TY - JOUR
T1 - GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
AU - Yano, Kenji
AU - Morinaka, Yoichi
AU - Wang, Fanmiao
AU - Huang, Peng
AU - Takehara, Sayaka
AU - Hirai, Takaaki
AU - Ito, Aya
AU - Koketsu, Eriko
AU - Kawamura, Mayuko
AU - Kotake, Kunihiko
AU - Yoshida, Shinya
AU - Endo, Masaki
AU - Tamiya, Gen
AU - Kitano, Hidemi
AU - Ueguchi-Tanaka, Miyako
AU - Hirano, Ko
AU - Matsuoka, Makoto
N1 - Funding Information:
ACKNOWLEDGMENTS. We thank Dr. T. Akagi (Okayama University) for suggestions on population genetics, and Y. Hattori (Nagoya University) for technical assistance. This work was supported by the Grant-in-Aid for Advanced Integrated Intelligence Platform Project, JSPS Fellows (Grant 16J08722), Young Scientists (B) (Grant 17K15209), Scientific Research (A) (Grant 17H01458), Postdoctoral Fellowships (Grant 19F19103), and Scientific Research on Innovative Areas (Grants 16H06464 and 16H06468).
Funding Information:
19. C. Dai, H. W. Xue, Rice early flowering1, a CKI, phosphorylates DELLA protein SLR1 to negatively regulate gibberellin signalling. EMBO J. 29, 1916–1927 (2010). Materials and Methods Detailed descriptions of plant materials, population genetic analyses, and molecular methods can be found in the SI Appendix. ACKNOWLEDGMENTS. We thank Dr. T. Akagi (Okayama University) for suggestions on population genetics, and Y. Hattori (Nagoya University) for technical assistance. This work was supported by the Grant-in-Aid for Advanced Integrated Intelligence Platform Project, JSPS Fellows (Grant 16J08722), Young Scientists (B) (Grant 17K15209), Scientific Research (A) (Grant 17H01458), Postdoctoral Fellowships (Grant 19F19103), and Scientific Research on Innovative Areas (Grants 16H06464 and 16H06468). 20. M. Nei, Genetic distance between populations. Am. Nat. 106, 283–292 (1972). 21. W. Wang et al., Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018). 22. X. Huang et al., A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012). 23. S. Ge, T. Sang, B. R. Lu, D. Y. Hong, Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. U.S.A. 96, 14400–14405 (1999). 24. C. J. Holberg et al., Factor analysis of asthma and atopy traits shows 2 major compo-nents, one of which is linked to markers on chromosome 5q. J. Allergy Clin. Immunol. 108, 772–780 (2001). 25. D. I. Boomsma, C. V. Dolan, A comparison of power to detect a QTL in sib-pair data using multivariate phenotypes, mean phenotypes, and factor scores. Behav. Genet. 28, 329–340 (1998). 26. L. Goh, V. B. Yap, Effects of normalization on quantitative traits in association test. BMC Bioinformatics 10, 415 (2009). 27. Y. Wu et al., The QTL GNP1 encodes GA20ox1, which increases grain number and yield by increasing cytokinin activity in rice panicle meristems. PLoS Genet. 12, e1006386 (2016). 28. K. Yano et al., Isolation of a novel lodging resistance QTL gene involved in strigo-lactone signaling and its pyramiding with a QTL gene involved in another mechanism. Mol. Plant 8, 303–314 (2015). 29. D. Fujita et al., NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc. Natl. Acad. Sci. U.S.A. 110, 20431–20436 (2013). 30. G. H. Zhang et al., LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol. Plant 7, 1350–1364 (2014). 31. K. Miura et al., OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet. 42, 545–549 (2010). 32. Y. Jiao et al., Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet. 42, 541–544 (2010). 33. J. Wang et al., Tissue-specific ubiquitination by IPA1 INTERACTING PROTEIN1 modu-lates IPA1 protein levels to regulate plant architecture in rice. Plant Cell 29, 697–707 (2017). 34. S. Wang et al., Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Res. 27, 1142–1156 (2017). 35. Y. Hayami, Demand for fertilizer in the course of Japanese agricultural development. Am. J. Agric. Econ. 46, 766–779 (1964). 36. A. Sasaki et al., Green revolution: A mutant gibberellin-synthesis gene in rice. Nature 416, 701–702 (2002). 37. M. Ashikari et al., Loss-of-function of a rice gibberellin biosynthetic gene, GA20 ox-idase (GA20ox-2), led to the rice ‘green revolution’. Breed. Sci. 52, 143–150 (2002). 38. S. Li et al., Modulating plant growth-metabolism coordination for sustainable agri-culture. Nature 560, 595–600 (2018). PLANT BIOLOGY
Publisher Copyright:
© 2019 National Academy of Sciences. All rights reserved.
PY - 2019/10/15
Y1 - 2019/10/15
N2 - 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.
AB - 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.
KW - gibberellin
KW - GWAS
KW - PCA
KW - Plant architecture
KW - SPINDLY
UR - http://www.scopus.com/inward/record.url?scp=85073310825&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85073310825&partnerID=8YFLogxK
U2 - 10.1073/pnas.1904964116
DO - 10.1073/pnas.1904964116
M3 - Article
C2 - 31570620
AN - SCOPUS:85073310825
SN - 0027-8424
VL - 116
SP - 2162
EP - 21267
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 42
ER -