Identification, characterization and validation of the genes involved in salt tolerance of the rice (Oryza sativa L. indica) landrace Horkuch and its segregating population using RAD-genotyping and RNA-sequencing under salinity stress

Abstract

Plants being sessile organisms, possess excellent means of sensing and regulation to adjust with the environment and its change. Molecular exploration of indigenous landraces adapted to various stresses in such environments can therefore be useful in understanding their mechanism of adaptation and tolerance. Due to climate change the world is losing more and more cultivable lands affected by drought, flooding salinity, etc., leading to food insufficiencies. The rice landrace Horkuch (Oryza sativa) is adapted to the saline conditions in the southern coast of Bangladesh and maintains efficient photosynthesis and detoxification under salt stress, but does not have enough yield to meet the farmers’ needs. Therefore, this study was aimed at finding the genetic loci and genes responsible for this tolerance and their heritability in populations derived from it. To this end, reciprocal crosses were made from salt tolerant Horkuch and high yielding but sensitive IR29. A set of the reciprocal F 2:3 population containing 300 individuals was genotyped using DArTSeq™ for discovering SNP markers and phenotyped under salt stress, both at seedling and reproductive stages when rice is most sensitive. DArTSeq™ is a restriction site associated, species-based intelligently designed next generation sequencing method which allowed reliable discovery of a large number of SNPs. A robust combined Linkage map was generated from the polymorphic SNPs identified from both populations followed by identification of multiple novel QTLs. QTLs for root length, potassium content and sodium content at seedling stage as well as spikelet fertility, days to maturity, seed breadth, plant height, grain weight, harvest index, etc., have been identified at the reproductive stage. Selected plants from the population, containing several phenotypic QTLs (pQTLs) from both seedling and reproductive stage were identified. These can therefore be used for introgression and pyramiding of multiple tolerance loci into commercial genotypes. A subset of the same combined population were studied for the gene expression patterns under 150mM stress at seedling and reproductive stage using 3ʹ tag-based RNAseq method. Certain correlations were observed between the superior physiological performance of the tolerant versus sensitive progenies and the differential pattern of gene expression in leaf and root tissues under salt stressed and control. Potential list of candidate genes were generated based on the differential expression related to G protein coupled receptor signaling pathway, carbohydrate metabolic process, potassium transport, calcium dependent signaling, water deprivation, better ROS scavenging, growth and photosynthesis.