Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

作者：Caijing Li, Jindong Liu, Jianxin Bian, Jianxin Bian, Tao Jin, Baoli Zou, Shilei Liu, Xiangyu Zhang, Peng Wang, Jingai Tan, Guangliang Wu, Qin Chen, Yanning Wang, Qi Zhong, Shiying Huang, Mengmeng Yang, Tao Huang, Haohua He, Jianmin Bian, Jianmin Bian · 发表于：BMC Plant Biology · 年份：2021 · DOI：10.1186/s12870-021-03317-7 · 被引用次数：38 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Plant Molecular Biology Research、Rice Cultivation and Yield Improvement

BACKGROUND: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. RESULTS: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2-2, qSR3-1, qSR3-2, qSR3-3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2-1, qSR3-4, qSR3-5, qSR3-6, qSR3-7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring t...