Salt tolerance is an important complex trait in rice which helps the plant to survive under salt stress condition. The complexity of salt tolerance is governed by many genes which could be identified efficiently by genome wide association study (GWAS). In the present study, we evaluated 180 diverse rice accessions for salinity tolerance at reproductive stage and successfully genotyped them using simple sequence repeats markers covering all 12 chromosomes. Eleven physiological parameters which include Na⁺, K⁺, Ca²⁺, Mg²⁺ content in stem and leaves and two important morphological traits grain yield and salt injury score were measured under control and saline conditions at reproductive stage. Population structure analysis revealed four subgroups and admixture level ranged from 0.70 to 57.2%. Association study using mixed linear model controlling both structure and kinship, identified 28 significant marker-trait associations and out of which 19 associations were identified for Na⁺, K⁺, Na⁺/K⁺ uptake in stem and leaves. The phenotypic variance for these associations ranged from 5.12 to 13.37%. The position of several associated markers was found close to candidate genes like transcription factors, membrane transporters, signal transducers which have previously shown to play active roles of salinity tolerance in rice. The present GWAS was successful in unravelling genomic regions that regulate ionic homoeostasis in rice. Furthermore, the salinity tolerant accessions identified during the screening could become important resource for breeding programs.

耐盐性是水稻的一项重要复杂性状，可帮助植物在盐胁迫条件下生存。耐盐性的复杂性由许多基因决定，这些基因可以通过全基因组关联研究（GWAS）有效地鉴定。在本研究中，我们评估了180种不同水稻种质在生殖阶段的耐盐性，并使用覆盖所有12条染色体的简单序列重复标记成功地对它们进行了基因分型。11种生理参数，包括Na ⁺，K ⁺，Ca 2 ⁺，Mg ²⁺在对照和盐分条件下，在繁殖期测定茎叶的含量和两个重要的形态学特征，即籽粒产量和盐害得分。人口结构分析显示四个亚组，混合水平为0.70％至57.2％。使用控制结构和亲缘关系的混合线性模型进行关联研究，确定了28个重要的标记-性状关联，其中有19个关联被确定为Na ⁺，K ⁺，Na ⁺ / K ⁺吸收茎和叶。这些关联的表型方差范围为5.12％至13.37％。发现几个相关标记的位置接近候选基因，如转录因子，膜转运蛋白，信号转导子，这些基因先前已显示出在水稻中耐盐度的积极作用。目前的GWAS成功地揭示了调节水稻离子同调的基因组区域。此外，筛选过程中确定的耐盐耐性材料可能成为育种计划的重要资源。