Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height

Abstract

Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b^∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.

Keywords: durum wheat; grain yield; haplotype; loci under selection; plant height; protein loss; quality traits.

FIGURE 1

Changes in genetic diversity (π) of the Durum wheat Cooperative Test in Canada from 1950 to 2010.

FIGURE 2

Population structure of the breeding panel as revealed by discriminant analysis of principal components. The axes represent the first two Linear Discriminants. Each color represents a sub-population.

FIGURE 3

Genome-wide analysis of loci under selection using Arlequin (red), BayeScan (green), and Lositan (blue). The horizontal black dash line indicates the threshold for selection with Arlequin and Lositan while the horizontal green dash line shows the selection threshold for BayeScan.

FIGURE 4

Venn diagram of loci under selection detected by Arlequin, BayeScan, and Lositan.

FIGURE 5

Heatmap of correlation coefficients between all traits measured in the durum wheat breeding panel. The color intensity (red for positive, blue for negative) increases with higher correlation. Absolute values > 0.15 were significant at α = 0.05. ^∗Should be read as star (e.g., Semolina b^∗ is “Semolina b star”).