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.
Highlights
IntroductionDurum wheat (Triticum turgidum L. ssp. durum Desf. Husn., 2n = 4x = 28; genome AABB) is an important crop in Canada, grown on an average of approximately 2 million hectares and comprising about 25% of total wheat area (Canada, 2018)
Canadian durum wheat is classified into four Canada Western Amber Durum (CWAD) wheat milling grades defined by the Canadian Grain Commission (Dexter and Edwards, 1998)
Genetic diversity in the registration trials changed over time, declining during the first 20 years of breeding in Canada when the germplasm shifted from introduced cultivars in the 1940s and 1950s to locally-bred lines in the 1970s (Figure 1)
Summary
Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn., 2n = 4x = 28; genome AABB) is an important crop in Canada, grown on an average of approximately 2 million hectares and comprising about 25% of total wheat area (Canada, 2018). Durum breeding in Canada has made steady genetic progress to improve yield and agronomic traits This was done concomitantly with improvements in end-use quality attributes such as grain protein concentration, yellow pigment concentration and gluten strength, while improving or maintaining resistance to disease (Clarke J.M. et al, 2010). Grain protein concentration and gluten strength are crucial factors in pasta manufacturing and cooking quality (Feillet and Dexter, 1996). These and other quality trait targets have indirectly driven durum wheat breeders to design hybridization programs within narrow limits, using a similar set of standard cultivars as donors of these quality traits. High grain protein concentration is a requirement for durum cultivar registration in Canada and this likely limited grain yield gain (Clarke J.M. et al, 2010) due to the generally negative relationship between grain yield and protein concentration (Clarke et al, 2009)
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