Fine Mapping and Expression Analysis of QTLs for Salinity Tolerance in Rice Oryza Sativa L cv CSR 27

Abstract

Soil salinity is a major abiotic stress limiting rice production in about thirty percent of the rice growing area worldwide. This trait is controlled by quantitative trait loci (QTLs), showing continuous phenotypic variation in the rice populations. Identification of genes controlling quantitative traits is difficult using any single approach due to complex inheritance of the trait and limited resolving power of the individual techniques. In this study, a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of candidate genes for salt tolerance in rice. A population of 216 recombinant inbred lines (RILs) derived from a cross between salt-tolerant variety CSR 27 and salt-susceptible variety MI 48 of rice was used to map quantitative trait loci (QTL) for salt ion concentrations in different tissues and salt susceptibility index (SSI) for spikelet fertility, grain weight and grain yield. Nine significant QTLs were mapped on chromosome 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. The QTL intervals on chromosome I and 8 mapped earlier in F2 population were narrowed down to 0.4 Mbp and 8 Mbp, respectively. In total, 2681 genes were located in the nine QTL intervals, making it difficult to pinpoint the candidate genes responsible for the trait. Similarly, microarray transcriptome profiling of the seedlings of tolerant and susceptible parents grown under control and salt stress showed 798 and 2407 differentially expressed gene probes, respectively. Further, by analyzing pools of RNA extracted from ten each of extreme tolerant and extreme susceptible RILs (bulked transcriptome profiling) to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to thirty only. Two of these genes, namely integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals...