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

Durum wheat was introduced in the southern prairies of western Canada in the late 19th 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 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 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 favourable 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.