Key message <p>Fine mapping of <i>qSSISFH8.1</i>, a quantitative trait locus (QTL) for reproductive stage salinity tolerance in rice to a 640&#xa0;kb region, and qRT-PCR analysis of differentially expressed candidate genes in the region. An indel marker was designed and validated for marker-assisted introgression of the trait into elite rice cultivars</p> Abstract <p>Rice (<i>Oryza sativa</i> L.) is cultivated globally as a staple food crop for about fifty percent of the human population. However, popular high-yielding rice cultivars are sensitive to soil salinity during seedling and reproductive stages of growth. Most of the reported QTL for salinity tolerance in rice span large chromosomal regions, making it difficult to identify the underlying causal genes or utilize these in marker-assisted breeding. Here we present fine mapping of <i>qSSISFH8.1</i>, a robust QTL for reproductive stage salinity tolerance derived from rice landrace Nona Bokra. A population of 4300 F₂ plants from cross between QTL-NIL (near-isogenic lines) with contrasting alleles was genotyped for the QTL-flanking markers to identify 146 recombinants. Thirteen SNPs were identified by targeted re-sequencing of genes in the QTL region and used to group the recombinants based on the crossing over breakpoints. Phenotyping of these recombinants for salinity tolerance in controlled microplots helped narrow down the QTL interval to 640&#xa0;kb. Analysis of differential expression of genes in the region in response to salinity stress and allelic sequence variation, identified genes coding for brassinosteroid insensitive 1-associated receptor kinase, prohibitin, tetraspanin, ATPase 1 and an uncharacterized expressed protein as potential candidates for salinity tolerance underlying <i>qSSISFH8.1</i>. We developed and validated an easy-to-use indel marker ‘RSST8.1indel’ for introgression of the QTL into salinity-sensitive elite rice cultivars.</p>