Genetic architecture of flag leaf length and width in rice (Oryza sativa L.) revealed by association mapping

Rice flag leaf is the main photosynthetic organ and plays a key role in grain yield. In this study, 106 loci associated with flag leaf length and width were identified using association mapping in a rice mini core collection. Analyzing the phenotypic effects of each allele represented 156 positive and 167 negative alleles, with a few alleles showing inconsistent effect in different environments. Among the 106 loci, 69 were environment-specific loci, 16 were environmentally stable and 21 were environmentally sensitive. Fifteen associated markers were shared by two traits and were designated as pleiotropic markers. According to the frequency distribution of alleles in different variety types, 343 alleles were categorized into three types based on geographic source and usage in breeding. Among these, 156 were used alleles, 138 were unused and 49 were foreign alleles. The results further our understanding of the genetic mechanisms of flag leaf length and width.