Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

Zilong Guo; Wanneng Yang; Yu Chang; Xiaosong Ma; Haifu Tu; Fang Xiong; Ni Jiang; Hui Feng; Chenglong Huang; Peng Yang; Hu Zhao; Guoxing Chen; Hongyan Liu; Lijun Luo; Honghong Hu; Qian Liu; Lizhong Xiong

doi:10.1016/j.molp.2018.03.018

Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

Mol Plant. 2018 Jun 4;11(6):789-805. doi: 10.1016/j.molp.2018.03.018. Epub 2018 Mar 31.

Authors

Zilong Guo¹, Wanneng Yang², Yu Chang¹, Xiaosong Ma³, Haifu Tu¹, Fang Xiong¹, Ni Jiang⁴, Hui Feng⁵, Chenglong Huang⁶, Peng Yang⁶, Hu Zhao¹, Guoxing Chen⁷, Hongyan Liu³, Lijun Luo³, Honghong Hu¹, Qian Liu⁴, Lizhong Xiong⁸

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
² National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China; College of Engineering, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: ywn@mail.hzau.edu.cn.
³ Shanghai Agrobiological Gene Center, Shanghai 201106, China.
⁴ Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China.
⁵ Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan 430070, China.
⁶ College of Engineering, Huazhong Agricultural University, Wuhan 430070, China.
⁷ MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China.
⁸ National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China. Electronic address: lizhongx@mail.hzau.edu.cn.

PMID: 29614319
DOI: 10.1016/j.molp.2018.03.018

Abstract

Understanding how plants respond to drought can benefit drought resistance (DR) breeding. Using a non-destructive phenotyping facility, 51 image-based traits (i-traits) for 507 rice accessions were extracted. These i-traits can be used to monitor drought responses and evaluate DR. High heritability and large variation of these traits was observed under drought stress in the natural population. A genome-wide association study (GWAS) of i-traits and traditional DR traits identified 470 association loci, some containing known DR-related genes. Of these 470 loci, 443 loci (94%) were identified using i-traits, 437 loci (93%) co-localized with previously reported DR-related quantitative trait loci, and 313 loci (66.6%) were reproducibly identified by GWAS in different years. Association networks, established based on GWAS results, revealed hub i-traits and hub loci. This demonstrates the feasibility and necessity of dissecting the complex DR trait into heritable and simple i-traits. As proof of principle, we illustrated the power of this integrated approach to identify previously unreported DR-related genes. OsPP15 was associated with a hub i-trait, and its role in DR was confirmed by genetic transformation experiments. Furthermore, i-traits can be used for DR linkage analyses, and 69 i-trait locus associations were identified by both GWAS and linkage analysis of a recombinant inbred line population. Finally, we confirmed the relevance of i-traits to DR in the field. Our study provides a promising novel approach for the genetic dissection and discovery of causal genes for DR.

Keywords: GWAS; drought resistance; drought response; image-based trait; natural variation; rice.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Genetic
Droughts*
Genome-Wide Association Study*
Oryza / genetics*
Oryza / physiology*
Phenotype