ECO2MALT - Evaluation et amélioration de la qualité brassicole de l'orge d'hiver pour la sélection de variétés adaptées aux systèmes de cultures à bas niveaux d'intrants

France is one of Europe's leading producers of malting barley and the world's leading exporter of malt. The inputs used on this crop contribute to greenhouse gas emissions from the agricultural sector and can indirectly lead to negative effects on consumer health. Currently, the production of malting barley withreduced use of chemical inputs is limited by the lack of suitable varieties and technical management practices to maintain production volumes and quality. The cost and time required to carry out grain quality analyses (micromalting) make the identification of varieties adapted to non-conventional technical itineraries difficult. The objectives of the work carried out in the CasDAR Eco2Malt project were to designand evaluate varietal ideotypes and technical management practices adapted to low-input malting barley production, and to propose rapid methods for estimating the malting quality of 6-row winter barley in order to speed up varietal selection. Through experimentation, we showed that current varieties grown in management with reduced nitrogen inputs (-30% - inputs at the usual dates) and without pesticides do not systematically achieve the protein content and calibrated yield required for malting barley. Through simulation, we showed that it is essential to delay fertilizer application when the doses are reduced to achieve high agronomic performance. We have also identified the varietal characteristics adapted to this technical management practices. Adapting both the genotypes and the nitrogen fertilisation strategy ensures the low-input technical management to achieve agronomic performance similar to that of nitrogen-intensive management, and to improve environmental performance. Some of the best performingideotypes at low input levels also achieve high performance at high input levels. In order to limit these costs of analysing the brewing potential of varieties during selection, a selection index has been developed and evaluated, making it possible to prioritise the characteristics of grains and/or wort to achieve brewing quality. The interest of models predicting the brewing potential of a line based on rapid grain analyses was tested. These results are intended to enable more lines to be characterised rapidly and thus facilitate the development of lines adapted to different contexts, including low inputs management practices.La France est l’un des premiers producteurs européens d’orge brassicole et le premier exportateur mondial de malt. Les intrants utilisés sur cette culture participent aux émissions de gaz à effet de serre du secteur agricole et peuvent indirectement entrainer des effets négatifs sur la santé desconsommateurs. Actuellement, la production d’orge brassicole avec un moindre recours aux intrants chimiques est limitée par le manque de variétés et d’itinéraires techniques adaptés permettant de maintenir les volumes et la qualité de la production. Le coût et le temps nécessaires pour réaliser les analyses de qualité des grains (micromaltages) rendent l’identification des variétés adaptées aux itinéraires techniques non-conventionnels délicate. Le travail réalisé dans le projet CasDAR Eco2Malt avait pour objectifs de concevoir et d’évaluer des idéotypes variétaux et des itinéraires techniques adaptés à une production d’orge brassicole en bas niveaux d’intrants, et de proposer des méthodes rapides d’estimation de la qualité brassicole des orges d’hiver 6 rangs pour accélérer la sélection variétale. A travers l’expérimentation, nous montrons que les variétés actuelles cultivées dans un itinéraire technique avec des apports d’azote réduits (-30% -apports aux dates habituelles) et sans pesticide nepermettent pas systématiquement d’atteindre les teneurs en protéines et le rendement calibré demandés pour les orges de brasserie. Par simulation, nous montrons qu’il est indispensable de retarder les apports d’engrais, lorsque les doses sont réduites pour atteindre des performances agronomiques élevées. Nous avons identifié les caractéristiques variétales adaptées à ce mode de conduite technique. Adapter à la fois les génotypes et la stratégie de fertilisation azotée permet à l’itinéraire technique à bas niveau d’intrants d’atteindre des performances agronomiques similaires à celles de la conduite intensive en azote, et d’améliorer les performances environnementales. Certains des idéotypes les plus performants en bas niveaux d’intrants obtiennent également des performances élevées en haut-niveaux d’intrants. Afin de limiter ces coûts d’analyses du potentiel brassicole des variétés lors de la sélection, un indice de sélection a été développé et évalué, permettant de hiérarchiser les caractéristiques des grains et ou du moult pour atteindre la qualité brassicole. L’intérêt de modèles prédisant le potentiel brassicole d’une lignée à partir des analyses rapides sur grain a été testé. Ces résultats ont pour objectif de permettre de caractériser plus de lignées rapidement et ainsi de faciliter le développement de lignées adaptées à différents contextes, dont les bas-intrants

Introduction de gènes de résistance à la rouille couronnée dans la sélection française d’avoine (Avena sativa L.)

International audienceThis program aimed at characterizing oat varieties (Avena sativaL.) originating from INRAE Clermont-Ferrand collection as well as from main oat-producing countries. These varieties and some of their progenies (F6) were evaluated for their crown rust tolerance. Simultaneously, these lines were molecularlyassessed for their allelic composition for known resistance genes. A consensus map of 178 SNP markers covering 26 linkage groups was established. An association study between rust-resistance phenotype and molecular markers willbe conducted which should result in the identification of linkage between some SNPs and resistance loci. The most relevant markers will further be used in marker-assisted selection programs. Moreover, several experimentations were conducted to develop a protocol for doubled-haploid (DH) line production. The most promising technique was the one involving anther culture.Ce programme porte sur la caractérisation de variétés d’avoine (Avena sativaL.) provenant de diverses origines et notamment de la collectionINRAE de Clermont-Ferrand mais également de variétés provenant des principaux pays producteurs. Ces différentes variétés collectées, ainsi que certains de leurs croisements (F6), ont été caractérisés aux champs pour leur tolérance à la rouille par les partenaires privés. Parallèlement, ces lignées ont été évaluées au laboratoire pour leur composition allélique au niveau des principaux gènes de résistance connus et marqués. Une carte génétiqueconsensus a été établie, elle comporte 178 marqueurs SNP répartis en 26 groupes de liaison. Au final, une étude d’association entre phénotypes résistants ou sensibles et diversité allélique aux gènes a permis d’identifier des marqueurs pertinents utilisables en sélection assistée. Dans le même temps, un ensemble d’expérimentations a été mené pour mettre au point une méthode de production de plantes haploïdesdoublées(HD). La technique la plus prometteuse est la culture d’anthères

Construction and evaluation of Near-Isogenic Lines for resistance to Aphanomyces euteiches in pea

International audienc

COLNATOR - Caractérisation de la collection nationale de ressources génétiques d’orge

The barley national collection, made of 570 French accessions, was evaluated during three years for tenagro-morphological traits in a multisite network (heading, plant height, loading, spike compactness, spikerow number, disease susceptibilities). Furthermore, the whole collection was genotyped for a set of 1056SNPs. Field evaluation results show a wide diversity for all observed traits. The use of empiric selectionindex on disease traits (barley leaf rust, powdery mildew, leaf blotch, net blotch, Ramularia leaf spot)makes it possible to define two different panels of 43 accessions (winter and spring types) showing highlevel of resistance for each studied pathogen. From SNPs genotyping data, clustering analysis of thewhole collection exhibits the importance of winter vs spring type and spike row number as factors toexplain genetic structure. A first approach of GWAS between markers and traits indicates a total of 1666significant associations (p<0.001). The whole evaluation dataset of this collection will be soon accessibleon internet (https://urgi.versailles.inra.fr/siregal/siregal/grc.do) and the national collection will be declaredas French contribution to TIRPAA (international treaty on genetic resources for food and agriculture).La collection nationale d’orge, regroupant 570 accessions françaises, a été évaluée pour une dizaine decaractères agro-morphologiques (précocité, hauteur, sensibilité à la verse, compacité et nombre de rangsde l’épi, sensibilité aux pathogènes : rouille naine, oïdium, rhynchosporiose, helminthosporiose,ramulariose), dans un réseau de dix sites. Par ailleurs, la collection a été génotypée pour 1056 SNPsrépartis sur l’ensemble du génome. Les résultats d’évaluation agronomique mettent en évidence unelarge variabilité pour l’ensemble des caractères observés. L’application d’un index empirique de sélectionsur les caractères de sensibilités aux maladies a permis de définir parmi la collection deux panels (typehiver et printemps) de 43 accessions chacun, montrant de bons niveaux de résistances aux cinqpathogènes étudiés. A partir des données SNPs, l’analyse de la structure de la collection a confirmél’importance du type hiver vs printemps et du nombre de rangs de l’épi comme facteurs structurants. Parla suite, une première approche de génétique d’association a permis de révéler au total 1666 associationsstatistiquement significatives entre phénotypes et génotypes aux marqueurs étudiés. L’ensemble desdonnées d’évaluation sera bientôt publiquement accessible sur le net(https://urgi.versailles.inra.fr/siregal/siregal/grc.do) et la collection nationale déclarée comme contributionfrançaise au traité international sur les ressources phytogénétiques

Complementary approaches towards the discovery of genes controlling yield in pea

International audiencePea is one of the most important grain legumes in the world. Improving pea yield is a critical breedingtarget in the current context of consumers’ increasing demand for plant proteins for food and feed. Becauseof its polygenic nature and the impact of the environment, breeding for higher yield is challenging. Weinvestigated the genetic determinism of yield (SW), seed number (SN) and thousand seed weight (TSW) usingboth linkage and linkage-disequilibrium approaches.Nine interconnected mapping populations, representing a total of 1,213 recombinant inbred lineswere phenotyped for SW, SN and TSW in six different field environments. These lines were genotyped usingthe GenoPea 13.2K SNP Array [1]. A multi-population quantitative trait loci (QTL) analysis [2] identified 19 QTLfor SW, 18 QTL for SN and 36 QTL for TSW. From this first QTL analysis, a metaQTL analysis [3] detected 27metaQTL and reduced confidence intervals.In addition, two panels of conventional winter pea (376 accessions) and spring pea (300 accessions)were phenotyped for the same traits in seven different field environments. These accessions were genotypedby re-sequencing after exome capture [4]. A Genome Wide Association analysis [5] detected markerssignificantly associated with the 3 traits.The combination of these two genetic approaches highlighted common regions on the pea genomethat represent genomic regions consistently involved in controling yield and its components in pea. Theseresults represent an important step towards marker assisted breeding programs for yield improvement

Complementary approaches towards the discovery of genes controlling yield in pea

International audiencePea is one of the most important grain legumes in the world. Improving pea yield is a critical breedingtarget in the current context of consumers’ increasing demand for plant proteins for food and feed. Becauseof its polygenic nature and the impact of the environment, breeding for higher yield is challenging. Weinvestigated the genetic determinism of yield (SW), seed number (SN) and thousand seed weight (TSW) usingboth linkage and linkage-disequilibrium approaches.Nine interconnected mapping populations, representing a total of 1,213 recombinant inbred lineswere phenotyped for SW, SN and TSW in six different field environments. These lines were genotyped usingthe GenoPea 13.2K SNP Array [1]. A multi-population quantitative trait loci (QTL) analysis [2] identified 19 QTLfor SW, 18 QTL for SN and 36 QTL for TSW. From this first QTL analysis, a metaQTL analysis [3] detected 27metaQTL and reduced confidence intervals.In addition, two panels of conventional winter pea (376 accessions) and spring pea (300 accessions)were phenotyped for the same traits in seven different field environments. These accessions were genotypedby re-sequencing after exome capture [4]. A Genome Wide Association analysis [5] detected markerssignificantly associated with the 3 traits.The combination of these two genetic approaches highlighted common regions on the pea genomethat represent genomic regions consistently involved in controling yield and its components in pea. Theseresults represent an important step towards marker assisted breeding programs for yield improvement

Barley soil borne mosaic viruses: Identification of predominant viruses affecting yield and malting quality, in order to orientate breeding towards a sustainable resistance

Genetic resistance is the only way to control mosaic damage in winter barley. At least 18 resistance genes are known, but until recently, rym4 was the most used by breeders to control Barley yellow mosaic virus-1 (BaYMV-1), predominant in France and Barley mild mosaic virus (BaMMV). However, since 2009, new significant damage has been observed in malting barley in a widening production area, indicating possible overcoming of resistance, with the development of BaYMV-2. The objectives of the Mosa-hordeum project were to: identify new viruses or pathotypes; develop new detection tools; confirm cultivar resistance observed in field using MB tools; confirm efficiency of resistance genes cited in literary reviews; quantify impact on yield and malting quality. A complete viral inventory was carried out 2013- 2016 on affected barley crops in 108 sites using: real-time PCR; Sanger sequencing; Next-Generation Sequencing; and serological tests. A new tool, based on derived Cleaved Amplified Polymorphic Sequences (dCAPS), developed to investigate BaYMV-1 and 2 distributions, demonstrated that BaYMV-2 is predominant (> 95%) in diseased samples. BaYMV-1 and BaMMV were also identified in co-infection with BaYMV-2 on susceptible cultivars. Comparison of yield components, malting and beer quality obtained on healthy/contaminated plots with couples of cultivars revealed variation in yield losses, up to 3t/ha, reduction in number of spikes and kernels/m², smaller kernels, slight increase in protein content and decrease of malt extract. Phylogenetic analyses indicated that the rym4 resistance-breaking ability of BaYMV-2 independently evolved on multiple occasions. In limited number of trials, rym5 resistance was overcome by a variant of BaMMV. The implantation of differentials in 21 contaminated trials confirmed the efficiency of 11 resistance genes against the BaYMV-2/BaMMV complex. To monitor BaYMV and BaMMV resistance for registration in the National List real-time PCR appears more efficient than dCAPS. These findings will help breeders achieve sustainable resistance

Barley soil borne mosaic viruses: Identification of predominant viruses affecting yield and malting quality, in order to orientate breeding towards a sustainable resistance

Genetic resistance is the only way to control mosaic damage in winter barley. At least 18 resistance genes are known, but until recently, rym4 was the most used by breeders to control Barley yellow mosaic virus-1 (BaYMV-1), predominant in France and Barley mild mosaic virus (BaMMV). However, since 2009, new significant damage has been observed in malting barley in a widening production area, indicating possible overcoming of resistance, with the development of BaYMV-2. The objectives of the Mosa-hordeum project were to: identify new viruses or pathotypes; develop new detection tools; confirm cultivar resistance observed in field using MB tools; confirm efficiency of resistance genes cited in literary reviews; quantify impact on yield and malting quality. A complete viral inventory was carried out 2013- 2016 on affected barley crops in 108 sites using: real-time PCR; Sanger sequencing; Next-Generation Sequencing; and serological tests. A new tool, based on derived Cleaved Amplified Polymorphic Sequences (dCAPS), developed to investigate BaYMV-1 and 2 distributions, demonstrated that BaYMV-2 is predominant (> 95%) in diseased samples. BaYMV-1 and BaMMV were also identified in co-infection with BaYMV-2 on susceptible cultivars. Comparison of yield components, malting and beer quality obtained on healthy/contaminated plots with couples of cultivars revealed variation in yield losses, up to 3t/ha, reduction in number of spikes and kernels/m², smaller kernels, slight increase in protein content and decrease of malt extract. Phylogenetic analyses indicated that the rym4 resistance-breaking ability of BaYMV-2 independently evolved on multiple occasions. In limited number of trials, rym5 resistance was overcome by a variant of BaMMV. The implantation of differentials in 21 contaminated trials confirmed the efficiency of 11 resistance genes against the BaYMV-2/BaMMV complex. To monitor BaYMV and BaMMV resistance for registration in the National List real-time PCR appears more efficient than dCAPS. These findings will help breeders achieve sustainable resistance