GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
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DOI：
10.1073/pnas.1904964116
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发表时间：
2019-10-15
影响因子：
11.1
通讯作者：
Matsuoka, Makoto
中科院分区：
文献类型：
--
作者：
Yano, Kenji;Morinaka, Yoichi;Matsuoka, Makoto
由于全球对作物高产的需求，阐明水稻结构的遗传控制至关重要。水稻构型是一个受株高、分蘖和穗部形态影响的复杂性状。对8个与水稻株型相关的典型性状进行主成分分析，结果表明，第一主成分PC1提供的信息最多。以PC1为因变量的全基因组关联研究（GWAS）分离了一个编码水稻SPINDLY（OsSPY）的基因，该基因激活赤霉素（GA）信号抑制蛋白SLR1。在9种具有不同GA反应水平的同基因植株中证实了GA信号对水稻构型调控的作用。进一步的群体遗传学分析表明，OsSPY基因与半矮秆和小穗性状相关的功能等位基因在水稻育种过程中被选择。总之，在GWAS中使用PCA将有助于揭示涉及具有复杂特征的性状的基因。
Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.