Shedding light on response of Triticum aestivum cv. Kharchia Local roots to long-term salinity stress through transcriptome profiling

Abstract

Among the various abiotic stresses, salinity is one of the major limitations for production and productivity of wheat. Kharchia Local is the most salt-tolerant wheat cultivar developed from farmers’ selection on salt affected areas of India. Here, to investigate the molecular response of Kharchia Local under salinity stress, transcriptome sequencing of root tissue samples at the anthesis stage was performed. Illumina sequencing generated a total of 82.84 million clean reads and were assembled into 1,18,200 unigenes. A set of 10,805 unigenes were differentially expressed in response to salinity stress. Around 8232 unigene-derived SSRs were mined from these DEGs that can be used as functional molecular markers. Expression pattern of salinity stress-responsive unigenes was validated using real time PCR and results were found to be consistent with that of transcriptome profiling. Functional annotation of DEGs against GO, KEGG, COG and BLASTX using nr protein database was performed. This revealed the upregulation of genes involved in various biological processes including ROS homeostasis, ion transport, signal transduction, ABA biosynthesis and osmoregulation. Genes encoding expansin, xyloglucan endotransglucosylase/hydrolase, dehydrins and peroxidases that take part in enhancement of root growth were found to be upregulated under salinity. This could be the reason for better root growth of Kharchia Local under long-term salinity stress as compared to its susceptible counterpart. The present investigation provides primary information on transcriptome profiling of Kharchia Local roots under long-term salinity stress at the anthesis stage. In conclusion, the data generated in this study provide useful insights in understanding the molecular mechanism of salinity stress tolerance and will also serve as a valuable genomic reservoir for functional characterization of salinity responsive genes to develop tolerant genotypes.