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

Abstract

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.

Genome-wide association mapping and genomic prediction for kernel color traits in intermediate wheatgrass (Thinopyrum intermedium)

“…However, we did compare the MTA and HTA positions with previously reported QTL in IWG to investigate if any loci were pleiotropic. We did not find any significant marker discovered in this study within the LD block (0.46 Mbp [ 3 ];) of previously reported markers in IWG. Additionally, as the QTL were of small to medium effects, several cycles of breeding and selection are likely necessary to increase the frequency of alleles conferring deep purple color to the grain, and fix them in the breeding population.…”

“…A genet is defined as a genetically unique organism and refers to individual plants in an outcrossing species such as IWG [ 8 ]. The population, part of the fourth breeding selection cycle (referred to as UMN_C4 hereafter), is owned by the University of Minnesota and has been described in a previous report [ 3 ]. Briefly, UMN_C4 was obtained from open-pollination of 73 cycle 3 (UMN_C3) genets that were selected based on their superior genomic estimated breeding values (GEBVs) for larger seed size, better threshability, reduced seed shattering, higher grain yield, and reduced plant height.…”

“…The process of haplotype discovery has also been previously described [ 3 ]. In short, HAPLOVIEW 4.2 [ 50 ] was implemented to construct haplotype blocks for each chromosome and blocks were constructed using a confidence interval algorithm [ 51 ].…”

“…To search for candidate genes in regions surrounding the significant SNP markers and haplotype blocks, putative protein coding sequences within 0.46 megabase pairs (Mbp) of the significant loci were obtained from the T. intermedium v2.1 annotation [ 45 ]. The distance of 0.46 Mbp was used because the genome-wide average linkage disequilibrium in UMN_C4 was found to be 0.23 Mbp [ 3 ]. A protein BLAST-search was carried out on NCBI’s website [ 58 ] using the T. intermedium protein coding sequences with % identity > 80% and E-value ≤1E-10; only the best 10 alignments per T. intermedium protein coding sequence were retained for further analysis.…”

“…The crop is a cool-season perennial grass species and is being domesticated as a novel food crop by multiple institutions including the University of Minnesota (UMN). Initiated in 2011, the UMN’s IWG breeding and domestication program has completed four breeding cycles and released a food-grade IWG cultivar named ‘MN-Clearwater’ in 2019 [ 2 , 3 ]. Besides the use of IWG grain as food, the crop also can provide substantial services towards ecosystem preservation such as improved carbon sequestration, reduced nutrient runoff and leaching to groundwater, and reduced soil erosion [ 4 , 5 ].…”