Geng Leiyue, Zhang Wei, Zou Tuo, Du Qi, Ma Xiaoding, Cui Di, Han Bing, Zhang Qixing, Han Longzhi
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, China.
Front Plant Sci. 2023 Jan 24;14:1065334. doi: 10.3389/fpls.2023.1065334. eCollection 2023.
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 () was the most promising, as it is known to be associated with salt stress, and its differential expression between the tolerant and sensitive RIL bulks highlights its important role in salt stress response pathways. Our findings provide five stable salt tolerance-related QTLs and one promising candidate gene, which will facilitate breeding for improved salt tolerance in rice varieties and promote the exploration of salt stress tolerance mechanisms in rice.
盐度是影响全球水稻产量的最普遍的非生物胁迫之一。了解耐盐性的遗传基础是培育耐盐水稻品种的关键。已经鉴定出许多QTL来帮助剖析水稻耐盐遗传机制，但只有位于显著QTL中的极少数基因得到了深入研究或精细定位。在此，结合连锁图谱和转录组分析来鉴定稳定QTL潜在的耐盐相关功能候选基因。构建了一个由吉冷1号（盐敏感）和密阳23号（耐盐）杂交衍生的重组自交系（RIL）群体。随后，利用从全基因组重测序开发的2921个重组 bin 标记构建了高密度遗传图谱。通过连锁分析共鉴定出12个控制盐胁迫下标准评价得分的QTL，分布在第2、3、4、6、8和11号染色体上。值得注意的是，本研究检测到5个QTL区间为环境稳定QTL，并通过比较转录组分析验证了它们的功能。通过比较两个亲本和两个混合群体的转录组图谱，我们发现了551个盐胁迫特异性差异表达基因。其中，位于稳定QTL区间的1个差异表达基因被认为是耐盐的有前景的候选基因。根据基因注释，基因（）最有前景，因为已知它与盐胁迫相关，并且其在耐盐和敏感RIL混合群体之间的差异表达突出了其在盐胁迫响应途径中的重要作用。我们的研究结果提供了5个稳定的耐盐相关QTL和1个有前景的候选基因，这将有助于改良水稻品种的耐盐性育种，并促进水稻耐盐胁迫机制的探索。
