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Salt tolerance mechanisms are regulated by balance in cell ionic concentrations such as K⁺, Na⁺, H⁺, Ca²⁺, and Mg²⁺. In this study, we examined major QTLs for the traits K⁺/Na⁺ homeostasis, shoot magnesium content (Mg²⁺), shoot calcium content (Ca²⁺), and shoot length. The QTLs for K⁺/Na⁺ homeostasis <i>Sod K/Na.1</i> are associated with three candidate genes: <i>LOC_Os02g48290</i>, <i>LOC_Os02g48340, and LOC_Os02g48350</i>, and <i>Sod_Ca.1</i> is associated with the gene <i>LOC_Os08g15020.</i> Three significant candidate gene haplotypes for shoot length, <i>Sod_SL.1</i> (<i>LOC_Os10g36690</i>), sodium content <i>Sod_Na.1</i> (<i>LOC_Os01g41770</i>), and magnesium content <i>Sod_Mg.1</i> (<i>LOC_Os10g31040</i>) were identified. The identified candidate genes encode dehydration response proteins, leucine rich repeat proteins, citrate transporter proteins, and diacylglycerol O-acyltransferase (DGATs), and play a key role in salt and abiotic stress tolerance. The identified novel QTLs and potential candidate genes could be used for functional characterization to help further supplement our understanding of the genetic makeup of sodicity stress tolerance in rice.