Genetic Variation in Cultivated and Non-Cultivated Barley: From SNPs to Copy Number Variants.

Technological advances in barley genomics are having an impact on our understanding of genetic diversity and barley breeding. Recently, a new 9K-SNP iSelect Illumina platform was developed for barley and used to genotype the National Small Grain Collection barley core subset. The subset comprises 2,419 accessions of cultivars and breeding lines, landraces, and genetic stocks representing worldwide barley diversity. A total of 2298 accessions and 6090 informative SNPs passed our quality control checks and were used for principal coordinates (PCO), population structure, and linkage disequilibrium analyses. Aleurone color, awn roughness, growth habit, hull cover, lemma color, row type, spike density and 1000 kernel weight were previously measured in the core collection and will be subjected to genome-wide association mapping. These SNP data will be also used to identify a set of representative accessions which captures most of the germplasm diversity and can be scored for additional traits of agronomic interest. Additionally, a Comparative Genomic Hybridization (CGH) array was developed for barley in collaboration with Roche NimbleGen and has been employed to study the extent of copy number variation (CNV) in a set of cultivated and wild barleys representing barley diversity. A significant percentage (14.9%) of the genome is affected by CNV, indicating that this kind of structural variation can account for much of the phenotypic diversity and plasticity of the crop. Wild accessions alone contribute to most of the CNVs identified, demonstrating the higher levels of diversity present in the wild relative of barley. Telomeric regions are richer in structural variants in all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. An enrichment of genes involved in defense, cell death and signal transduction was found among genes affected by CNV.