Salt stress is a major abiotic stress affecting the productivity of rice crop worldwide. This study screened a set of 71 rice genotypes collected from coastal parts of Goa and Karnataka states in India for seedling stage salinity tolerance to identify genotypes alternative to standard salt-tolerant donors Pokkali, FL478, etc. Phenotyping for seedling stage tolerance was carried out under micro plots at an induced salinity of 12 dS/m. For haplotyping, 14 Saltol QTL linked simple sequence repeat (SSR) markers on chromosome 1 were utilized. On the basis of the response to salt stress, 10 genotypes were found tolerant, 16 moderately tolerant, 29 sensitive and 15 as highly sensitive. Among the SSR markers, marker RM10871 was the most polymorphic with a polymorphic information content of 0.90, exhibiting 14 different alleles followed by RM10793 (0.84) and RM3412 (0.80) with 8 and 7 alleles, respectively. These markers also exhibited high values for the effective number of alleles (Ne) and gene diversity (I). The haplotype analysis revealed that the allelic constitution of the Saltol region of 10 tolerant genotypes from our study varied in comparison to the reference tolerant check FL478. Further, the haplotype of three tolerant genotypes, namely, Goa Dhan 2, Panvel 1 and Goa wild rice (GWR) 005 appears to be completely different from the FL478 haplotype indicating tolerance in these genotypes is controlled by genomic region other than Saltol. These three genotypes with probable novel regions for seedling stage salt tolerance can be considered for enhancing salinity tolerance of rice cultivars.

中文翻译：

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不同地方品种、野生稻和水稻渐渗系Sa​​ltol QTL区域的单倍型分析（Oryza sativa L.）

盐胁迫是影响全球水稻产量的主要非生物胁迫。本研究筛选了一组从印度果阿邦和卡纳塔克邦沿海地区收集的 71 种水稻耐盐性水稻基因型，以鉴定替代标准耐盐供体 Pokkali、FL478 等的基因型。诱导盐度为 12 dS/m 的微型图。对于单倍型，14萨尔托使用了 1 号染色体上的 QTL 连锁简单序列重复 (SSR) 标记。根据对盐胁迫的反应，发现10个基因型耐受，16个中等耐受，29个敏感，15个高度敏感。在 SSR 标记中，标记 RM10871 的多态性最高，多态性信息含量为 0.90，表现出 14 个不同的等位基因，其次是 RM10793 (0.84) 和 RM3412 (0.80)，分别具有 8 个和 7 个等位基因。这些标记的有效等位基因数 (Ne) 和基因多样性 (I) 也表现出较高的值。单倍型分析表明，萨尔托与参考耐受检查 FL478 相比，我们研究的 10 个耐受基因型的区域有所不同。此外，三种耐受基因型的单倍型，即 Goa Dhan 2、Panvel 1 和果阿野生稻 (GWR) 005 似乎与 FL478 单倍型完全不同，表明这些基因型中的耐受性受除基因组区域以外的基因组区域控制。萨尔托。这三种基因型可能具有苗期耐盐性的新区域，可考虑用于提高水稻品种的耐盐性。