Marker Association Analysis with Three Agronomic Traits in Hard Winter Wheat Lines under Diverse Environments

Genetic performance for a quantitative trait is often controlled by gene-by-gene and genotype-by-environment (GE) interaction effects. As an important component, a GE interaction effect is highly related to crop stability. As genetic association mapping has been widely used to determine markers associated with traits of interest, stability analysis based on genetic markers/genes of importance could help develop widely adapted or specifically adapted cultivars. With linear mixed model approach, in this study we analyzed a wheat data set from the USDA Hard Winter Wheat Regional Nursery Program in 2010. The data included 32 genetic markers and 48 genotypes with three important agronomic traits: grain yield, plant height, and heading date, which were measured under multi-environments. Our results showed that four important DNA markers: Rht2, PPO18NED, Lr34JagTM, and Waxy-A1-AFC-AR2FAM, were significantly associated with all these three traits. Among these, Rht2 contributed 50.34%, 78.65%, and 53.90% of the phenotypic variation for grain yield, plant height, and heading date, respectively. Compared to their main effects, however, genotype-by-environment interaction effects were less important under these diverse environments.