TCAP Genotyping: Beyond the Arrays.

The TCAP project “Improving barley and wheat germplasm for changing environments” is using high-density genotyping data as a tool to discover and select for new allelic diversity. The project has developed a database of genotypes for thousands of accessions evaluated with the wheat and barley high-density SNP arrays that, combined with the wealth of phenotypic data generated, has led to increased understanding of the genetic architecture of important traits in both species. However, given that advances in DNA sequencing technologies have resulted in increased outputs and reduced costs, sequencing based genotyping protocols have been integrated into the project. Progress conducting genotyping by sequencing (GBS) on TCAP materials will be presented. GBS is being used to generate high-density linkage maps in bi-parental populations and in the wheat and barley nested association mapping populations.  In winter wheat, GBS is being done on elite panels evaluated for nitrogen use efficiency and yield that were also genotyped using the iSelect wheat array having 90,000 SNP, resulting in a database of SNP genotypes and GBS tags for approximately 1200 lines of hard and soft winter wheat. In barley, the low temperature tolerance (LTT) genomic selection population is in the fifth cycle and a population of wild barley introgression lines is undergoing genomic selection for multiple traits. SNPs identified by mapping sequences to the barley reference genome are being used to update the genomic selection models developed using 384-SNP arrays specific to these populations. The GBS protocols produce greater numbers of markers for genome-wide analyses at lower costs, reduce issues of ascertainment bias and have eliminated the need for development of population specific marker assays when doing genomic selection.