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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. [ABSTRACT FROM AUTHOR]

Common bunt, caused by Tilletia caries (DC.) Tul. & C. Tul. and T. laevis J.G Kuhn, is an economically important disease of wheat ( Triticum aestivum L.) worldwide. The resistance in the winter wheat cultivar ‘Blizzard’ is effective against known races of common bunt in western Canada. The incorporation of resistance from Blizzard into field-ready cultivars may be accelerated through the use of molecular markers. Using the maize pollen method, a doubled haploid population of 147 lines was developed from the F1 of the second backcross of Blizzard (resistant) by breeding line ‘8405-JC3C’ (susceptible). Doubled haploid lines were inoculated at seeding with race T19 or T19 and L16 and disease reaction was examined under controlled conditions in 1999 and natural conditions in 2002, and 2003. Resistant:susceptible-doubled haploid lines segregated in a 1:1 ratio for bunt reaction, indicating single major gene segregation. Microsatellite primers polymorphic on the parents were screened on the population. Initial qualitative segregation analysis indicated that the wheat microsatellite markers Xgwm374, Xbarc128 and Xgwm264, located on wheat chromosome 1BS, were significantly linked to the resistance locus. Qualitative results were confirmed with quantitative trait locus analysis. The genetic distance, calculated with JoinMap®, between the bunt resistance locus and overlapping markers Xgwm374, Xgwm264 and Xbarc128 was 3.9 cM. The three markers were validated on doubled haploid populations BW337/P9502&DAF1BB and Blizzard/P9514-AR17A3E evaluated for common bunt reaction in the growth chamber in 2007. These markers will be useful in selecting for the common bunt resistance from Blizzard and assist in identifying the resistance among potential new sources of resistance. [ABSTRACT FROM AUTHOR]

[This corrects the article DOI: 10.1371/journal.pone.0170941.].

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat., Competing Interests: The authors have declared that no competing interests exist.