Identification of QTLs for reproductive stage salinity tolerance in rice using a cross between CSR28 and BRRI dhan28

Salinity poses a serious threat to rice (Oryza sativa L.) production in coastal regions across the globe. Since salinity tolerance is a complex and polygenic trait, understanding the salt-tolerance mechanisms is key for rice breeding. Breeding efforts can be aided by quantitative trait locus (QTL) mapping for complementary salt tolerance mechanisms in plants. While numerous studies are available on salinity tolerance at the seedling stage, limited studies have been conducted on reproductive stage tolerance in rice due to the difficulty in achieving reliable stage-specific phenotyping techniques. In this study, a BC₁F₂ mapping population consisting of 435 individuals derived from a cross between a salt-tolerant Indian variety, CSR28, and a salt-sensitive Bangladeshi mega variety, BRRI dhan28, was evaluated for yield components after exposure to salinity stress of EC 10 dS/m during the reproductive stage. After selecting extremely tolerant and sensitive progenies, 190 individuals were genotyped by kompetitive allele-specific PCR (KASP) genotyping with 152 high-quality single nucleotide polymorphic (SNP) markers. Consequently, 15 QTLs were identified under reproductive stage salt stress, including plant height, panicle length, number of filled and unfilled spikelets, percent filled spikelets, grain yield, and the Na⁺-K⁺ ratio. Notably, three QTLs, one each for the number of filled spikelets (qNFS10.1), percent filled spikelets (qPFS10.1), and grain yield (qGY10.1), were mapped at the same position (75.9 cM) on chromosome 10. These promising QTLs can be examined further to dissect the molecular mechanisms underlying reproductive stage salinity tolerance in rice.