Li Caijing, Lu Changsheng, Zou Baoli, Yang Mengmeng, Wu Guangliang, Wang Peng, Cheng Qin, Wang Yanning, Zhong Qi, Huang Shiying, Huang Tao, He Haohua, Bian Jianmin
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, China.
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, China.
Front Plant Sci. 2022 Jul 15;13:934515. doi: 10.3389/fpls.2022.934515. eCollection 2022.
Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as , and , are located in these QTL candidates. Among the 25 novel QTLs, co-localized with on chromosome 1, and and co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for () and seven for (), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for and four for ) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the , and genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.
盐胁迫是限制水稻产量的因素之一，研究人员的一项重要任务是培育耐盐性强的水稻。在本研究中，使用211份水稻种质来测定耐盐发芽性（STG）指标，并利用36727个单核苷酸多态性（SNP）进行全基因组关联研究（GWAS）。相对发芽势（RGE）、相对发芽指数（RGI）、相对活力指数（RVI）、相对平均发芽时间（RMGT）、相对芽长（RSL）和相对根长（RRL）用于测定水稻的STG指标。在60和100 mM NaCl条件下，在9个染色体区域共鉴定出43个数量性状基因座（QTL），其中RGE相关的有15个、RGI相关的有6个、RVI相关的有7个、RMGT相关的有3个、RSL相关的有1个、RRL相关的有11个。对于这些与STG相关的QTL，有18个QTL与先前的研究共定位，一些已鉴定的耐盐基因，如 、 和 位于这些QTL候选区域。在25个新的QTL中， 与1号染色体上的 共定位， 与3号染色体上的 共定位。根据RNA测序数据库，发现16个基因，包括9个 （ ）相关基因和7个 （ ）相关基因，在对照和盐处理之间的表达水平存在显著差异。此外，分析了这些差异表达基因的表达模式，发现9个基因（5个 相关基因和4个 相关基因）在发芽期的胚中高表达。对这9个基因的单倍型分析表明，在 、 和 基因中具有优良单倍型的水稻品种具有较高的STG。GWAS验证了已知的耐盐基因，并鉴定出了新的基因座，这些基因座可以丰富当前与耐盐性相关的基因库。本研究中鉴定出的具有高STG和显著基因座的资源在耐盐性育种中可能具有潜在用途。
