School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
Sci Rep. 2020 Dec 4;10(1):21259. doi: 10.1038/s41598-020-78256-8.
Salinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.
盐度是水稻种植的主要非生物限制因素。水稻种质中存在丰富的耐盐特性天然变异。由于很少有研究关注对盐胁迫反应不同的水稻基因型的基因组水平变异，因此需要对不同遗传材料进行基因组重测序，以阐明耐盐机制的分子基础。对两个耐盐（Pokkali 和 Nona Bokra）和三个盐敏感（Bengal、Cocodrie 和 IR64）水稻基因型的全基因组序列进行了分析。共生成了 4.13 亿个读数，平均基因组覆盖率为 93%，平均测序深度为 18X。对 DNA 多态性的分析表明，2347 个非同义 SNP 和 51 个移码突变可以区分耐盐和盐敏感基因型。将全基因组多态性信息与 QTL 定位和表达谱数据相结合，鉴定出 396 个在编码区具有大效应变异的差异表达基因。这些基因参与多种耐盐机制，如离子转运、氧化应激耐受、信号转导和转录调控。本研究中鉴定的全基因组 DNA 多态性和有前途的候选基因代表了耐盐水稻品种分子育种的宝贵资源。
