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Salt stress causes severe reduction in the growth and yield of rice plants. The ability to maintain cellular ion homeostasis is of importance to help the plant survive under salt stress. Salt overly sensitive 1 (SOS1), a plasma membrane Na+/H+ antiporter, has been proven to play critical roles in Na+ exclusion out of the cell, hence contributing to salt tolerance in plants. In this study, we analyzed the natural nucleotide polymorphisms occuring within the entire coding sequence as well as the upstream region of the OsSOS1 gene by comparing the sequences of two contrasting rice genotypes, namely, Nipponbare (salt-sensitive) and Pokkali (salt-resistant). In total, six nucleotide polymorphisms were identified in the coding sequence, and 44 nucleotide substitutions, 225-bp-insertion and 65-bp-deletion were observed in the upstream region of the OsSOS1 gene. Futher in silico analysis revealed that two out of six nucleotide polymorphisms in the coding sequence were non-synonymous (A1600G, G2204A) which led to two amino acid substitutions (T534A, S735N, respectively) positioned in the C-terminal domain of OsSOS1 transporter, but caused no effect on protein properties. In the upstream region of OsSOS1 gene, 44 single nucleotide polymorphisms and two INDELs were identified, in which nucleotide substitutions at position -1392, -1389, -822, -583, +57 and an insertion at position -1035 caused change in cis-regulatory elements. Analysis of OsSOS1 expression revealed that salt induced the expression of the gene in the roots, but not in the leaves in both investigated rice cultivars.
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