Impact of Breeding and Selection on the Evolution of the Wheat D-Genome in a Historical Soft Red Winter Wheat Panel

The D-genome of wheat (Triticum aestivum L.) is the most recent set of chromosomes added to the wheat genome during hybridization of the tetraploid AABB durum wheat with the diploid DD grass. Known to be the least polymorphic of all three genomes, the D genome houses important genes involved in shaping agronomic traits such as disease resistance, yield, and grain quality. Therefore, to study the impact of breeding and selection on the evolution of the D-genome, a panel of 380 soft red winter wheat lines from 1814 to 2015 was genotyped using the genotyping by sequencing method followed by reference-based SNP calling. The SNPs were filtered for minor allele frequency of ≥ 0.05 and missing data of ≤ 25%. The resulting 2,509 D-genome SNPs (15,032 across all 3 genomes) and the associated sequence tags were used in subsequent population genomic analyses. Estimation of pairwise differences (Tajima’s D) within segregating sites showed non-neutral evolution of the loci. While the values ranged from -0.55 to 4.26, 75% of the values were >0 suggesting these loci are under positive selection, likely from selective sweeps during the course of breeding. Regions with positive selection were found to be in moderately high LD (D’ up to 0.7) with loci in different chromosomes undergoing minor positive selection (Tajima’s D 1.6-2.2). Knowledge of the extent of selection in different regions of the D genome along with LD and recombination rates could help understand the reason behind the low polymorphic nature of this genome in current wheat germplasm.