Integrating linkage mapping and comparative transcriptome analysis for discovering candidate genes associated with salt tolerance in rice

作者：Leiyue Geng, Wei Zhang, Tuo Zou, Qi Du, Xiaoding Ma, Di Cui, Bing Han, Qixing Zhang, Longzhi Han · 发表于：Frontiers in Plant Science · 年份：2023 · DOI：10.3389/fpls.2023.1065334 · 被引用次数：23 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、GABA and Rice Research、Plant Stress Responses and Tolerance

Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. Understanding the genetic basis of salt tolerance is key for breeding salt-tolerant rice varieties. Numerous QTLs have been identified to help dissect rice salt-tolerance genetic mechanisms, yet only rare genes located in significant QTLs have been thoroughly studied or fine-mapped. Here, a combination of linkage mapping and transcriptome profiling analysis was used to identify salt tolerance-related functional candidate genes underlying stable QTLs. A recombinant inbred line (RIL) population derived from a cross between Jileng 1 (salt-sensitive) and Milyang 23 (salt-tolerant) was constructed. Subsequently, a high-density genetic map was constructed by using 2921 recombination bin markers developed from whole genome resequencing. A total of twelve QTLs controlling the standard evaluation score under salt stress were identified by linkage analysis and distributed on chromosomes 2, 3, 4, 6, 8 and 11. Notably, five QTL intervals were detected as environmentally stable QTLs in this study, and their functions were verified by comparative transcriptome analysis. By comparing the transcriptome profiles of the two parents and two bulks, we found 551 salt stress-specific differentially expressed genes. Among them, fifteen DEGs located in stable QTL intervals were considered promising candidate genes for salt tolerance. According to gene annotations, the gene OsRCI2-8 ( Os06g0184800 ) was the...