Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

Huang, X. and Zhao, Y. and Li, C. and Wang, A. and Zhao, Q. and Li, W. and Guo, Y. and Deng, L. and Zhu, C and Fan, D. and Lu , Y. and Weng, Q. and Liu, K. and Zhou, T. and Jing, Y. and Si, L. and Dong, G. and Huang, T. and Lu, T. and Feng, Q. and Han, B. (2011) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 44. pp. 32-39.

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A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.

Item Type: Article
Additional Information: We thank the China National Rice Research Institute for providing the rice germplasm samples. We thank S. Griffiths and G. Moore for critical reading of the manuscript. We thank Z. Zhang and E.S. Buckler for helping us use the compressed MLM and Z. Ning for assistance with sequence alignment. This work was supported by the Chinese Academy of Sciences (KSCX2-YW-N-094), the Ministry of Agriculture of China (2011ZX08001-004 and 2011ZX08009-002), the National Natural Science Foundation of China (30821004) and the Ministry of Science and Technology of China (2011CB100205) to B.H.
Author Affiliation: Shanghai Institutes for Biological Sciences(China)
Subjects: Crop Improvement
Divisions: Other Crops
Depositing User: Mr Siva Shankar
Date Deposited: 29 Dec 2011 08:55
Last Modified: 29 Dec 2011 09:08
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