In human genetics,genome-wide association study (GWAS) is a commonly used method for discovering genes and genetic variants contributing to human traits,usually through statistical examination of the associations between whole-genome sequence variants and one specific trait.The first effort in human GWAS,using genotyping data of 96 patients and 50 healthy controls,successfully identified one gene associated with age-related macular degeneration (Haines et al.,2005).Soon afterward,a large genetics project (The Wellcome Trust Case Control Consortium,2007) that collected thousands of cases and controls in human populations uncovered many new genes underlying seven common diseases,convincingly demonstrating the power of GWAS in genetic mapping of human traits.Subsequently,the method of GWAS was introduced into plant genetics and improved the handling of various plant populations (Nordborg and Weigel,2008;McMullen et al.,2009).During recent years,many large-scale GWAS have been carried out in plants,including those in Arabidopsis,rice,and maize (Atwell et al.,2010;Huang et al.,2010;Li et al.,2013).In fact,plants have unique advantages for GWAS (Xiao et al.,2017).For example,the mapping populations could be permanent:genotyped or sequenced only once but phenotyped many times for various research purposes.