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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #271470
Title: Genome-wide and fine resolution association studies of 14 agronomic traits in rice land races

Author
item HUANG, XUEHUI - Chinese Academy Of Sciences
item SANG, TAO - Chinese Academy Of Sciences
item ZHAO, QIANG - Chinese Academy Of Sciences
item WEI, XINHUA - Chinese Academy Of Sciences
item FENG, QI - Chinese Academy Of Sciences
item ZHAO, YAN - Chinese Academy Of Sciences
item LI, CANYANG - Chinese Academy Of Sciences
item ZHU, CHUANRANG - Chinese Academy Of Sciences
item LU, TINGTING - Chinese Academy Of Sciences
item ZHANG, ZHIWU - Cornell University
item LI, MENG - Cornell University
item FAN, DANLIN - Chinese Academy Of Sciences
item GUO, YUNLI - Chinese Academy Of Sciences
item WANG, AHONG - Chinese Academy Of Sciences
item WANG, LU - Chinese Academy Of Sciences
item DENG, LIUWEI - Chinese Academy Of Sciences
item LI, WENJUN - Chinese Academy Of Sciences
item LU, YIQI - Chinese Academy Of Sciences
item WENG, QIJUN - Chinese Academy Of Sciences
item LIU, KUNYAN - Chinese Academy Of Sciences
item HUANG, TAO - Chinese Academy Of Sciences
item ZHOU, TAOYING - Chinese Academy Of Sciences
item JING, YUFENG - Chinese Academy Of Sciences
item LI, WEI - Chinese Academy Of Sciences
item ZHANG, LEI - Chinese Academy Of Sciences
item Buckler, Edward - Ed
item QIAN, QIAN - Chinese Academy Of Sciences
item ZHANG, QIFA - Huazhong Agricultural University
item LI, JIAYANG - Chinese Academy Of Sciences
item HAN, BIN - Chinese Academy Of Sciences

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.