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

Kenji Yano, Yoichi Morinaka, Fanmiao Wang, Peng Huang, Sayaka Takehara, Takaaki Hirai, Aya Ito, Eriko Koketsu, Mayuko Kawamura, Kunihiko Kotake, Shinya Yoshida, Masaki Endo, Gen Tamiya, Hidemi Kitano, Miyako Ueguchi-Tanaka, Ko Hirano, Makoto Matsuoka

Research output: Contribution to journalArticlepeer-review

99 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)2162-21267
Number of pages19106
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number42
Publication statusPublished - 2019 Oct 15


  • gibberellin
  • GWAS
  • PCA
  • Plant architecture


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