Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars

Abstract

Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was <1 cM, whereas in the centromeric region of 5A, LD extended for approximately 5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection.

Figure 1.

Orthogonal projections of the cloud of points representing the genetic distance among varieties, based on 36 unlinked SSR markers analyzed by multiple correspondence analysis. Subpopulations S1–S4 were inferred in Structure.

Figure 2.

Effect of selection of cultivars on LD. Solid, dark shading, and light shading indicate comparison-wise P < 0.0001, P < 0.001, P < 0.01, respectively, for r² estimates among 18 unlinked SSR markers on 149 varieties (above diagonal) and 95 selected varieties (below diagonal).

Figure 3.

Estimates of r² vs. linkage distance on chromosomes 2D and 5A. Horizontal straight lines indicate the 95th percentile of the distribution of unlinked r². Curves were fit by second-degree loess. Axis scales are different for each plot.

Figure 4.

Consensus map of loci tested on chromosome 2D and 5A. Underlined loci were positioned by comparison with the Wheat Composite 2004 map. (*) and (**) indicate loci associated with kernel traits at α_c = 0.05 and α_c = 0.01, respectively. In the triangles, black, dark shading, and light shading indicate comparison-wise significance of r² at P < 0.0001, P < 0.001, P < 0.01, respectively.

Figure 5.

Phenotypic effect of marker alleles at loci significantly associated with kernel length, width, and weight in NY and OH.