Candidate gene association mapping in spring wheat

Abstract

Association mapping (AM) is a form of quantitative trait locus (QTL) mapping that utilizes a collection of germplasm rather than a structured mapping population. Marker/trait associations are made through the application of a mixed-effects model that corrects for population stratification. The objective of this study was to evaluate the application of association mapping on a selection of elite spring wheat cultivars. We tested marker/trait associations for known "perfect" markers and markers identified as controlling traits of interest through traditional bi-parental mapping. We also wanted to evaluate the observed linkage disequilibrium (LD) surrounding genes of interest by utilizing closely linked sets of markers in specific regions of the spring wheat genome. Population structure was estimated with fifty-one unlinked microsatellite markers. Two phenotypic datasets were used for evaluation. The first was an unbalanced historical dataset, and the second was a balanced dataset taken from a two year replicated field trial. Marker/trait associations were identified for plant height, stem solidness, heading date, grain protein content, test weight, and seed color. Our analyses identified significant associations between Rht-D1 and plant height, Ppd-D1 and heading date, and Xgwm340 and stem solidness. No associations were identified between Rht-B1 and plant height, Ppd-B1 and heading date, nor Vrn-B1 and heading date. The extent of LD varied depending on breeding history and selection pressure. One LD block was identified around the stem solidness QTL and two blocks were found surrounding a productive tiller QTL. Smaller blocks of LD were observed surrounding the three genes controlling kernel color. No LD was observed surrounding the Rht-B1 locus.