Abstract
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.
Highlights
Marker-assisted selection (MAS) is increasing in use in plant breeding as a means to enrich selections from segregating populations for desirable alleles influencing economically important traits
Several of the quantitative trait loci (QTL) that we discovered were specific to lines from the diverse collection but most were identical by state in our breeding material, despite large phenotypic differences in trait expression [100, 101]
Large phenotypic variation was observed among the breeding lines for all of the traits (Table 1)
Summary
Marker-assisted selection (MAS) is increasing in use in plant breeding as a means to enrich selections from segregating populations for desirable alleles influencing economically important traits. Several QTL were reported in the literature, relatively few are practically used in breeding programs [5]. Reasons for their lack of practical use are mostly due to the difficulties with context dependencies caused by genotype-environmental interactions and/or epistasis, to the limitations of sampling bi-parental populations with multi-genic traits, and to lack of follow-through research to validate identified QTL [6,7,8]. Identification of marker-trait associations using association mapping techniques, could avoid some of these context dependencies
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