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

• Published in: Molecular plant Vol. 11; no. 6; pp. 789 - 805
• Main Authors: Guo, Zilong, Yang, Wanneng, Chang, Yu, Ma, Xiaosong, Tu, Haifu, Xiong, Fang, Jiang, Ni, Feng, Hui, Huang, Chenglong, Yang, Peng, Zhao, Hu, Chen, Guoxing, Liu, Hongyan, Luo, Lijun, Hu, Honghong, Liu, Qian, Xiong, Lizhong
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 04.06.2018
• Subjects: Databases, Genetic; drought resistance; drought response; Droughts; Genome-Wide Association Study; GWAS; image-based trait; natural variation; Oryza - genetics; Oryza - physiology; Phenotype; rice; drought response; drought resistance; GWAS; rice; image-based trait; natural variation
• ISSN: 1674-2052; 1752-9867
• DOI: 10.1016/j.molp.2018.03.018

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. A set of highly heritable image traits was identified to monitor dynamic drought responses and to evaluate drought resistance (DR) in rice. GWAS of the image-based and traditional traits revealed a comprehensive genetic architecture of DR in rice. Several image traits are closely correlated to DR in the field and have high potential to be indicative traits in DR breeding.