Haplotype Diversity of Advanced Breeding Lines and Their Role in Association Mapping Grain Pigment Qtl's in Durum Wheat:.

Association mapping (AM) is a powerful approach to identify genomic regions associated with important traits.  Each year, plant breeders phenotype their most promising lines in multi-environment regional yield trials making these lines useful for identification of desirable molecular markers linked to traits of interest, and to study haplotype variation to develop genome-wide selection strategies.  The objective was to study the feasibility of the association mapping approach applied to closely related lines grown in regional trials, and to study the haplotype variation at previously reported quantitative trait loci (QTL).  Seventy-two advanced breeding lines from Canadian durum breeding programs were chosen, and semolina yellow pigment was used as an example trait to demonstrate the feasibility of this approach. Sixty-four microsatellite markers previously associated with phenotypic variation in yellow pigment (YP) at 10 QTL were evaluated. To assess population structure, a pairwise genetic similarity matrix was calculated based on Rogers' Euclidean distance and a majority-rule consensus tree was reconstructed using UPGMA. A Bayesian clustering approach was also used to infer the number of subpopulations (K) and to assign individuals to subpopulations based on membership proportion in each subpopulation (Q matrix) with the software STRUCTURE. Marker-trait associations were tested with a linear mixed-effects model within the program TASSEL. The advanced breeding lines showed a high level of genetic similarity. Semolina pigment among the sub-populations was not significantly different. Our results demonstrate that those markers previously associated with yellow pigment in bi-parental mapping populations, were also significantly associated with semolina pigment in advanced breeding lines.  These results support the use of advanced, adapted breeding lines coupled with haplotype information as a mechanism to identify marker-trait associations and to train DNA markers for genome wide selection strategies.