An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice (Oryza sativa L.)

Abstract

Flag leaf angle (FLA) is an important outcrossing trait affecting the hybrid seed production in rice (Oryza sativa 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, OsFLA6 and OsFLA2; OsFLA6 was co-localized with the gene OsLIC. In addition, the accessions with large and small FLA values have corresponding high and low OsFLA6 expressions. OsFLA2TT allele could increase significantly the seed setting percentage in hybrid F1 seed production by field experiment. We also confirmed that the allele OsFLA2TT increased the FLA compared with that of the isogenic line carrying allele OsFLA2CC by transgenic complementation experiment. The allele frequencies of OsFLA6GGand OsFLA2TT decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement of FLA of parents of hybrid rice.

Identification of QTLs Conferring Rice Leaf Inclination Angle and Analysis of Candidate Genes

“…Cai et al [26] investi population using the cross combination of indica rice ZYQ8 and japonica ric terials, and detected nine QTLs controlling FLA, six of which were detecte somes 1, 2, 2, 7, 9 and 12 in Hainan, and three were detected on chromosom in Hangzhou. Jiang et al [27] conducted a genome-wide association study different environments, and detected a total of six QTLs, of which one wa that had not been studied by previous researchers, and verified the function date gene OsFLA2. Gui et al [28] identified leaf angle during rice heading a total of six QTLs in the past two years, of which five were reported for the fi researchers utilized different rice populations, genetic analysis and gene m rice leaf inclination angle has been performed in different environments, pro foundation for aggregating rice leaf angle dominant alleles and improv types.…”

“…Therefore, it is speculated that there may be effector sites controlling leaf inclination angle near these two intervals. Jiang et al [27] studied the phenotypic values of FLA in 353 rice germplasm under six different environments and obtained six QTLs. Among them, qFLA4 located on chromosome 4 partially overlaps with qTLIA4-2 in this study, suggesting that there may be a controlling leaf inclination near this site.…”

“…Cai et al [26] investigated the DH population using the cross combination of indica rice ZYQ8 and japonica rice JX17 as materials, and detected nine QTLs controlling FLA, six of which were detected on chromosomes 1, 2, 2, 7, 9 and 12 in Hainan, and three were detected on chromosomes 6, 8 and 12 in Hangzhou. Jiang et al [27] conducted a genome-wide association study on FLA in six different environments, and detected a total of six QTLs, of which one was a new locus that had not been studied by previous researchers, and verified the function of the candidate gene OsFLA2. Gui et al [28] identified leaf angle during rice heading and detected a total of six QTLs in the past two years, of which five were reported for the first time.…”

Stomatal properties of Arabidopsis cauline and rice flag leaves and their contributions to seed production and grain yield

“…Taken together, these results suggest that PM H + -ATPase is also critical for the stomatal properties of the flag leaf and grain yield. In addition, previous studies showed that the insertion angle of the flag leaf differs among rice varieties, which affects the photosynthetic activity ( Kobayashi et al , 2003 ; Jiang et al , 2022 ). Furthermore, cytokinin was suggested to increase the stomatal density in tomato and make a great contribution to leaf morphogenesis ( Farber et al , 2016 ; Muszynski et al , 2020 ).…”