Saltol is one of the most well-known quantitative loci (QTLs) for salinity tolerance in rice. It has been used to develop highly tolerant rice varieties in saline and coastal areas in Southeast Asia, South Asia, and Africa. However, the functional activity of Saltol is not well known, and the molecular marker application of readily developed linked markers in Saltol has not always been successful in the rice breeding programs for salinity tolerance improvement. Interestingly, two BC₂F₉ sister backcrossed inbred lines (BILs), which have been developed by marker-assisted backcrossing utilized the linked markers of Saltol to improve the salinity tolerance of MS11 (a temperate japonica growing in tropical condition). The BILs showed very different phenotypic and stress tolerance, although both contained the Saltol QTL. The genomic similarity of the two BILs was 73%, and we have identified the genomic sites of different genic constitutions between the lines utilizing background genotyping. The stress response of the two BILs showed difference in survival rate, grain yield under highly saline field condition, and SPAD, SES in hydroponic conditions. MS11-SaltolA showed salinity tolerance through Na⁺/K⁺ homeostasis with relatively high K⁺ ion uptake and low Na⁺ ion uptake in the seedling stage. Further genomic analyses with whole genome resequencing is ongoing to study on gene interactions. The developed highly tolerant MS11-SaltolA can be used as an improved donor in rice molecular breeding for high salinity tolerance.

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The SUBMERGENCE 1 (SUB1) locus, conferring tolerance to complete inundation, was identified, and gel-based DNA markers, AEX1 and GnS2, were previously developed for marker-assisted breeding (MAB). However, a high throughput and high specific method, at low cost, is still required to detect Sub1 alleles. Kompetitive Allele Specific PCR (KASP) markers enable high throughput analysis for a large number of seeds, as well as detection of both alleles, in a single reaction. In this study, we developed KASP markers that can distinguish specific alleles at Sub1A loci based on single nucleotide polymorphisms (SNPs). Marker validations were carried out by genotyping of a segregating population with the developed KASP markers. The results from KASP assay and gel-based marker analysis were consistent for Sub1A alleles. KASP markers developed for Sub1A would be helpful due to high accuracy, low cost, and a high throughput genotyping feature in MAB.

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