QTL mapping and candidate gene prediction for the sensitivity of flag leaf angle to exogenous GA₃ in rice (Oryza sativa L.)

The sensitivity of flag leaf angle (FLA) to GA(3) in rice is directly related to the yield and quality of hybrid F1 seed production. Mining the elite alleles and gene loci controlling FLA sensitivity to GA(3) is necessary. Here the GA(3) sensitivity index (GSI) was used as the measure of GA(3) sensitivity of FLA. The FLA(GSI) phenotypic values of 173 rice materials composing a natural population were investigated, showing a wide range of genetic variation. Combining the 1.2 million single nucleotide polymorphism (SNPs), a genome-wide association study was performed to detect the quantitative trait loci (QTLs). One QTL, qFLA(GSI)5, that was significantly associated with FLA(GSI) was newly detected. This QTL was mapped into the 7,807,710-8,007,710 bp region, which had 25 positional candidate genes. Based on the linkage disequilibrium analysis, the QTL region was narrowed down to 7,904,253-7,960,999 bp, which contained five candidate genes. Among the five candidate genes, only LOC_Os05g14160 contained nonsynonymous SNPs significantly associated with FLA(GSI). The FLA(GSI) of the AA allele was significantly higher than that of the GG allele. Hap2 can increase GA(3) sensitivity by 0.19-0.22. The results in this study provide a theoretical basis for improving the sensitivity of FLA to exogenous GA(3) in rice.