Barley (Hordeum vulgare) is the fourth most cultivated crop in the world and a model species for grasses. From a collection of spring barley genotypes comprising most of the genetic variation of cultivated barley around the world, we selected 23 inbreds to create, using a double round-robin crossing scheme, 45 segregating populations that represent such diversity. This is the first reported population for joint linkage and association mapping in barley. We use this genetic material for evaluating new predictors of phenotypic diversity. In this context we perform an in-depth characterization of the segregating populations as well as parental inbreds at the genomic, transcriptomic, methylomic, and metabolomic level, in order to unravel the molecular basis of the physiological differences between these genotypes. This information will then be exported to the segregating populations, which will enable us to uncover the genetic basis of the phenotypical and physiological differences that we observe.
A particular focus of our barley work is to study the extent of the barley dispensable genome: the fraction of the pan-genome which is composed of genes that are either absent or not expressed in specific genotypes. We are developing a bioinformatics approach to identify dispensable genes, also called Presence / Absence Variation (PAV), based on RNA sequencing data, and are validating some of these variants in the lab. An important aspect of this work is also to determine whether PAV has an impact on phenotypic traits of agricultural interest, an area of research that is receiving increasing attention in the community (Xu et al., 2017; Gabur et al., 2018). Our set of 23 genotypes and descending segregating populations are great resources to address these challenging questions and more. Other questions of interest to us are, for example, the genetic basis of recombination frequency, or the identification of novel genetic variants that control yield-related traits. Through these projects, we hope to make a significant contribution to improving yield in barley and advance our understanding of how this fascinating model crop for genetic studies adapted to very diverse environments around the globe.
- Barley genome-wide prediction for recombination and agronomic traits
- Methylation in Barley
- PAV/CNV in Barley
- Genetic regulation of grain size and weight in barley
The number, size and weight of grains are the major determinants of the quality and yield of barley. Although the genes regulating grain number are well studied in barley, the barley genes controlling grain size are poorly understood. Therefore, the aim of the project is to dissect the genetic architecture of grain size and weight in barley. We utilize forward genetics to map the genetic loci associated with grain size traits and grain weight in a multi-parent population developed from 23 diverse barley inbreds in a double-round robin (refer to thematic area ‘Barley’ for a detailed description of the mapping population). Besides, we apply reverse genetics tools to validate the candidate genes identified from the genetic mapping.
We observed a strong genotypic variance for the seed size traits and the heritability was more than 84 % across the multiple locations and years. In addition, we have detected major effect quantitative trait loci (QTL explaining 10 % or more phenotypic variance) distributed across seven barley chromosomes. Barley orthologs for genes associated with grains size in rice, wheat and maize were present in the QTL interval. To validate the candidate genes, we have further developed high-resolution populations for the fine mapping of the QTL. Also, we have applied targeted mutagenesis using CRISPR RNA/Cas9 to create knock-out lines for interesting candidate genes.