (UE1375) (PHACC), Florimond Desprez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Arvalis - Institut du Végétal, ARVALIS -Thiverval-Grignon, Laboratoire de la Santé des Végétaux - Unité de Mycologie (LSV-Mycologie), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Abstract

International audience; Fusarium head blight (FHB) is a cereal disease caused by a complex of plant pathogenic fungal species of the genera Fusarium andMicrodochium, with different epidemiological characteristics and producing or not different toxins. The FHB causes significant yieldlosses, health issues and technological quality concerns in all temperate areas worldwide. The composition of the species complexis different according to the cereal, depending on the climate of the year and the agronomic practices. These species may havedifferent susceptibilities to the fungicides used and different behaviors towards genetic resistance. Thus, investigating thesecharacteristics is required to implement integrated pest management strategies adapted to this disease. For more than 10 years,several research programs have led to significant progress in this area. Tools have been developed to more accurately characterizefungal populations and their interactions. Models have been developed to predict the risk and to adapt control measures. Themolecular mechanisms involved in the interaction between plant genes and the pathogenicity of fungal species are beginning to bedeciphered. Phenotyping methods are being developed to help in the characterization of varietal susceptibility and direct controlmethods using biocontrol products are under investigation. The goal of this paper is to review the main results obtained in thecontext of integrated management of fusarium head blight.; La fusariose de l’épi (FHB) est une maladie des céréales causée par un complexe d’espèces de champignons phytopathogènes desgenres Fusarium et Microdochium, ayant des caractéristiques épidémiologiques différentes et productrices ou non de différentestoxines. Le FHB entraîne d’importantes pertes de rendement et des problèmes de qualité sanitaire et technologique dans toutes lesrégions tempérées du globe. La composition du complexe d’espèces est différente selon les céréales, très dépendante du climat del’année et de l’itinéraire technique. Ces espèces peuvent avoir des sensibilités différentes aux fongicides utilisés et descomportements différents vis à vis des résistances présentes dans les variétés. Ainsi, il est essentiel de connaître ces caractéristiquespour mettre en œuvre les méthodes de lutte intégrée adaptées à cette maladie. Depuis plus de 10 ans, plusieurs programmes derecherche ont permis des avancées significatives sur cette thématique. Des outils ont été développés et ont permis de caractériserplus précisément les populations fongiques selon les céréales et leurs interactions. Des modèles ont été développés pour prédire lerisque et adapter les moyens de lutte. Les mécanismes moléculaires impliqués dans l’interaction entre les gènes de la plante et lapathogénicité des espèces fongiques commencent à être décryptés. Des méthodes de phénotypage se développent pour aider à lacaractérisation de la sensibilité variétale et des méthodes de lutte directe utilisant des produits de biocontrôle sont endéveloppement. L’objectif de cet article est de synthétiser les principaux résultats acquis dans l’objectif d’une protection intégréevis‐à‐vis de la fusariose des épis des céréales.

Published
2020

14. Multifaceted functional diversity for multifaceted crop yield: Towards ecological assembly rules for varietal mixtures

Author

Guillaume Maillet, Frédéric Compan, Hélène Fréville, Germain Montazeaud, Pierre Roumet, Martin Ecarnot, Cyrille Violle, Aline Rocher, Florian Fort, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Agropolis Fondation : SAADA_1605_057, European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, Assembly rules, grain protein content, [SDV]Life Sciences [q-bio], Biology, 010603 evolutionary biology, 01 natural sciences, community‐weighted mean, Grain quality, functional trait, 2. Zero hunger, Genetic diversity, Biomass (ecology), Ecology, varietal mixtures, Crop yield, grain yield, assembly rules, food and beverages, durum wheat, 15. Life on land, functional diversity, Productivity (ecology), Trait, Monoculture, 010606 plant biology & botany
Abstract

UMR AGAP équipe : Génomique évolutive et gestion des populations (GE²pop); International audience; 1.Ecological theories suggest that higher plant genetic diversity can increase productivity in natural ecosystems. So far, varietal mixtures, that is, the cultivation of different genotypes within a field, have shown contrasting results, notably for grain yield where both positive and negative mixing effects have been reported. Such discrepancy between ecological theories and agronomical applications calls for a better understanding of plant–plant interactions in crops.2.Using durum wheat Triticum turgidum ssp. durum as a model species, we investigated the effect of functional trait composition on productivity and grain quality of varietal mixtures by growing 179 highly diverse genotypes in pure stands and 197 two‐way mixtures in field conditions. We quantified the agronomic performance of the mixtures relative to their components grown in pure stands on two variables related to productivity, vegetative biomass yield and grain yield, and one variable related to grain quality, grain protein content. We then analysed the relationship between the relative performance of the mixtures and their functional composition that we characterized with trait means and trait differences on 19 above‐ and below‐ground traits. 3.We found that biomass and grain yield increased by 4% overall in mixtures relative to single varieties, but that mixing effects were non‐significant for grain protein content. The combined effects of trait means and trait differences explained 12%, 17% and 22% of the variability of relative grain yield, biomass yield and grain protein content, respectively, with different traits affecting productivity and grain quality. Clustering varieties into functional groups allowed us to identify the most beneficial associations for multifaceted agronomic performance.4.Synthesis and applications. Functional traits explained a significant part of the relative agronomic performance of mixtures compared to monocultures (12%–22%, depending on the yield component). They can thus serve as a basis to identify groups of varieties whose combinations are expected to generate positive mixing effects, especially for productivity, and without compromising grain quality. Selection could then target convergence between groups for some traits and divergence between groups for other traits using empirically derived relationships between functional traits and agronomic performance as a guideline.

Published
2020
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15. Genome wide association mapping for resistance to multiple fungal pathogens in a panel issued from a broad composite cross-population of tetraploid wheat Triticum turgidum

Author

Jacques David, Etienne Paux, Dimitri Sanchez, Elsa Ballini, Pierre Roumet, Aurélie Ducasse, Jean-Benoit Morel, Gilles Charmet, Delphine Audigeos, Jonathan Kitt, Muriel Tavaud, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARVALIS - Institut du Végétal [Boigneville], ARVALIS - Institut du végétal [Paris], CASDAR, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 0301 basic medicine, Leaf rust, [SDV]Life Sciences [q-bio], Population, Locus (genetics), Chitin, Plant Science, Paralogous Gene, Horticulture, Quantitative trait locus, Biology, Triticum turgidum, 01 natural sciences, 03 medical and health sciences, Septoria, Genetics, GWAS, Allele, Association mapping, education, Gene, 2. Zero hunger, education.field_of_study, Resistance inducers, food and beverages, Wheat blast, biology.organism_classification, 3. Good health, 030104 developmental biology, [SDE]Environmental Sciences, Septoria tritici blotch, Septoria nodorum blotch, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

BGPI : Equipe 4 : Interactions Céréales Agents Pathogènes (ICAP); Few resistance genes providing defence against the major fungal diseases septoria tritici blotch (STB), septoria nodorum blotch, leaf rust (LR), and an emerging wheat blast disease have been identified in durum wheat. We identified sixteen fungal disease-associated QTL through genome-wide association mapping of 180 inbred lines sampled from a durum wheat Composite Cross-population. Two STB resistance-associated QTL mapped to chromosome 3A, one of which colocalizes with Stb6, a known resistance gene previously identified in bread wheat. This partial resistance could be conferred by a new allele of Stb6 or another paralogous gene. The second locus is associated with a reduction in pycnidia density, a recently identified and poorly understood form of resistance. A resistance QTL strongly associated with LR, and colocalizing with Lr61, was observed in a 3.24 Mbp region on chromosome 6B. QTL mapping of LR resistance following treatment by chitin used in the context of inducer treatment was also investigated. Using a combination of resistance alleles at these loci could confer durable resistance to multiple fungal diseases and aid durum wheat breeders in their fight against these fungal pathogens.

Published
2020
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16. Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

Author

Denis Vile, Agathe Roucou, Marie-Christine Breuil, Aymé Spor, Cyrille Violle, Pierre Roumet, Laurent Philippot, David Bru, Florian Fort, Arnaud Mounier, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), European Research Council (ERC) Starting Grant Project 'Ecophysiological and biophysical constraints on domestication in crop plants' (Grant ERC-StG-2014-639706-CONSTRAINTS), INRAE Pari Scientifique (IDIOME-Ble)., European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro

Subjects
0301 basic medicine, Genotype, Science, 030106 microbiology, Introgression, Microbial communities, Triticum turgidum, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Plant Roots, Article, Domestication, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Ophiostomataceae, Abundance (ecology), Mycorrhizae, Botany, Relative species abundance, Soil Microbiology, Triticum, 2. Zero hunger, Rhizosphere, Multidisciplinary, Bacteria, Ecology, biology, Obligate, Microbiota, Domestication des plantes, fungi, food and beverages, 15. Life on land, biology.organism_classification, Rhizobiales, Tetraploidy, Phenotype, 030104 developmental biology, Medicine, Mycobiome
Abstract

International audience; Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations. Crop domestication events led to spectacular modifications of plant traits increasing their suitability to human requirements. Cereals and especially wheat have been domesticated in the Middle East 1. Domestication process led to dramatic phenotypic changes in cultivated species in relation to cultivation conditions and human needs. The Domestication syndrome 2 refers to the whole set of phenotypic changes occurred during this process, including: loss of dormancy, increasing seed size, modifying seed dispersal mode and apical dominance as well photoperiod sensitivity. open

Published
2020
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17. How plant structure impacts the biochemical leaf traits assessment from in-field hyperspectral images: A simulation study based on light propagation modeling in 3D virtual wheat scenes

Author

Martin Ecarnot, Gilles Rabatel, Nathalie Al Makdessi, Pierre Roumet, Nathalie Gorretta, Pierre-Antoine Jean, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agropolis Foundation : 1202-008, 'Investissements d'avenir' program (Labex Agro) : ANR-10-LABX-0001-01, France Agrimer and l'Agence Nationale de la Recherche (ANR) through the Phenoble and Phenome programmes, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Feature vector, simulation models, Soil Science, three dimensional model, modèle de simulation, 01 natural sciences, 3D virtual scenes, modelling, leaf nitrogen content, Partial least squares regression, biochimie végétale, modélisation, triticum durum, 0105 earth and related environmental sciences, Remote sensing, Mathematics, caribu, diffusion de la lumière, Spectrometer, Ecology, canopy light propagation, modèle 3d, Simulation modeling, Hyperspectral imaging, Regression analysis, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Field (geography), multiple scattering, Principal component analysis, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

AGAP : équipe GE2pop (Génomique évolutive et gestion des populations); Light propagation modeling in 3-dimensional virtual scenes has been successfully applied to many fields, including plant canopies. However, its application to detailed analyses on how multiple scattering affects spectral-based biochemistry assessments has never been proposed. In this article, a wheat canopy model has been built using simulation models included in the open source software platform Open-Alea. Adel-Wheat, a 3D dynamic model of the aerial growth of winter wheat, has been associated with spectra collected on wheat leaves with an ASD spectrometer, and then used as input of the Caribu light propagation model. Caribu calculates the proportion of direct and scattered light for all polygons of the 3D scene. Principal component analysis was first applied to analyze the distribution of resulting spectra in the spectral feature space. Then the influence of canopy structure on quantitative regression models has been considered. For this purpose, a typical agronomical problem, i.e. nitrogen content retrieval, was addressed, using a Partial Least Square regression model. This study exhibits some important results concerning the distribution of collected spectra in the spectral feature space due to multiple scattering, and underlines the physical interpretation of these results. In the short term, it shows that satisfactory nitrogen content prediction (error about 0.5% of dry matter) can be obtained at the plant level, when considering only the plant top leaves. Moreover, its paves the way for future researches to develop spectral analysis tools able to overcome such multiple scattering phenomena.

Published
2017
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18. Shifts in plant functional strategies over the course of wheat domestication

Author

Florian Fort, Agathe Roucou, Cyrille Violle, Martin Ecarnot, Pierre Roumet, Denis Vile, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, plant functional trait, Vegetative reproduction, media_common.quotation_subject, human selection, domestication syndrome, phenotypic space, Root system, Biology, 010603 evolutionary biology, 01 natural sciences, phenotypic integration, Crop, Cultivar, Domestication, ComputingMilieux_MISCELLANEOUS, media_common, 2. Zero hunger, Biomass (ecology), Ecology, fungi, Longevity, plant functional strategies, food and beverages, 15. Life on land, plant economics spectrum, ecophysiological trade-off, functional coordination, Agronomy, Trait, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Agroecology, 010606 plant biology & botany
Abstract

AGAP : équipe GE2pop; International audience; 1. Human selection, changes in environmental conditions and management practices drove the phenotypic trajectory of crops during domestication. The characterization of the crop domestication syndrome lies mostly on reproductive characters. However, biophysical and ecophysiological constraints during vegetative growth are also at play and can strongly impact crop phenotypes. It has been argued that a broadened examination of crop phenotypes through a functional trait-based lens should improve our understanding of the domestication syndrome. 2. We used a collection of 39 genotypes representative of key steps during tetraploid wheat domestication and grew them in a common garden experiment. We quantified the vegetative phenotype of each genotype through the measurements of 13 functional traits related to root, leaf and whole-plant dimensions. 3. In modern cultivars, compared to ancestral forms, leaf longevity was shorter, while net photosynthetic rate, leaf production rate and nitrogen content were higher. Modern cultivars had a shallower root system and exhibited a larger proportion of fine roots, preferring to invest biomass above-rather than below-ground. We found ancestral forms to be integrated phenotypes characterized by coordination between above-and below-ground functioning. Conversely, in modern forms, human selection appeared to have broken this coordination and to have generated a new type of network of trait covariations. 4. Synthesis and applications. The examination of leaf, root and whole-plant traits of wheat accessions indicated a strong shift in plant functional strategies over the course of domestication. Elite genotypes tended to better optimize resource-use acquisition strategies than ancestral ones. The characterization of the crop phenotype based on vegetative traits thus suggests a much more complete domestication syndrome. Our findings highlight the benefits of using a functional trait-based characterization of crop phenotypes to document the extent of domestication syndrome and to further advance the agroecological management of cereals.

Published
2018
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19. Impact de la Domestication sur le Microbiome rhizosphérique chez le blé

Author

Aymé Spor, Agathe Roucou, Florian Fort, Laurent Philippot, Pierre Roumet, Denis Ville, Cyrille Violle, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Inconnu, INRA, Dpt BAP & EA : Projet Idiome ( 2017-2018), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, holobionte, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

20. Génétique et amélioration des plantes au sein du réseau PhytoMic

Author

Pierre Roumet, Aymé Spor, Laurent Philippot, ProdInra, Migration, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agroécologie [Dijon], and Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

21. Genetic variability of nitrogen use efficiency in rainfed upland rice

Author

Alain Ramanantsoanirina, Nourollah Ahmadi, Pierre Roumet, Tatiana Rakotoson, Philippe Letourmy, Isabelle Ratsimiala Ramonta, Julie Dusserre, Tuong-Vi Cao, Louis-Marie Raboin, Centre National de la Recherche Appliquée au Développement Rural, Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Faculté des sciences, Université de Goma, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Cariplo Foundation, and Agropolis Foundation

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, madagascar, Disponibilité nutriments (sol), variabilité génétique, Upland rice, 01 natural sciences, F30 - Génétique et amélioration des plantes, Région d'altitude, upland rice, genetic variability, 2. Zero hunger, biology, food and beverages, 04 agricultural and veterinary sciences, Nutrition des plantes, Rendement des cultures, Fertilizer, Génotype, Limiting factor, Efficacité d'utilisation, Intéraction génotype environnement, Azote, low input, Soil Science, Oryza sativa, Context (language use), Teneur en azote, engineering.material, Oryza, Variation génétique, Riz pluvial, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetic variability, nitrogen utilization efficiency, Panicle, Méthode statistique, Sol, rice, nitrogène, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, oryza, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, nitrogen uptake efficiency, Agronomy and Crop Science, F04 - Fertilisation, 010606 plant biology & botany
Abstract

AGAP : équipe GE2pop; In sub-Saharan Africa and in Madagascar, upland rice is mostly grown for subsistence by resource-poor farmers in low-input production systems with low yields. In this context, soil nitrogen availability is a major limiting factor. To determine the appropriate breeding strategy to improve nitrogen use efficiency (NUE), the genetic variability and the level of G × N interaction of NUE need to be evaluated. NUE and its components are complex quantitative traits and the study of their relationship with other simpler traits should help understand the mechanisms involved in NUE and identify ways to improve it. A study was conducted at mid-altitude in Madagascar using 13 adapted tropical japonica rice varieties over three cropping seasons with two contrasted levels of applied N (high N with 90–120 kg N ha−1 as urea and low N without mineral fertilizer) in rainfed upland conditions. Year × N and Year × G interactions were significant due to contrasted rainfall distributions across the three cropping seasons. Agronomic efficiencies of N fertilization were low (11.5 kg grain kg−1 N in the best year) because of N loss through leaching or volatilization. Our results also suggest gaseous loss of N by plants between flowering and harvest, particularly under the high N treatment. The experiment revealed significant genetic variability for NUE, nitrogen uptake efficiency (NUPE) and nitrogen utilization efficiency (NUTE) in both high N and low N treatments but a low level of G × N interaction. The variation in NUPE accounted for more of the variation in NUE than the variation in NUTE. There was no correlation between NUPE and NUTE, either under high N or under low N. We found no negative relationship between grain yield and grain N concentration under low N. The relationship between NUE and agronomic and N-related traits differed from one year to the next, illustrating the plasticity of the contribution of the different agronomic traits to NUE as a function of the contrasted climatic conditions (particularly the rainfall distribution pattern). However, two traits, the number of panicles per m2 and the harvest index were consistently positively correlated with NUE. The difference between total N uptake at flowering and at harvest was positively correlated with NUE, particularly under the low N treatment.

Published
2017
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22. Monitoring Nitrogen Leaf Resorption Kinetics by Near-Infrared Spectroscopy during Grain Filling in Durum Wheat in Different Nitrogen Availability Conditions

Author

Pierre Roumet, Martin Ecarnot, Nicolas Verzelen, Ingrid Vilmus, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 2. Zero hunger, Triticum spp, Kinetics, food and beverages, chemistry.chemical_element, Biology, Grain filling, Photosynthesis, Nitrogen, Resorption, protéine végétale, Horticulture, Human fertilization, chemistry, Agronomy, Yield (chemistry), [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Grain yield, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Agronomy and Crop Science
Abstract

In wheat (Triticum spp.), the N content of leaves during the grain filling period (GFP) plays a key role in maintaining photosynthetic activity and determining the amount of N available for grain protein content (GPC). We documented flag N leaf resorption in durum wheat (Triticum turgidum L.) plants under a nonlimiting level of N in 2010 and under two different levels of N fertilization in 2011. During the GFP, we monitored changes in flag leaf N content by a nondestructive method based on near-infrared spectroscopy. The datasets were modeled for each plant; parameters were extracted and analyzed to determine which source of variation (genotype and/or N availability) predominated. Different genotypic profiles were highlighted opposing Ixos versus Primadur when comparing two different levels of N availability, with Ixos flag leaves being the most affected by a low level of N preanthesis. High postanthesis N availability delayed the beginning of N resorption (t0) and there was a strong negative correlation between t0 and the resorption duration. Delayed N resorption was associated with better grain yield components. A high proportion of the variation of grain yield per spike and GPC was explained by multiple linear regressions combining the width of the flag leaf and N dynamic parameters under the nonlimiting N availability. The negative correlation between yield and GPC may result from the initiation of N resorption during grain filling, potentially increasing yield if delayed or increasing GPC if occurring early.

Published
2014
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23. Predicting wheat maturity and stay–green parameters by modeling spectral reflectance measurements and their contribution to grain yield under rainfed conditions

Author

Emel Özer, Pierre Roumet, Germain Montazeaud, Martin Ecarnot, José Crossa, Marta S. Lopes, Ibrahim Ozturk, Handan Karatoğma, Fatih Özdemir, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Adanson fellowship - French Agropolis Fondation, CGIAR Research Program (CRP) WHEAT, European Union, and Benefit-sharing Fund of the ITPGRFA

Subjects
0106 biological sciences, 0301 basic medicine, Senescence, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Population, Soil Science, drought, Grain filling, Biology, 01 natural sciences, Normalized Difference Vegetation Index, 03 medical and health sciences, stay-green, Low rainfall, Botany, education, 2. Zero hunger, Abiotic component, Maturity (geology), education.field_of_study, prediction, Reflectivity, 030104 developmental biology, climate change, Agronomy, Grain yield, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

AGAP : équipe GE2pop; International audience; The normalized difference vegetation index (NDVI) continues to provide easy and fast methodologiesto characterize wheat genetic resources in response to abiotic stresses. This study identifies ways tomaximize green leaf area duration during grain filling and develops NDVI models to predict physio-logical maturity and different stay −green parameters to increase grain yield of rainfed winter wheatunder terminal drought. Three wheat populations were evaluated: one containing 240 landraces fromAfghanistan, the second with 250 modern lines and varieties, tested for two years under low rainfall con-ditions in Turkey, and the third with 291 landraces from Central and Western Asia (grown for one yearin the same location). The onset of senescence, maximum “greenness”, rate of senescence and residual“greenness” at physiological maturity were estimated using sequential measurements of NDVI and haveshown significant correlations with grain yield under low rainfall rainfed conditions. Trade-offs wereidentified among the different stay −green attributes, e.g. delayed onset of senescence and high maxi-mum “greenness” resulted in accelerated rates of senescence and highest yields and were most evidentin the landrace populations. It is concluded, that the use of rate of senescence to select for stay −greenmust be coupled with other stay −green components, e.g. onset of senescence or maximum “greenness”to avoid the effects of the trade-offs on final grain yield. The NDVI decay curves (using the last three NDVImeasurements up to maturity) were used to estimate days to maturity using the NDVI decay during thesenescence period and days to heading. A training and testing set (20 and 80% of each population, respec-tively) were used for calibrations allowing for correlations between predicted and observed maturity ofup to r = +0.85 (P < 0.0001). This procedure will facilitate large −scale wheat phenotyping in the future.

Published
2016
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24. Genetic Diversity in a Soybean Collection

Author

M. Tavaud-Pirra, P. Sartre, Sylvain Santoni, Pierre Roumet, Randall L. Nelson, N. Texier, Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), United States Department of Agriculture (USDA), and Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
2. Zero hunger, 0106 biological sciences, Germplasm, 0303 health sciences, Genetic diversity, [SDV]Life Sciences [q-bio], food and beverages, Biology, 01 natural sciences, 03 medical and health sciences, Population bottleneck, Evolutionary biology, Botany, Genetic structure, Genotype, Microsatellite, Allele, Domestication, human activities, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany
Abstract

Contact: Muriel.Tavaud@supagro.inra.fr; International audience; Soybean [Glycine max (L.) Merr.] was domesticated in China, and cultivated landraces were initially distributed throughout Asia and more recently extended to Europe and America. Previous studies of genetic diversity suggest a strong genetic bottleneck between Asian and North American soybean genetic pools. However, little is known about the potentially useful genetic diversity present in European soybean germplasm. We evaluated genetic diversity by phenotypic characterization and by comparing nuclear and cytoplasmic microsatellites in 301 genotypes of an INRA soybean collection with those of 31 European breeding lines and 17 ancestors from American cultivars (representing 83% of the North America diversity). We showed that the INRA collection contains 14 and 8% more diversity than the European breeding lines and American ancestors, respectively, based on Nei diversity (He). The genetic structure of this INRA collection does not correlate with either geographic origin or phenotypic differentiation. We generated a core collection composed of 50 accessions from the INRA collection and European breeding lines. This core collection contains 203 of the 226 microsatellite marker alleles available for this germplasm and is also representative of the diversity of morphological traits in temperate regions (maturity 000 to 111), which will be useful for future breeding programs

Published
2009
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25. Detection of Fusarium head blight contamination in wheat kernels by multivariate imaging

Author

Laetitia Pinson-Gadais, Dominique Bertrand, Pierre Roumet, Benoit Jaillais, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Unité de recherche Mycologie et Sécurité des Aliments (MSA), Data Frame, French National Research Agency [ANR], ANR-08-ALIA-013, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Groupe Français de Chimiométrie (GFC). Paris, FRA., and ANR-08-ALIA-0013,NOMAC,Nouvelles ressources pour maîtriser le devenir digestif des nutriments des produits céréaliers(2008)

Subjects
0106 biological sciences, Fusarium, Veterinary medicine, Multivariate statistics, genetic structures, [SDV]Life Sciences [q-bio], Multispectral image, 01 natural sciences, Chemometrics, Fusarium culmorum, multispectral imaging, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, fusarium, 2. Zero hunger, biology, 010401 analytical chemistry, food and beverages, durum wheat, Contamination, biology.organism_classification, chemometrics, 0104 chemical sciences, Agronomy, Principal component analysis, Kernel (category theory), 010606 plant biology & botany, Food Science, Biotechnology
Abstract

AGAP : équipe GE²pop; The objective of this study was to evaluate the safety quality of wheat kernels and more specifically the infection of wheat by Fusarium culmorum. We have developed a new non-destructive methodology based on multispectral imaging and chemometrics to detect wheat contamination. This method has been applied to evaluate the tolerance to Fusarium Head Blight (FHB) on six accessions of durum wheat. Two of the accessions are parental lines, one susceptible and one resistant to Fusarium, and the other four are their offspring lines. Multispectral images of dorsal and ventral sides of all kernels were acquired with an in-house imaging system and processed with chemometrical tools, including principal component analysis (PCA) and multiple linear regression (MLR). According to the quantitative PCR (qPCR) results, PCA was able to detect infested kernels and to identify affected areas with kernels. Moreover, regression analysis of the images allowed the degree of contamination for each pixel to be estimated, and thus mapping of contamination for each kernel. (C) 2015 Elsevier Ltd. All rights reserved.

Published
2015
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26. Direct Estimation of Mutation Rate for 10 Microsatellite Loci in Durum Wheat, Triticum turgidum (L.) Thell. ssp durum desf

Author

David Bru, Sylvain Santoni, Thomas Bataillon, Anne-Céline Thuillet, Jacques David, Pierre Roumet, Pierre Sourdille, UMR 1097 UMR INRA / ENSAM / IRD : Diversité et Génome des Plantes Cultivées, Institut National de la Recherche Agronomique (INRA)-Génétique et amélioration des plantes (G.A.P.)-UMR INRA / ENSAM / IRD : Diversité et Génome des Plantes Cultivées (DGPC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and ProdInra, Archive Ouverte

Subjects
0106 biological sciences, Mutation rate, Time Factors, Biology, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, GENETIQUE VEGETALE, Molecular Biology, Alleles, Triticum, Ecology, Evolution, Behavior and Systematics, Triticum turgidum, 030304 developmental biology, Likelihood Functions, 0303 health sciences, Models, Genetic, Genetic Variation, Agronomy, Mutagenesis, Microsatellite, Microsatellite Repeats
Abstract

absent

Published
2002
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27. Anchoring durum wheat diversity in the reality of traditional agricultural systems: varieties, seed management, and farmers’ perception in two Moroccan regions

Author

Marie-Hélène Muller, Ali Sahri, Mustapha Arbaoui, Pierre Roumet, Lamyae Chentoufi, Ahmed Birouk, Loubna Belqadi, Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II - IAV (MOROCCO) (IAV), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Muller, Marie-Helene, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, In situ conservation, Health (social science), réseau d'échanges informels, Biodiversity, Triticum turgidum, 01 natural sciences, montagne de l'atlas, céréale, maroc, Traditional agriculture, agrosystème traditionnel, agriculture de subsistance, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Triticum, media_common, 2. Zero hunger, 0303 health sciences, Food security, Vegetal Biology, Agricultural and Biological Sciences(all), Agroforestry, Biologie du développement, Agriculture, système agricole traditionnel, Development Biology, Agricultural sciences, Varietal diversity, Morocco, Geography, Seeds, General Agricultural and Biological Sciences, Cultural Studies, Crops, Agricultural, modernisation agricole, diversification agricole, media_common.quotation_subject, Modernization theory, Health(social science), 03 medical and health sciences, Interviews, Perception, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecosystem, 030304 developmental biology, business.industry, Research, Subsistence agriculture, 15. Life on land, pays méditerranéen, Farmers’ knowledge, Complementary and alternative medicine, Agronomy, Crop diversity, blé dur, gestion des semences, business, Sciences agricoles, Biologie végétale, 010606 plant biology & botany
Abstract

Background: Traditional agrosystems are the places were crop species have evolved and continue to evolve under a combination of human and environmental pressures. A better knowledge of the mechanisms underlying the dynamics of crop diversity in these agrosystems is crucial to sustain food security and farmers’ self-reliance. It requires as a first step, anchoring a description of the available diversity in its geographical, environmental, cultural and socio-economic context. [br/] Methods: We conducted interviews with farmers cultivating durum wheat in two contrasted traditional agrosystems of Morocco in the Pre-Rif (163 farmers) and in the oases of the Atlas Mountains (110 farmers). We documented the varietal diversity of durum wheat, the main characteristics of the farms, the farming and seed management practices applied to durum wheat, and the farmers’ perception of their varieties. [br/] Results: As expected in traditional agrosystems, farmers largely practiced diversified subsistence agriculture on small plots and relied on on-farm seed production or informal seed exchange networks. Heterogeneity nevertheless prevailed on many variables, especially on the modernization of practices in the Pre-Rif region. Fourteen (resp. 11) traditional and 5 (resp. 3) modern varieties were identified in the Pre-Rif region (resp. in the Atlas Mountains). The majority of farmers grew a single variety, and most traditional varieties were distributed in restricted geographical areas. At the farm level, more than half of the varieties were renewed in the last decade in the Pre-Rif, a more rapid renewal than in the Atlas Mountain. Modern varieties were more prevalent in the Pre-Rif region and were integrated in the traditional practices of seed production, selection and exchange. They were clearly distinguished by the farmers from the landraces, the last ones being appreciated for their quality traits. [br/] Conclusions: The surveyed traditional agrosystems constitute open, dynamic and heterogeneous entities. We suggest that competing factors could favour or limit the cultivation of improved varieties and the erosion of original durum wheat diversity. This first description opens the way to focused further investigations, including complementing variety names with cultural, genetic and phenotypic information and unravelling the multidimensional factors and consequences of modern variety adoption.

Published
2014
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28. Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history

Author

Morgane Ardisson, Pierre Roumet, Lamyae Chentoufi, Ali Sahri, Marie-Hélène Muller, Ahmed Birouk, Loubna Belqadi, Mustapha Arbaoui, Muller, Marie-Helene, Département de Production, Protection et Biotechnologies Végétales, Institut Agronomique et Vétérinaire Hassan II - IAV (MOROCCO) (IAV), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Light, Traditional agrosystems, Flowers, Biology, Breeding, Genetic diversity, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Evolutionary dynamics, Variety names, Triticum, Durum wheat, Ecology, Evolution, Behavior and Systematics, Local adaptation, 2. Zero hunger, Food security, Vegetal Biology, business.industry, Genetic Variation, food and beverages, Agriculture, Landraces, 15. Life on land, Agricultural sciences, Tetraploidy, Morocco, Phenotype, Agronomy, Crop diversity, Seeds, business, Sciences agricoles, Biologie végétale, Research Article, Microsatellite Repeats
Abstract

Background Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers’ varietal taxonomy and practices and the historical background of the crop. Results On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns. Conclusions This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0264-2) contains supplementary material, which is available to authorized users.

Published
2014
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29. Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population

Author

Yan Holtz, Gautier Sarah, Frédéric Choulet, Morgane Ardisson, Clémence Genthon, Jacques David, Muriel Tavaud-Pirra, Pierre Roumet, Sylvain Santoni, Gérard Poux, Vincent Ranwez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), flagship project Agropolis Resource Center for Crop Conservation, Adaptation and Diversity (ARCAD) - Agropolis Fondation 0900-001, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, dispensable, Population, SNP, Plant Science, Biology, 01 natural sciences, DNA sequencing, diversity, 03 medical and health sciences, Genetics, genotyping by sequencing, repeatability, education, Molecular Biology, Genotyping, 030304 developmental biology, Genetic association, Synteny, 2. Zero hunger, 0303 health sciences, Genetic diversity, education.field_of_study, food and beverages, durum wheat, Marker-assisted selection, RNAseq, SNP genotyping, Agronomy and Crop Science, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 010606 plant biology & botany, Biotechnology
Abstract

The genetic diversity in durum wheat, Triticum turgidum durum, has been strongly reduced since the domestication of the wild Triticum turgidum dicoccoides. Monitoring durum wheat composite crosses incorporating related tetraploid taxa, such as wild and domesticated emmer wheat, is a suitable evolutionary pre-breeding method. Transcriptome sequencing paves the way for a genomic survey of single nucleotide polymorphisms (SNPs) segregating in such populations, offering the possibility of genotyping by sequencing to use these resources in genome-wide association studies (GWAS) and genomic selection (GS) programs. Evolutionary Pre-breeding pOpulation (EPO) is an evolutionary durum wheat pre-breeding population. Sequencing the transcriptome of 179 durum wheat lines (175 from EPO) led to the detection of 103,262 SNPs on two reference transcriptomes: one from the International Wheat Genome Sequencing Consortium and one assembled de novo on durum wheat. Using strict filtering to remove dubious heterozygous SNPs, EPO genetic diversity was eventually described with 76,188 high-confidence SNPs. The percentage of missing genotyping data depended on the expression level, and 88 individuals out of 175 were genotyped per SNP on average. Using the 3B pseudo-molecule of bread wheat, the transcription and diversity levels were shown to be higher in distal regions than in proximal regions, but SNPs were available throughout the chromosomes. Assuming good synteny with Hordeum, the trend was similar on the 14 chromosomes of the durum wheat genome. EPO hosts a high level of diversity, has a number of SNPs in low linkage disequilibrium (< 40 Mb) and would be well suited for GWAS and GS programs.

Published
2014
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30. Germination of Immature Soybean Seeds to Shorten Reproductive Cycle Duration

Author

Pierre Roumet and Frédérique Morin

Subjects
animal structures, Sucrose, Immature soybean, food and beverages, Embryo, Embryo culture, Biology, Reproductive cycle, Horticulture, chemistry.chemical_compound, Point of delivery, chemistry, Germination, embryonic structures, Botany, Composition (visual arts), Agronomy and Crop Science
Abstract

The soybean [Glycine max (L.) Merrill] reproductive cycle represents more than 50% of the length of the total growth cycle. Immature embryo culture could be used to shorten this cycle. This study was conducted to develop an efficient technique to shorten the soybean reproductive cycle and to make it possible to develop recombinant lines from populations more rapidly. The importance of a pod pretreatment before embryo extraction, the effects of embryo age on germination rate, embryo position in the pod, and the composition of the germination medium (supplemented with sucrose or not) were analyzed to define an optimal technique. Plant recovery rate and genotype effects on germination were evaluated with 22 genotypes representing a broad genetic background. It was necessary to pretreat immature seed by exposing pods to 26°C for 4 d to induce germination. Best results (up to 100% germination) were obtained from embryos sampled at the end of lag phase of seed development (approximately 18 d after flowering). For three-seeded pods, the central embryos generally had a higher germination rate than distal and proximal embryos (25 and 44 percentage points, respectively). Whatever the embryo position in the pod, adding sucrose significantly increased the germination of embryos sampled 14 to 18 d after flowering. Plantlets were obtained from 73% of the germinated embryos and the length of cycle was reduced from 130 to 140 d to 65 to 70 d. Average germination of the 22 genotypes was 80%; thus, this technique, paired with the single seed descent method, provides soybean breeders with a tool to develop lines quickly.

Published
1997
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31. Assessing leaf nitrogen content and leaf mass per unit area of wheat in the field throughout plant cycle with a portable spectrometer

Author

Frédéric Compan, Pierre Roumet, Martin Ecarnot, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Correlation coefficient, near-infrared spectroscopy, Leaf mass, Soil Science, chemistry.chemical_element, Biology, 01 natural sciences, leaf nitrogen content, wheat, Partial least squares regression, Calibration, Dry matter, Spectrometer, 04 agricultural and veterinary sciences, Nitrogen, Horticulture, Agronomy, chemistry, non-destructive-non invasive tool, Content (measure theory), 040103 agronomy & agriculture, leaf mass per unit area, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Leaf nitrogen content (LNC) and leaf mass per unit area (LMA) were assessed by near-infrared spectroscopy (NIRS) on fresh and dried plants of durum wheat (Triticum turgidum ssp). Individual leaves were scanned with a portable spectrometer and reference analyses of LNC and LMA were then carried out. Partial least squares (PLS) regression was used for calibration and cross-validation. INC was accurately predicted for both fresh and dry leaves whatever the phenologic stage (correlation coefficient of calibration R(2)cal ranging from 0.932 to 0.958, standard error of cross-validation SECV ranging from 0.215 to 0.320% (dry matter)). LMA was predicted with R(2)cal = 0.942 and SECV = 4.84g m(-2). The combination of these two calibrations made it possible to predict leaf nitrogen per unit area (R(2)cross-validation = 0.94, SECV = 0.248 gN m(-2)) and provides a relevant and non-destructive tool for following the dynamics of three major leaf parameters.

Published
2013
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33. Elite durum wheat genetic map and recombination rate variation in a multiparental connected design

Author

Christiane Borries, Morgane Ardisson, Jacques David, Pierre Roumet, Sylvain Santoni, Laurence Vaissayre, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Population, Recombination rate, Plant Science, Horticulture, Biology, CARTOGRAPHIE GENETIQUE, 01 natural sciences, Genome, Diallel cross, 03 medical and health sciences, half diallel design, Genetics, genetic linkage map, education, Triticum turgidum, 030304 developmental biology, 2. Zero hunger, Linkage (software), 0303 health sciences, education.field_of_study, durum wheat, variation des taux de recombinaison, Variation (linguistics), Inbred population, Agronomy and Crop Science, 010606 plant biology & botany, variation of recombination rate
Abstract

UMR 1334 AGAP : Equipe AFEF ‘Architecture et Fonctionnement des Espèces fruitières’ ; Team AFFS ‘Architecture and Functioning of Fruit Species’ Contact : Pierre.Roumet@supagro.inra.fr; Genetic maps published for elite durum wheat (Triticum turgidum durum Desf.), were mainly related to Italian and North American pools. To provide additional information dedicated to durum elite pool, a recombinant inbred population (217 RILs) derived form 2 French commercial varieties (Ixos and Primadur), has been mapped with 529 loci (98 AFLPs, 67 SSRs, 1 ISBP and 363 DArTs). Genetic map spanned a total of 2,082 cM (5.7 cM/marker on average). Recombination rate variation over the genome was documented through the analysis of six segregating populations representing a total of 48 RILs x 6, issued from an half diallel design based on four elite lines-Neodur, Ixos, Lloyd and Primadur-including the 2 previous genitors. Each set of three genetically connected populations (48 RILs x 3) was used to build the consensus parental maps for each genitor. To construct the four consensus parental maps, marker ordering was determined on 217 RILs map which was an extended population of the most polymorphic cross (Ixos x Primadur). Sizeable, recombination rate variation has been observed between the four parental maps both at the marker pair scale and at the linkage group scale. Two of the parents, Lloyd and Primadur, had strong, opposite effects increasing and decreasing, respectively the recombination rate. Additional studies are proposed to increase our understanding of this variation, with the identification of environmental or genetic factors affecting recombination rate.

Published
2012
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34. Potential of field hyperspectral imaging as a non destructive method to assess leaf nitrogen content in Wheat

Author

Gilles Rabatel, Nathalie Vigneau, Pierre Roumet, Martin Ecarnot, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Q@limediterannee competitive cluster, Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Domaine expérimental de Melgueil (MONTP MELGUEIL UE), and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Soil Science, Mineralogy, chemistry.chemical_element, 01 natural sciences, HYPERSPECTRAL, Non destructive, ANALYSE SPECTRALE, NITROGEN CONCENTRATION, 2. Zero hunger, Physics, [SDE.IE]Environmental Sciences/Environmental Engineering, Hyperspectral imaging, Forestry, 04 agricultural and veterinary sciences, Nitrogen, CHIMIOMETRIE, REFLECTOMETRIE, REFLECTANCE, chemistry, TENEUR EN AZOTE, CONCENTRATION D'AZOTE, BLE, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, DURUM WHEAT, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Contact: Pierre.Roumet@supagro.inra.fr; L'azote est le facteur le plus limitant de la croissance des plantes, aussi sa mesure durant le cycle est un élément clé du contrôle des cultures. De nombreuses techniques de mesure non destructives basées sur les propriétés optiques de feuilles ont été proposées pour remplacer la méthode classique coûteuse et destructive de l'indice de nutrition azotée (NNI). Notre objectif est ici d'étudier la possibilité d'accéder à la teneur en azote des feuilles à partir du spectre de réflectance 400-1000nm de plantes entières, mesuré par une caméra hyperspectrale, et en prenant en compte les difficultés inhérentes à un éclairage naturel variable et à l'éventualité de réflexions spéculaires. Dans un premier temps, nous avons étalonné un modèle chimiométrique entre la teneur en azote et le spectre de réflectance de feuilles disposées à plat (R² = 0.903, SEP = 0.327 %DM), qui valide le capteur et notre procédé de correction en réflectance. Nous avons ensuite étalonné un modèle entre la teneur en azote et le spectre de feuilles en place pour des cultures sous serre (R² = 0.889, SEP = 0.481% DM) ou au champ (R² = 0.881, SEP = 0.366 %DM). La réunion des deux jeux de données nous permet d'obtenir également un modèle pertinent pour les deux types de conditions de cultures à la fois (R² = 0.875, SEP = 0.496 %DM), suggérant que cette technique est prometteuse pour la mesure non destructive de teneur en azote. Cet outil pourra être utilisé pour le suivi dynamique du statut azoté ou pour générer des cartographies spatiales de la teneur en azote dans la plante. / Nitrogen is the most important crop limiting factor, thus plant nitrogen status during plant cycle is a key parameter for crop monitoring. Many new techniques, based on leaf optical properties have been proposed for a non-destructive diagnosis to replace Nitrogen Nutrition Index which is a costly and destructive method. We intend here to study leaf nitrogen concentration accessibility from reflectance (4001000 nm) spectra of whole plants from a field hyperspectral imaging set-up including difficulties related to variable solar lighting and potential specular reflexion. Firstly, we calibrated a chemometrical model between leaf nitrogen concentration and reflectance spectra of flat leaves (R2 = 0.903, SEP = 0.327%DM), which validated the sensor and our reflectance correction process. As a second step, we calibrated a chemometrical model between nitrogen concentration and reflectance spectra of individual leaves from isolated plants grown in pots in greenhouse (R2 = 0.889, SEP = 0.481%DM) or underfield conditions (R2 = 0.881, SEP = 0.366%DM). Pooling the two datasets provided us a relevant model to predict leaf nitrogen content for the two culture conditions (R2 = 0.875, SEP = 0.496% DM) suggesting that this technique is promising to assess nitrogen plant parameters with a non destructive method. This tool could be used to follow-up plant nitrogen dynamics criteria or to generate nitrogen spatial cartographies.

Published
2011
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35. Calibration of a chemometrical model from field hyperspectral close-range images: Taking into account leaf inclination and multiple reflection effects

Author

Martin Ecarnot, Gilles Rabatel, Pierre Roumet, Nathalie Vigneau, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Equipe Rhizogenèse (RHIZOGéNèSE- UMR DIA-PC), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), and Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
010504 meteorology & atmospheric sciences, Field (physics), [SDE.IE]Environmental Sciences/Environmental Engineering, 0211 other engineering and technologies, Hyperspectral imaging, 02 engineering and technology, 01 natural sciences, Signal, Quality (physics), Content (measure theory), [SDE]Environmental Sciences, Calibration, Reflection (physics), Specular reflection, 021101 geological & geomatics engineering, 0105 earth and related environmental sciences, Mathematics, Remote sensing
Abstract

International audience; The aim of the study was to test the potentiality of field close-range hyperspectral images to obtain nitrogen content of wheat leaves in field. Field measurements imply several potential disturbances of the recorded signal: illumination level, specular reflection, multiple reflections, etc. Chemo-metrical model calibration procedure has to take them into account. We tested the following methodology. First we calibrated a chemometrical model between nitrogen content and non-disturbed reflectance signal of flat isolated leaves. Thus we evaluated the quality of such a model. Then, we identified and qualified each phenomenon effects and proposed a solution to overcome each issue. Finally, we verified that all the disturbances could be taken into account while preserving satisfactory model prediction quality.; Le but de l'étude était de tester le potentiel de l'imagerie hyperspectrale de proximité au champ pour évaluer la teneur en azote des feuilles de blé. La mesure au champ génère des perturbations importantes dans le signal mesuré: niveau d'éclairement, réflexions spéculaires, réflexions multiples, etc. L'étalonnage chimiométrique doit les prendre en compte. Nous avons testé la méthodologie suivante: tout d'abord nous avons étalonné un modèle entre la teneur en azote et le signal de réflectance non perturbé de feuilles à plat et isolées. Puis nous avons identifié et formalisé les divers phénomènes perturbants et avons proposé une solution pour s'en affranchir. Finalement, nous avons vérifié que toutes les perturbations pouvaient être prises en compte en préservant une qualité suffisante du modèle de prédiction.

Published
2010
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36. Environment characterisation for the interpretation of environmental effect and genotype environment interaction

Author

Xavier Lacaze, Pierre Roumet, Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Crops, Agricultural, multiplicative model, Kernel Number, Genotype, Nitrogen, Climate, Biology, Environment, grain Protein content, 01 natural sciences, Models, Biological, Statistics, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Computer Simulation, Gene–environment interaction, Triticum, Plant Proteins, water deficit, 2. Zero hunger, Agricultural chemistry, Analysis of Variance, business.industry, Explained sum of squares, Water, durum wheat, Agriculture, 04 agricultural and veterinary sciences, General Medicine, Regression, Biotechnology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Main effect, Crop simulation model, business, Agronomy and Crop Science, Cropping, 010606 plant biology & botany
Abstract

International audience; Increasing attention is being paid to environment characterisation as a means of identifying the environmental factors determining grain protein content (GPC) in durum wheat. New insights in crop physiology and agronomy have led to the development of crop simulation models. Those models can reconstruct plant development for past cropping seasons. One major advantage of these models is that they can also indicate the intensity of limiting factors affecting plants during particular developmental stages. The main environmental factors determining GPC in durum wheat can be investigated by introducing the intensity of limiting factors into genotype × environment (G×E) models. In our case, limiting factors corresponding to water deficit and nitrogen availability were calculated for the development period between booting and heading. These variables were then introduced into a clustering model. This model is an extension of factorial regression applied to discrete environment and genotypic variables. This procedure effectively described the environment main effect: around 30.9% of the sum of squares of the environment main effect was accounted for, using less than 33% of the degrees of freedom. It also partially accounted for G×E interaction. Our methodology, coupling the use of crop simulation and G×E analysis models, is of potential value for improving our understanding of the main development stages and identification of environmental limiting factors for the development of GPC.

Published
2004
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37. Identification of soybean plant characteristics that indicate the timing of drought stress

Author

Dominique Desclaux, Tung-Thanh Huynh, Pierre Roumet, ProdInra, Migration, Unité de recherches de génétique et amélioration des plantes, and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Greenhouse, Biology, 01 natural sciences, LEGUMINEUSE A GRAINS, Crop, CROISSANCE VEGETATIVE, Botany, Cultivar, Gene–environment interaction, ComputingMilieux_MISCELLANEOUS, Plant stem, 2. Zero hunger, fungi, food and beverages, Edaphic, 04 agricultural and veterinary sciences, 15. Life on land, [SDV] Life Sciences [q-bio], Point of delivery, Agronomy, Plant morphology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

large scale and conducted at locations where these tools may not be available. Moreover, it is often difficult to Low-cost, phenotype-based techniques are needed to help crop find, among the great number of collected data, the breeders interpret genotype 3 environment interactions. Our objecperiod when water was limiting and if a water deficit tive was to determine how drought stress imposed on soybean [Glycine max (L.) Merr.] at various growth stages affected selected plant occurred, to deduce if it had an impact on crop developcharacteristics. Determinate (Spot) and indeterminate (Weber) soy- ment. To avoid these problems and help to focus the bean cultivars were grown under greenhouse conditions and subjected research among all climatic and edaphic data, Meynard to two levels of drought stress (30 and 50% plant-available water) and David (1992) proposed for wheat (Triticum aestiduring vegetative (V4‐R1), flowering (R1‐R3), pod lengthening (R3‐ vum L.) an environmental diagnosis based on cultivar R5), or seed-filling (R5) stages. Mean internode length was the most observations. Yield components are determined at spedrought sensitive factor during the vegetative and flowering stages. cific growth stages and each is subject to the enviSignificant height differences for the determinate cultivar accurately ronmental conditions that prevail during this period. differentiated between stress periods, with shorter plants being associAnalysis of each component value could thus provide ated with vegetative stress. The number of pods per vegetative dry a post-harvest assessment of when environmental stress matter unit was significantly affected by stress during pod lengthening. Early stress during seed fill reduced the number of seeds per pod, occurred and how severe it was. The main interest of whereas late stress (after the abortion limit stage) decreased seed the method is to avoid wide ranging research on limiting weight. These results suggest that precise periods of drought stress factors from a common climatic database by focusing can be determined by measuring a posteriori several morphological on specific periods, and to provide complementary obfactors and yield components of determinate and indeterminate soy- servations. Indeed, when describing an environment, bean genotypes at physiological maturity. the important point is to know whether plants have suffered from a water deficit rather than simply that this deficit occurred.

Published
2000

38. Impact of drought stress on the phenology of two soybean (Glycine max L. Merr) cultivars

Author

Pierre Roumet, Dominique Desclaux, Station d'amélioration des plantes, and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Senescence, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Drought stress, Phenology, Ontogeny, fungi, food and beverages, Soil Science, 04 agricultural and veterinary sciences, Biology, 01 natural sciences, Point of delivery, Agronomy, Glycine, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Cultivar, Agronomy and Crop Science, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany, Main stem
Abstract

Drought stresses modify the phenology of plants, and thus affect the yield components. The impact of various periods of water stress on the organ appearance rate and on the durations of the main vegetative and reproductive periods was studied under greenhouse conditions on soybean cultivars differing by type of growth. The two cultivars, Weber and Spot, maturity group I, indeterminate and determinate respectively, were subjected to drought stress (30% PAW) during a main developmental stage: i.e., vegetative, flowering, pod lengthening or seed filling. Drought stress seemed to trigger a signal that caused an early switch of plant development from vegetative to reproductive. Appearance of nodes initiated during stress was delayed, resulting in a small number of nodes produced, whereas flower and pod appearance were hastened. Each reproductive phase was shorter under stress, mainly because of the appearance of new organs that prevented the emergence of organs belonging to the earlier ontogenetic phases. The seed-filling stage and the final stage in seed abortion began earlier in stressed plants and the duration of the maturation period was significantly reduced by stress during seed filling, leading to accelerated senescence. The cultivars differed mostly with respect to their strategies of partitioning between the main stem and branches. Under stress, the duration of the main reproductive phase was increased on the main stem but reduced on the branches in cultivar Weber, whereas the opposite response was noted in cultivar Spot.

Published
1996

39. Une histoire des blés durs en France : des origines néolithiques à nos jours

Author

Laurent Bouby, Michel Chauvet, Pierre Roumet, Ruas Marie-Pierre, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, parc scientifique agropolis, Pl@ntUse, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Abecassis Joël, Massé Jack, Allaoua Kamel, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Ruas, Marie-Pierre, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV]Life Sciences [q-bio], [SDE.MCG]Environmental Sciences/Global Changes, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, [SDV.SA.STA] Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, sources écrites, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, génétique, [SHS]Humanities and Social Sciences, [SDV.SA.HORT] Life Sciences [q-bio]/Agricultural sciences/Horticulture, domestication, [SHS.ENVIR] Humanities and Social Sciences/Environmental studies, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, carpologie, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, archéobotanique, ComputingMilieux_MISCELLANEOUS, [SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy, [SHS.ANTHRO-SE] Humanities and Social Sciences/Social Anthropology and ethnology, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, céréales, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, [SDE.ES]Environmental Sciences/Environmental and Society, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, [SHS.HIST] Humanities and Social Sciences/History, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SDE.ES] Environmental Sciences/Environmental and Society, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SHS.HIST]Humanities and Social Sciences/History, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience

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