Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice

作者：Guogen Zhang, Zhiyuan Bi, Jing Jiang, Jingbing Lu, Keyang Li, Di Bai, Xinchen Wang, Xueyu Zhao, Min Li, Xiuqin Zhao, Wensheng Wang, Jianlong Xu, Zhikang Li, Fan Zhang, Yingyao Shi · 发表于：Frontiers in Plant Science · 年份：2023 · DOI：10.3389/fpls.2023.1170641 · 被引用次数：16 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Plant Stress Responses and Tolerance、GABA and Rice Research

Introduction Saline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. Methods To understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES). Results Totally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs ...