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Rice is sensitive to salinity at both the seedling and reproductive stages, and it reduces the grain yield from 50 to 100%. In this study, 27 SNP markers significantly associated with 15 QTLs were identified. Three major QTLs were associated with shoot length (<i>Sal_SL 7.1</i>), shoot sodium content (<i>Sal_Na 1.1</i>) and shoot magnesium content (<i>Sal_Mg 2.1</i>). Five QTLs for root length (<i>Sal_RL 1.1</i>, <i>Sal_RL 3.1</i>, <i>Sal_RL 6.1 Sal_RL 8.1</i> and <i>Sal_RL 12.1</i>), shoot K⁺/Na⁺ homeostasis (<i>Sal_K/Na 1.1</i>, <i>Sal_K/Na 4.1</i>, <i>Sal_K/Na 5.1</i>, <i>Sal_K/Na 7.1</i> and <i>Sal_K/Na 10.1</i>) and single QTLs for shoot potassium (<i>Sal_K 6.1</i>) and calcium content (<i>Sal_Ca 5.1</i>) were also detected. QTL <i>Sal_K/Na 1.1</i> was found responsible for the ionic ratio associated with the <i>Saltol</i> region, and <i>Sal_K/Na 10.1</i> was associated with the gene <i>OSCA1;4</i>, which is a hyperosmolality-gated calcium-permeable channel that acts as an osmosensor under salt stress condition. A candidate gene haplotype analysis revealed ten significant genes, <i>LOC_Os06g03940</i>, <i>LOC_Os10g42820</i>, <i>LOC_Os07g36230</i>, <i>LOC_Os02g06410</i>, <i>LOC_Os06g48610</i>, <i>LOC_Os12g12950</i>, <i>LOC_Os03g12050</i>, <i>LOC_Os08g02690</i>, <i>LOC_Os07g47560</i>, and <i>LOC_Os05g08840</i>, responsible for abiotic stress tolerance. The identified potential candidate genes can be used for functional characterization to understand the complex mechanism of salinity tolerance in rice.