Toward Genomic Selection in Intermediate Wheatgrass (Thinopyrum intermedium): using Genotyping-by-Sequencing for Simultaneous SNP Discovery, Genetic Map Construction, and Trait Mapping

Genotyping-by-sequencing (GBS) combines molecular marker discovery and genotyping and has been successfully utilized in species with large, complex genomes, such as barley and wheat. Intermediate wheatgrass (Thinopyrum intermedium) is a perennial species that shows great promise as a dual grain and biofuel crop. It is also an importance source of disease resistance genes for wheat. Intermediate wheatgrass, however, is an allohexaploid with an estimated 14 GB genome, no reference, and minimal marker development. The combination of a large and understudied genome makes genetic studies and genomic assisted breeding for intermediate wheatgrass intractable. To address these constraints, the objectives of this project are to discover SNPs, generate a genetic map, and map important agronomic traits. From several full-sib families and breeding populations, 380 individuals were genotyped with GBS. Thousands of high-quality SNPs were discovered and used to confirm known relationships and reveal new pedigree information. Preliminary analysis suggests that GBS can be utilized in Thinopyrum intermedium for de novo genotyping to develop high-density genetic maps and genomic selection models for crop improvement.