A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits.
A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits.
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DOI：
10.1186/s12870-018-1504-1
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发表时间：
2018-11-14
影响因子：
5.3
通讯作者：
Jouannic S
中科院分区：
文献类型：
--
作者：
Ta KN;Khong NG;Ha TL;Nguyen DT;Mai DC;Hoang TG;Phung TPN;Bourrie I;Courtois B;Tran TTH;Dinh BY;LA TN;DO NV;Lebrun M;Gantet P;Jouannic S
提高产量是水稻育种的重要课题。穗部结构是水稻产量的关键组成部分之一，并且表现出很大的多样性。为了确定穗结构的形态和遗传决定因素，我们使用越南地方品种的原始样本进行了详细的表型分析和全基因组关联研究（GWAS）。使用新开发的图像分析工具，在两年内对圆锥花序的形态特征进行评分：轴长度；一级、二级和三级分支数量；初级和次级分支的平均长度；轴和初生分枝节间的平均长度。我们观察到每穗的小穗数量和次生分枝数量对数据集中的整体表型多样性有很大贡献。两年来，通过 GWAS 检测到了与 7 个性状相关的 29 个稳定 QTL。其中一些 QTL 与已经参与穗发育的基因相关。重要的是，本研究揭示了与小穗数量、二级分枝数量和一级分枝数量性状相关的新QTL的存在。我们对穗结构变异的表型分析表明，对于所使用的样品组，形态多样性在很大程度上取决于初级分枝上不确定与确定的腋生分生组织命运之间的平衡，支持轴和初级分枝之间腋生分生组织命运差异的概念。我们的全基因组关联研究确定了涵盖所有研究性状的众多基因组位点，并将对旨在提高产量的育种计划感兴趣。本研究检测到的新QTL为鉴定控制水稻穗发育和产量的新基因提供了基础。本文的在线版本 (10.1186/s12870-018-1504-1) 包含补充材料，可供授权用户使用。
Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice. The online version of this article (10.1186/s12870-018-1504-1) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/dnares/dsu046
发表时间：
2015-04
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Kumar V;Singh A;Mithra SV;Krishnamurthy SL;Parida SK;Jain S;Tiwari KK;Kumar P;Rao AR;Sharma SK;Khurana JP;Singh NK;Mohapatra T
通讯作者：
Mohapatra T
影响因子：
16.6
作者：
Crowell S;Korniliev P;Falcão A;Ismail A;Gregorio G;Mezey J;McCouch S
通讯作者：
McCouch S
影响因子：
3.7
作者：
Begum H;Spindel JE;Lalusin A;Borromeo T;Gregorio G;Hernandez J;Virk P;Collard B;McCouch SR
通讯作者：
McCouch SR
DOI：
10.1111/tpj.12681
发表时间：
2015-01
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Matsuda F;Nakabayashi R;Yang Z;Okazaki Y;Yonemaru J;Ebana K;Yano M;Saito K
通讯作者：
Saito K
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.