Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai 600113, Tamil Nadu, India.
Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram 603203, Tamil Nadu, India.
Gene. 2019 Sep 10;713:143976. doi: 10.1016/j.gene.2019.143976. Epub 2019 Jul 12.
Naturally evolved saline tolerant rice landraces found along the coastline of India are a valuable genomic resource to explore the complex, polygenic nature of salinity tolerance. In the present study, a set of 28 genome wide SSR markers, 11 salt responsive genic SSR markers and 8 Saltol QTL linked SSR markers were used to estimate genetic relatedness and population structure within a collection of 47 rice landraces (including a tolerant and 2 sensitive checks) originating from geographically divergent coastal regions of India. All three marker types identified substantial genetic variation among the landraces, as evident from their higher PIC values (0.53 for genomic SSRs, 0.43 for Genic SSRs and 0.59 for Saltol SSRs). The markers RM431, RM484 (Genomic SSRs), OsCAX (D), OsCAX (T) (Genic SSRs) and RM562 (Saltol SSR) were identified as good candidates to be used in breeding programs for improving salinity tolerance in rice. STRUCTURE analysis divided the landraces into five distinct populations, with classification correlating with their geographical locations. Principal coordinate and hierarchical cluster analyses (UPGMA and neighbor joining) are in close agreement with STRUCTURE results. AMOVA analysis indicated a higher magnitude of genetic differentiation within individuals of groups (58%), than among groups (42%). We also report the development and validation of a new Cleavage Amplified Polymorphic Sequence (CAPS) marker (OsHKT1;5V395) that targets a codon in the sodium transporter gene OsHKT1;5 (Saltol/SKC1 locus) that is associated with sodium transport rates in the above rice landraces. The CAPS marker was found to be present in all landraces except in IR29, Kamini, Gheus, Matla 1 and Matla 2. Significant molecular genetic diversity established among the analyzed salt tolerant rice landraces will aid in future association mapping; the CAPS marker, OsHKT1;5V395 can be used to map rice landraces for the presence of the SNP (Single Nucleotide Polymorphism) associated with increased sodium transport rates and concomitant salinity tolerance in rice.
在印度沿海地区发现的自然进化的耐盐水稻地方品种是探索耐盐性这一复杂多基因性状的宝贵基因组资源。本研究利用一套 28 个基因组 SSR 标记、11 个盐响应基因 SSR 标记和 8 个 Saltol QTL 连锁 SSR 标记，对来自印度地理上不同沿海地区的 47 个水稻地方品种（包括一个耐盐品种和 2 个敏感对照品种）进行遗传关系和群体结构分析。所有三种标记类型都在地方品种中鉴定出了大量的遗传变异，这从它们更高的 PIC 值（基因组 SSR 为 0.53，基因 SSR 为 0.43，Saltol SSR 为 0.59）中可以看出。标记 RM431、RM484（基因组 SSR）、OsCAX（D）、OsCAX（T）（基因 SSR）和 RM562（Saltol SSR）被鉴定为可用于改良水稻耐盐性的育种计划中的良好候选标记。STRUCTURE 分析将地方品种分为五个不同的群体，分类与地理位置相关。主坐标和层次聚类分析（UPGMA 和邻接法）与 STRUCTURE 结果非常吻合。AMOVA 分析表明，个体内的遗传分化程度高于群体间的遗传分化程度（个体内为 58%，群体间为 42%）。我们还报告了一个新的 Cleavage Amplified Polymorphic Sequence (CAPS) 标记（OsHKT1;5V395）的开发和验证，该标记针对钠离子转运体基因 OsHKT1;5 中的一个密码子（Saltol/SKC1 位点），该基因与上述水稻地方品种的钠离子转运率有关。该 CAPS 标记存在于除 IR29、Kamini、Gheus、Matla 1 和 Matla 2 以外的所有地方品种中。对分析的耐盐水稻地方品种进行的分子遗传多样性研究将有助于未来的关联图谱分析；CAPS 标记 OsHKT1;5V395 可用于对水稻地方品种进行图谱绘制，以鉴定与钠离子转运率增加和水稻耐盐性相关的 SNP（单核苷酸多态性）的存在。
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