Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two "high-yield rice" varieties and two "low-yield rice" varieties with contrasting photosynthesis and grain yield characteristics. A total of 2,089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil.

The rice chromosome segment substitution lines (CSSLs) of 'Khao Dawk Mali 105' ('KDML105') genetic background were developed by backcrossing with 'KDML105' rice and transferring the region from chromosome 1 of DH212 which was expected to contain the full putative salt tolerance genetic region. Line of CSSL11, CSSL12, and CSSL16 contained the full putative salt tolerance genetic region were evaluated with the parental lines, 'KDML105' and DH212 at seedling stage of rice. The physiological responses in rice plants were grown under normal condition and 75 mM of NaCl, and then comparative photosynthetic parameters, chlorophyll fluorescence parameters, PhiPS2, ETR, NPQ, as well as growth analysis. In this article, the data of physiological response evaluation in rice at seedling stage after salt stress treatment can be found. This can be useful as the information of the photosynthesis response to salt stress to other rice cultivars and related species.