Genome‐wide association study identifies genomic regions under selection for domestication and agronomic traits in intermediate wheatgrass

Intermediate wheatgrass (IWG) (Thinopyrum intermedium, Kernza) is a perennial forage grass undergoing neo-domestication as a grain crop. IWG provides numerous ecosystem services and has the potential to benefit rural communities as an alternative crop option with high market value. However, IWG has only been under development as a perennial grain crop for the past few decades and at the University of Minnesota (UMN) since 2011. Improvements in grain-related traits, market development, and agronomic management are needed for the long-term viability of IWG as a Midwestern grain crop. In this study, 225 parent genets (genetically unique individuals) from UMN IWG breeding Cycles 2, 3, 4, and 5 were cloned, planted, and evaluated for 2 years at two locations. Plants were genotyped using genotyping-by-sequencing to get 12,072 single nucleotide polymorphisms and phenotyped for key domestication and agronomic traits. A genome-wide association study (GWAS) identified 36 quantitative trait loci (QTLs) for shattering, seed size, and yield traits, which individually explained an average of 13% of the phenotypic variation. Several QTLs mapped to the same homoeologous chromosomes or regions as previously identified domestication and agronomic loci in IWG and other cereal species. Changes in allele frequencies for significant QTL across breeding cycles were examined, which identified 12 alleles under selection. Several favorable alleles remain at minor frequencies, indicating substantial potential for continued genetic improvement. Integration of GWAS hits as fixed effects within genomic selection models could enable recurrent selection schemes that strategically increase favorable allele frequencies and stack positive traits for long-term gain.