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

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 a...

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Autores principales: Yano, Kenji, Morinaka, Yoichi, Wang, Fanmiao, Huang, Peng, Takehara, Sayaka, Hirai, Takaaki, Ito, Aya, Koketsu, Eriko, Kawamura, Mayuko, Kotake, Kunihiko, Yoshida, Shinya, Endo, Masaki, Tamiya, Gen, Kitano, Hidemi, Ueguchi-Tanaka, Miyako, Hirano, Ko, Matsuoka, Makoto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800328/
https://www.ncbi.nlm.nih.gov/pubmed/31570620
http://dx.doi.org/10.1073/pnas.1904964116
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author Yano, Kenji
Morinaka, Yoichi
Wang, Fanmiao
Huang, Peng
Takehara, Sayaka
Hirai, Takaaki
Ito, Aya
Koketsu, Eriko
Kawamura, Mayuko
Kotake, Kunihiko
Yoshida, Shinya
Endo, Masaki
Tamiya, Gen
Kitano, Hidemi
Ueguchi-Tanaka, Miyako
Hirano, Ko
Matsuoka, Makoto
author_facet Yano, Kenji
Morinaka, Yoichi
Wang, Fanmiao
Huang, Peng
Takehara, Sayaka
Hirai, Takaaki
Ito, Aya
Koketsu, Eriko
Kawamura, Mayuko
Kotake, Kunihiko
Yoshida, Shinya
Endo, Masaki
Tamiya, Gen
Kitano, Hidemi
Ueguchi-Tanaka, Miyako
Hirano, Ko
Matsuoka, Makoto
author_sort Yano, Kenji
collection PubMed
description 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.
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spelling pubmed-68003282019-10-24 GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture Yano, Kenji Morinaka, Yoichi Wang, Fanmiao Huang, Peng Takehara, Sayaka Hirai, Takaaki Ito, Aya Koketsu, Eriko Kawamura, Mayuko Kotake, Kunihiko Yoshida, Shinya Endo, Masaki Tamiya, Gen Kitano, Hidemi Ueguchi-Tanaka, Miyako Hirano, Ko Matsuoka, Makoto Proc Natl Acad Sci U S A Biological Sciences 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. National Academy of Sciences 2019-10-15 2019-09-30 /pmc/articles/PMC6800328/ /pubmed/31570620 http://dx.doi.org/10.1073/pnas.1904964116 Text en Copyright © 2019 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/ https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Yano, Kenji
Morinaka, Yoichi
Wang, Fanmiao
Huang, Peng
Takehara, Sayaka
Hirai, Takaaki
Ito, Aya
Koketsu, Eriko
Kawamura, Mayuko
Kotake, Kunihiko
Yoshida, Shinya
Endo, Masaki
Tamiya, Gen
Kitano, Hidemi
Ueguchi-Tanaka, Miyako
Hirano, Ko
Matsuoka, Makoto
GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title_full GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title_fullStr GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title_full_unstemmed GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title_short GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
title_sort gwas with principal component analysis identifies a gene comprehensively controlling rice architecture
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800328/
https://www.ncbi.nlm.nih.gov/pubmed/31570620
http://dx.doi.org/10.1073/pnas.1904964116
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