Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa).

Haijiao Dong,Gang Hu,Gongwei Wang,Zhongmin Han,Shuangle Li,Yongzhong Xing,Hu Zhao,Chang Liu,Gaiyu Yang,Weibo Xie,Kenneth M Olsen

doi:10.1371/journal.pgen.1007323

Abstract

As a major component of ideal plant architecture, leaf angle especially flag leaf angle (FLA) makes a large contribution to grain yield in rice. We utilized a worldwide germplasm collection to elucidate the genetic basis of FLA that would be helpful for molecular design breeding in rice. Genome-wide association studies (GWAS) identified a total of 40 and 32 QTLs for FLA in Wuhan and Hainan, respectively. Eight QTLs were commonly detected in both conditions. Of these, 2 and 3 QTLs were identified in the indica and japonica subpopulations, respectively. In addition, the candidates of 5 FLA QTLs were verified by haplotype-level association analysis. These results indicate diverse genetic bases for FLA between the indica and japonica subpopulations. Three candidates, OsbHLH153, OsbHLH173 and OsbHLH174, quickly responded to BR and IAA involved in plant architecture except for OsbHLH173, whose expression level was too low to be detected; their overexpression in plants increased rice leaf angle. Together with previous studies, it was concluded that all 6 members in bHLH subfamily 16 had the conserved function in regulating FLA in rice. A comparison with our previous GWAS for tiller angle (TA) showed only one QTL had pleiotropic effects on FLA and TA, which explained low similarity of the genetic basis between FLA and TA. An ideal plant architecture is expected to be efficiently developed by combining favorable alleles for FLA from indica with favorable alleles for TA from japonica by inter-subspecies hybridization.

Highlights

Leaf angle is the inclination between leaf and stem, which is an important agronomic trait that attracts attention
The flag leaf angle (FLA) of 529 O. sativa accessions shared a similar distribution in Hainan and Wuhan, China (Fig 1)
We found that indica rice has a smaller FLA with a narrower distribution than japonica rice in Hainan and Wuhan (Fig 1)

Summary

Introduction

Leaf angle is the inclination between leaf and stem, which is an important agronomic trait that attracts attention. Scientists in plant developmental biology have paid much attention to the mechanism of leaf angle formation. Endogenous hormones, especially brassinosteroids (BRs), play important roles in controlling rice leaf angle by promoting the growth of cells on the adaxial side of the lamina joint [9, 10]. OsSPY and D1/RGA1 are two genes in the GA signaling pathway that regulate leaf angle in a BR-GA crosstalk manner in rice [17, 18]. Increased Leaf Angle 1 (ILA1), different from the abovementioned leaf angle-related genes, regulates mechanical tissue formation in the rice leaf lamina joint [19]. There are many findings on the development of leaf angle of rice that are helpful for understanding its molecular mechanism

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Conclusion