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15 Pags.- 5 Figs.- 3 TAbls.- Supp. Mat. Copyright Owner, the Authors. Under LicenceCC BY 4.0., One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT—assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit., Support was provided by the USDA-NIFA TCAP Project no. 2011-68002-30029.

Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L.) elite material families and old cultivars, which reflect the breeding history of barley in Germany. Crosses of parents selected from the training set were used to create a set of double-haploid families consisting of 750 genotypes. Those were used to confirm prediction ability estimates based on a cross-validation with the training set material using 11 different genomic prediction models. Population structure was inferred with dimensionality reduction methods like discriminant analysis of principle components and the influence of population structure on prediction ability was investigated. In addition to the size of the training set, marker density is of crucial importance for genomic prediction. We used genome-wide linkage disequilibrium and persistence of linkage phase as indicators to estimate that 11,203 evenly spaced markers are required to capture all QTL effects. Although a 9k SNP array does not contain a sufficient number of polymorphic markers for long-term genomic selection, we obtained fairly high prediction accuracies ranging from 0.31 to 0.71 for the traits earing, hectoliter weight, spikes per square meter, thousand kernel weight and yield and show that they result from the close genetic relatedness of the material. Our work contributes to designing long-term genetic prediction programs for barley breeding.

Barley (Hordeum vulgare) is the fourth cereal in the world. In our days, environmental conditions are changing and climatic hazards multiply. The Limagrain barley breeding team wants to develop adapted varieties to these new constraints. For this, it is necessary to understand the genetic determinism of abiotic stress tolerance and barley phenology. The theme of this internship proposes to explore two important aspects for adaptability and which are closely related: earliness and frost tolerance. To better understand the genetic determinants of earliness and frost tolerance, genome wide association studies (GWAS) and genomic selection were performed. 183 QTLs were detected in 40 populations of inbred lines and for a set of six variables. Some of these loci colocalize with genes important in earliness and frost tolerance mechanisms. The identified QTLs will be directly used to improve the material from which they were detected. Data analysis will be improved by taking into account environmental variables and a comparison between genomic selection and association analysis.; L’orge (Hordeum vulgare) est la quatrième céréale mondiale. De nos jours, les conditions environnementales sont changeantes et les aléas climatiques se multiplient. L’équipe de sélection orge de Limagrain souhaite développer des variétés adaptées à ces nouvelles contraintes. Pour cela, il est nécessaire de mieux comprendre le déterminisme génétique de la tolérance aux stress abiotiques et la phénologie de l’orge. Le thème de ce stage propose d’étudier deux aspects importants pour l’adaptabilité recherchée et qui sont étroitement liés : la précocité et la tolérance au froid. Afin de mieux connaître les déterminants génétiques de la précocité et de la tolérance au froid, des études d’association et de sélection génomique ont été réalisées. Au total, 183 QTLs ont été détectés dans 40 populations de lignées en cours de sélection et pour un ensemble de 6 variables. Une partie de ces loci colocalise avec des gènes importants des mécanismes de précocité et de tolérance au froid. Les QTLs identifiés pourront être directement utilisés pour améliorer le matériel dans lequel ils ont étaient détectés. Un approfondissement du traitement des données prenant davantage en compte des variables environnementales est envisagé ainsi qu’une comparaison entre sélection génomique et analyse d’association.