QTL mapping and analysis for drought tolerance in rice by genome-wide association study

Yueming Yi; Muhammad A Hassan; Xinxin Cheng; Yiru Li; Huan Liu; Wuyun Fang; Qian Zhu; Shimei Wang

doi:10.3389/fpls.2023.1223782

QTL mapping and analysis for drought tolerance in rice by genome-wide association study

Front Plant Sci. 2023 Jul 25:14:1223782. doi: 10.3389/fpls.2023.1223782. eCollection 2023.

Authors

Yueming Yi^{1

2}, Muhammad A Hassan^{1

3}, Xinxin Cheng², Yiru Li^{1

2}, Huan Liu^{1

3}, Wuyun Fang^{1

3}, Qian Zhu^{1

3}, Shimei Wang^{1

3}

Affiliations

¹ Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.
² College of Agriculture, Anhui Science and Technology University, Fengyang, China.
³ Key Laboratory of Rice Genetics and Breeding in Anhui Province, Hefei, China.

Abstract

Rice drought resistance is a complicated quantitative feature involving a range of biological and agronomic variables, but little is known about the underlying genetics and regulatory mechanisms that regulate drought tolerance. This study used 120 recombinant inbred lines (RILs), derived from a cross between drought tolerant Lvhan 1 and susceptible Aixian 1. The RILs were subjected to drought stress at the first ear stage, and phenotypic data of 16 agronomic and physiological traits under varying conditions were investigated. Genome-wide association study (GWAS) on the drought resistance index of traits was carried out. A total of 9 quantitative trait loci (QTLs) associated with drought-related traits were identified on chromosomes 2, 6, 7, 8, 9, and 10, which includes QTLs for plant height (PH) qPH10.1, effective panicles number (EPN) qEPN6.1, panicle length (PL) qPL9.1, thousand-grain weight (TGW) qTGW2.1, qTGW6.1, qTGW8.1, leaf length (LL) qLL7.1, leaf width (LW) qLW7.1, and leaf area (LA) qLA7.1. The fraction of phenotypic variation explained by individual QTL varied from 10.6% to 13.9%. Except for days to flowering (DTF), the mean values of all traits under normal water management conditions were considerably higher than those under drought conditions. Except for the DTF, the drought resistance index of all rice traits was less than 1, indicating that drought treatment reduced the EPN, FGPP, SSR, PH, and LA, which affected the growth and development of rice. The drought resistance index of DTF was 1.02, indicating that drought prolonged the heading time of rice and diminish the yield parameters. Along with identifying QTLs, the results also predicted ten candidate genes, which are directly or indirectly involved in various metabolic functioning related to drought stress. The identification of these genomic sites or QTLs that effectively respond to water scarcity will aid in the quest of understanding the drought tolerance mechanisms. This study will facilitate the marker-assisted rice breeding and handy in the breeding of drought-tolerant rice varieties.

Keywords: agronomic yield traits; drought tolerance; genome-wide association studies; quantitative trait loci (QTL); rice.

Grants and funding

The work was supported by a grant from the Anhui Natural Science Foundation Project (2208085QC82; 1908085MC93), the Young Talent Project of Anhui Academy of Agricultural Sciences, Asian Cooperation Fund Project (125001012000210004), and Anhui Provincial Key Research and Development Program (202104f06020017).