Genome-wide association mapping in plants.

KEY MESSAGE: We present new association mapping methods which address the unique challenges of analyzing genome-wide data from multi-environment plant studies. Association studies on a genome-wide scale are being performed in plants. Unlike human studies, plant studies contain replicates whose data may be recorded across different environments. Plant studies also often employ elaborate experimental designs for controlling extraneous phenotypic variation. As a result, the genome-wide analysis of data from plant studies can be challenging. In this paper, we present QK-based association mapping for the analysis of data from plant association studies. In doing so, we have developed: (a) a general multivariate QK framework for association mapping in plant studies of arbitrary complexity; (b) a new weighted two-stage analysis approach for QK-based association mapping; (c) a heuristic procedure for determining when two-stage analysis is appropriate; and (d) a Monte Carlo sampling procedure for controlling the genome-wide type I error rate. We conduct a simulation study to evaluate the performance of our genome-wide mapping technique. We also analyze data from a multi-environment association study in wheat.