RNA-seq based Transcriptomic Variations and Expression Analysis of SKC1 gene involved in Salt Tolerance in Green Super Rice

Abstract

Rice (Oryza sativa) is the important staple food crop worldwide, especially in Southeast Asia. About one third of rice cultivation area is under saline soil. Salinity stress is among the major abiotic stresses globally, that inhibits the rice growth and affects crop productivity. Plants have adopted the multiple tolerance mechanisms to tackle salinity stress. This study was carried out to identify such mechanism of salt tolerance at normal field, saline field, and hydroponic condition. The present study investigates the saline tolerance mechanism among the 22 GSR lines along with two local checks. In this study, we screened the experimental rice genotypes with the help of morpho-physiological, biochemical and genetic regulators under normal and salinity stress conditions. Field trial conducted during June, 2020 according to triplicated randomized complete block design (RCBD) with two treatments i.e. normal and salinity condition at NIGAB and Pindibhattian respectively. Morphology based attributes i.e., plant height (PH), number of tillers (NT), grain yield per plant (GY), straw yield per plant (SY), harvest index (HI), salt susceptibility index (SSI), 1000-grain weight (GW), and grain length (GL) were measured at maturity stage. Hydroponic experiment was also conducted at seedling stage to screen the saline tolerant lines. Morpho-physiological attributes include; shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW) and root dry weight (RDW) were taken under control, 140mM and 200mM salt stress. Based on the salinity tolerance ranking, three saline tolerant (NGSR S13, NGSR S19, NGSR S20) and three saline susceptible lines (NGSR S3, NGSR S12, and NGSR S16) were selected for further molecular evaluation experiment. Using online transcriptome data, five differential expressed genes and two already reported genes (SKC1 and qSE3) were selected for expression evaluation in salt tolerant and susceptible lines. RT-PCR was performed to understand the genetic mechanism underlying salinity tolerance among the salt tolerant and susceptible lines. In future, functional validation of the salinity tolerant genes in rice and other crops will help us to understand the genetic mechanism underlying salinity tolerance. Salinity tolerant lines are useful genetic resource for salinity breeding programs.