The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Abstract

Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries' breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms 'response-to-auxin' and 'response-to-wounding.' Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

The Use of Low-Density SNP Array for Identification of Interspecific Introgressions of Genetic Material from the Bread Wheat into Homologous Chromosomes of the Durum Wheat

“…Wound response genes are often expressed in response to pathogen exposure [25]. Nine wound response genes were found on chromosome 1A between 12 Mbp and 13 Mbp on pseudochromosomes of bread wheat assembly [26]. The introgression region identified in this work includes these coordinates.…”