Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa).
Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa).
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DOI：
10.1371/journal.pgen.1007323
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发表时间：
2018-04
期刊：
影响因子：
4.5
通讯作者：
Xing Y
中科院分区：
文献类型：
--
作者：
Dong H;Zhao H;Li S;Han Z;Hu G;Liu C;Yang G;Wang G;Xie W;Xing Y
叶片角度是水稻理想株型的重要组成部分，尤其是剑叶角度对水稻产量的贡献很大。本研究利用世界范围内的种质资源，阐明了弗拉的遗传基础，为水稻的分子设计育种提供了理论依据。全基因组关联分析（GWAS）在武汉和海南分别检测到40个和32个弗拉QTL。两种条件下共检测到8个QTL。其中，在籼、粳亚群体中分别检测到2个和3个QTL。此外，对5个弗拉QTL候选位点进行了单倍型水平的关联分析。这些结果表明，不同的遗传基础之间的弗拉籼和粳稻亚群。OsbHLH153、OsbHLH173和OsbHLH174这三个候选基因对BR和IAA的反应都非常迅速，但OsbHLH173的表达水平很低，无法检测到，它们在植株中的过表达增加了水稻叶片的角度。结合前人的研究结果，认为bHLH亚家族16中的6个成员在水稻弗拉的调控中具有保守的功能。与我们以前的分蘖角（TA）的GWAS相比，只有一个QTL对弗拉和TA具有多效性效应，这解释了弗拉和TA之间的遗传基础相似性较低。通过亚种间杂交，将籼型弗拉的有利等位基因与粳型TA的有利等位基因结合，有望有效地构建理想的株型。水稻叶角是决定植株密度的理想植株构型的主要组成部分。许多叶角相关基因已经基于突变体进行了表征，但这些基因的自然变异和遗传改良的潜在价值尚未得到评估。本文利用GWAS技术对水稻弗拉的遗传基础进行了研究。目前已鉴定出数十个数量性状基因座（QTL），但在籼粳亚种群之间普遍检测到的弗拉QTL却很少。小叶角等位基因主要来源于籼稻。三个新的OsbHLH基因已被证实通过过表达调节叶角。结合以往的研究，bHLH亚家族16的所有6个成员在调节叶角方面具有保守的功能。在同一个材料中，只有一个QTL对弗拉和TA具有多效性效应，表明弗拉和TA的遗传基础不同。小TA等位基因主要来自粳稻。建议通过亚种间杂交，同时利用弗拉和TA的有利等位基因，培育紧凑型品种。
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. Rice leaf angle is a major component of ideal plant architecture that determines plant density. Many leaf angle-related genes have been characterized based on mutants, but natural variations of these genes and potential values in genetic improvement have not been evaluated. Here we explore the genetic basis of rice FLA in rice by GWAS. Dozens of quantitative trait loci (QTLs) have been identified, but few FLA QTLs have been commonly detected between indica and japonica subpopulations. Alleles for small leaf angle mostly come from indica rice. Three novel OsbHLH genes have been confirmed to regulate leaf angle by overexpression. Together with previous studies, all 6 members of bHLH subfamily 16 have a conserved function in regulating leaf angle. Only one QTL has been identified with pleiotropic effects on FLA and TA in the same collection, indicated the diverse genetic basis between FLA and TA. Alleles for small TA mostly come from japonica rice. We suggest to breed compact plant type cultivars by simultaneously utilizing favorable alleles for FLA and TA via inter-subspecies hybridization.
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