An Analysis of Natural Variation Reveals That Controls Flag Leaf Angle in Rice ( L.).

Flag leaf angle (FLA) is an important outcrossing trait affecting the hybrid seed production in rice ( L.). Natural variation of FLA has been reported in rice, but the molecular basis for this variation is largely unknown. In this study, we investigated the phenotypic values of FLA in 353 rice natural accessions in six environments, which indicated that there was abundant phenotypic variation. We performed a genome-wide association study on FLA using 1.3 million single nucleotide polymorphisms (SNPs). A total of six quantitative trait loci (QTLs) were identified significantly associated with FLA, of which five were located in previously reported QTLs/genes and one was novel. We identified two causal gene loci for FLA, namely, and ; was co-localized with the gene . In addition, the accessions with large and small FLA values have corresponding high and low expressions. 2 allele could increase significantly the seed setting percentage in hybrid F seed production by field experiment. We also confirmed that the allele increased the FLA compared with that of the isogenic line carrying allele by transgenic complementation experiment. The allele frequencies of decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement of FLA of parents of hybrid rice.