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United States Department of Agriculture

Agricultural Research Service


Location: Plant, Soil and Nutrition Research

Title: Genome-wide and fine resolution association studies of 14 agronomic traits in rice land races

item Huang, Xuehui
item Sang, Tao
item Zhao, Qiang
item Wei, Xinhua
item Feng, Qi
item Zhao, Yan
item Li, Canyang
item Zhu, Chuanrang
item Lu, Tingting
item Zhang, Zhiwu
item Li, Meng
item Fan, Danlin
item Guo, Yunli
item Wang, Ahong
item Wang, Lu
item Deng, Liuwei
item Li, Wenjun
item Lu, Yiqi
item Weng, Qijun
item Liu, Kunyan
item Huang, Tao
item Zhou, Taoying
item Jing, Yufeng
item Li, Wei
item Zhang, Lei
item Buckler, Edward - Ed
item Qian, Qian
item Zhang, Qifa
item Li, Jiayang
item Han, Bin

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2010
Publication Date: 10/24/2010
Citation: Huang, X., Sang, T., Zhao, Q., Wei, X., Feng, Q., Zhao, Y., Li, C., Zhu, C., Lu, T., Zhang, Z., Li, M., Fan, D., Guo, Y., Wang, A., Wang, L., Deng, L., Li, W., Lu, Y., Weng, Q., Liu, K., Huang, T., Zhou, T., Jing, Y., Li, W., Zhang, L., Buckler IV, E.S., Qian, Q., Zhang, Q., Li, J., Han, B. 2010. Genome-wide and fine resolution association studies of 14 agronomic traits in rice land races. Nature Genetics. 42:961-967.

Interpretive Summary: Uncovering the genetic basis of how diverse landraces have adapted to various agro-climatic conditions since domestication is critical to the food security of the world. The small genome of rice provides an excellent test for applying the latest genome sequencing and statistical genetics tools. This study successfully identified genomic variation across these diverse varieties of rice, and for many simpler traits was very successful in identifying key gene controlling these traits. However, the landraces analysis was less successful for complex traits involved in large-scale adaptation, which suggests that other approaches that involve specially created genetic populations will be needed. This study highlights the power of novel approaches to now tap genetic diversity in diverse rice landraces.

Technical Abstract: Here we report genome sequences of 517 diverse rice land races and the identification of ~3.6 million single nucleotide polymorphisms. A high-density haplotype map of rice genome was constructed using a highly accurate imputation method developed for next-generation sequencing data. Initial genome-wide association studies revealed 80 loci with strong association signals underlying fourteen agronomic traits. We further inspected the genetic architecture of the fourteen agronomic traits that explained ~36% of the phenotypic variance on average, which is much higher than those of GWAS in human. The peak signals for six known loci tied to the previously identified genes at high resolution.

Last Modified: 10/19/2017
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