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Significance Rice architecture is an important agronomic trait for determining yield; however, the complexity of this trait makes it difficult to elucidate the molecular mechanisms. This study applied a strategy of using principal components (PCs) as dependent variables for a genome-wide association study (GWAS).SPINDLY was identified to regulate rice architecture by suppressing gibberellin (GA) signaling. Further study using GA-signaling mutants confirmed that levels of GA responsiveness regulate rice architecture, suggesting that the utilization of a favorableSPINDLY allele will improve crop productivity. The strategy presented in this study of performing GWAS using PC scores will provide valuable information for plant genetics and will improve our understanding of complex traits at the molecular level.

GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture