Salt stress responses and SNP‐based phylogenetic analysis of Thai rice cultivars

Abstract

Genetic diversity is important for developing salt‐tolerant rice (Oryza sativa L.) cultivars. Certain Thai rice accessions display salt tolerance at the adult or reproductive stage, but their response to salinity at the seedling stage is unknown. In this study, a total of 10 rice cultivars/line, including eight Thai cultivars and standard salt‐tolerant cultivar and susceptible line, were screened using a hydroponic system to identify salt‐tolerant genotypes at the seedling stage. Different morphophysiological indicators were used to classify tolerant and susceptible genotypes. Phylogenetic analyses were performed to determine the evolutionary relationships between the cultivars. Results showed that ‘Lai Mahk’, ‘Jao Khao’, ‘Luang Pratahn’, and ‘Ma Gawk’ exhibited salt stress tolerance comparable with the standard salt‐tolerance check ‘Pokkali’. Whole‐exome single‐nucleotide polymorphism (SNP)‐based phylogenetic analysis showed that the Thai rice cultivars were monophyletic and distantly related to Pokkali and IR29. Lai Mahk and Luang Pratahn were found closely related when using the whole‐exome SNPs for the analysis. This is also the case for the analysis of SNPs from 164 salt‐tolerance genes and transcription regulatory genes. The tolerant cultivars shared the same haplotype for 16 genes. Overall, the findings of this study identified four salt‐stress‐tolerant Thai rice cultivars, which could be used in rice breeding programs for salinity tolerance.

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

“…Our comparative analysis of multi-traits and loci also allows us to obtain a bird's eye view of the relationships between several phenotypic and physiological properties, as well as to characterise trait-specific and multi-trait loci (Figures 2, 3). Indeed, analyses of the links between multiple traits have been performed in earlier studies, using the correlations between the phenotype and trait properties e.g., Ninsuwan et al (2013), Wang et al (2013) and Habila et al (2022). However, for the first time in this work, we also examined the correlations between the traits in terms of the similarities of QTL confidence scores assigned to all the SNPs across the genome (Figure 4).…”

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice

“…The numbers of tillers (TILs), panicles (PANs), filled grains (FGs) and unfilled grains (UFGs) were measured after harvesting. The data are expressed as stress susceptibility indices (SSIs), which were calculated by dividing the mean under salt stress by the mean under control conditions [40]. The SSIs were used to draw box plots using the ggplot2 [37] R package.…”

Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

“…Therefore, breeding salt-tolerant rice varieties is the only promising step for ensuring food security in the future ( Niu et al, 2022 ). Molecular studies have opened new doors to fully sequence rice genome and hunt for candidate genes in salt breeding programs ( Habila et al, 2022 ). QTL and genes have shown tremendous results in developing tolerant varieties; however, further studies are needed to get a clear picture ( de Ocampo et al, 2022 ).…”