Crop improvement relies on the ability to identify and exploit genetic diversity. Genomics resources provide the opportunity to efficiently identify and exploit diversity for crop improvement. In the past several years a tremendous amount of genomic resources have been developed in barley, including a genome sequence of the gene-containing portion of the genome, thousands of SNP markers, genotyping centers, databases, and genotyping-by-sequencing (GBS), comparative genomic hybridization (CGH) and gene capture technologies. Coupled with these genomics resources are the availability of germplasm and mutant collections, specialized mapping populations and breeding germplasm.
Two nation-wide projects, the Barley Coordinated Agricultural Project (CAP) and Triticeae CAP, have coupled these germplasm resources with genomics technologies with the intent to integrate genomics technologies within breeding programs. The Barley CAP genotyped and phenotyped advanced breeding lines from 10 U.S. barley breeding programs. These data are stored and easily accessed in The Hordeum Toolbox database (now called The Triticeae Toolbox). These data were used to conduct association mapping to identify quantitative trait loci for over 20 traits including: resistance to Fusarium head blight and African stem rust (Ug99).
Subsequently, in collaboration with the USDA-ARS funded small grain genotyping centers, marker-assisted selection and genomic selection have been implemented for various traits. The TCAP is focused on identifying and exploiting genetic diversity for climate change related traits including water and nitrogen use efficiency, low temperature tolerance, and resistance to several fungal pathogens.
Key germplasm that the TCAP is exploring includes the National Small Grain Core Collection (NSGCC) for barley, nested association mapping and wild barley introgression populations, and elite barley breeding lines. As in the barley CAP, the TCAP approach is focused on genotyping and phenotyping these genetic materials and using the combined datasets to identify QTL. Of note is the extent of the worldwide genetic diversity that these germplasm resources and populations contain.
The NSGCC comprises 2,571 accessions of cultivars and breeding lines, landraces, and genetic stocks representing worldwide barley diversity. The genetic diversity of the NSGCC is being captured in two nested association mapping populations. The wild barley introgression population represents a resource that captures over 90% of the genetic variation from wild barley in a cultivated background. Finally, the elite breeding lines include a subset of the barley CAP breeding lines, representing the U.S. breeding materials, and a worldwide collection of low temperature tolerant barleys.
To complement our efforts to examine genetic diversity in barley with SNP markers, GBS, CGH and gene capture technologies have been developed. GBS provides the opportunity to quickly and cheaply map tens of thousands of markers and has been used to increase the density of barley genetic maps. Using the CGH array, our results showed that 15.6% of the genome is affected by copy number variation and presence/absence variation (CNV/PAV). Gene capture approaches will be used in the near future to assess the genetic variation at virtually every gene in the barley genome. Taken together, these projects represent a substantial coordinated effort to develop and exploit genetic diversity in barley for crop improvement.