Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice

In hybrid rice seed production, rice varieties with a small flag leaf angle (FLA) experience obstacles to cross-pollination at the early heading stage, and farmers usually need to remove flag leaves to achieve artificial pollination. Therefore, the cultivation of rice varieties with large FLAs can not only save a substantial amount of labour in the leaf-cutting process during artificial pollination but also accelerate the mechanization of hybrid rice seed production.

In this study, 431 rice accessions were included in a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) and the superior haplotypes for rice FLA in 2022 and 2023. The aim of the study was to identify new QTLs and provide germplasm resources for the genetic improvement of rice FLA. The population exhibited rich phenotypic variation in FLA in both years. The FLA GWAS was performed with more than 3 million single-nucleotide polymorphisms (SNPs), and eight QTLs associated with FLA were detected; of these, six QTLs located on rice chromosomes 1, 2, 8 and 9 were novel and detected in both years. In addition, these QTLs were analysed by haplotype analysis and functional annotation, and FLA2 and FLA9, which encode xyloglucan fucosyltransferase and cytokinin-O-glucosyltransferase 2, respectively, were identified as candidate genes for FLA regulation in rice. Quantitative real-time polymerase chain reaction (qRT‒PCR) results validated FLA2 and FLA9 as candidate genes. The results of this study showed that the elite alleles of FLA2 and FLA9 can increase FLA in rice. Excellent parents for FLA improvement were predicted through pyramiding breeding.

A total of six new QTLs and two candidate genes (FLA2 and FLA9) were identified by a GWAS of 431 rice accessions over two years. The elite alleles and excellent parents predicted in our study can provide important information for the functional analysis of rice FLA-related genes and improvement through pyramiding breeding.