Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass

Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication traits in the fourth cycle IWG breeding population at the University of Minnesota: height, seed length, seed width, shattering, threshability, and seed mass. A weak population structure was observed and linkage disequilibrium (r2) declined rapidly: 0.23 mega base pairs at conventional r2 value of 0.2. Broad-sense heritabilities were overall high and ranged from 0.71–0.92. Association analysis was carried out using 25,909 single SNP markers and 5379 haplotype blocks. Thirty-one SNP markers and 17 haplotype blocks were significantly associated with the domestication traits. These associations were of moderate effect as they explained 4–6% of the observed phenotypic variation. Ten SNP markers were also detected by the haplotype association analysis. One SNP marker on Chromosome 8, also discovered in haplotype block analysis, was common between seed length and seed mass. Increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG’s domestication traits.