Genome-Wide Association Analysis of Grain Pigment Colour in Elite Durum Wheat Breeding Lines, Using Single SNP- and Haplotype-Based Approach in Durum Wheat

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes can be described as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile effort. In the present study, we used single SNPs- and haplotype-based approach to search for loci associated with grain pigment colour in durum wheat; the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. A total of 169 breeding lines were genotyped using the 90K Infinium assay, and 12,234 high quality SNPs were generated and used to access the population structure and the linkage disequilibrium pattern. A total of 5,082 SNPs, mapped on a durum consensus map, were clustered into 324 haplotypes. Combining multiple SNPs into haplotypes increased the average PIC from 0.27 (single SNPs) to 0.5 (haplotypes). The haplotype-based analysis identified a total of 11 loci associated with grain pigment color traits, including all of the six loci identified by the single SNPs-based analysis. Furthermore, the haplotype-based analysis resulted in substantial increase of the phenotypic variance explained (21.3% on average) and the allelic effect (29.8% on average). These results clearly show a benefit of haplotype-based analysis for dissecting grain pigment colour in durum wheat. A routine use of haplotype-based analysis in comparison with single SNPs analysis will provide more insight about the potential of combining SNPs into haplotypes in genome-wide association studies.