Comparative transcriptome responses of leaf and root tissues to salt stress in wheat strains with different salinity tolerances

Background: Salinity stress is a major adverse environmental factor that can limit crop yield and restrict normal land use. The selection of salt-tolerant strains and elucidation of the underlying mechanisms by plant breeding scientists are urgently needed to increase agricultural production in arid and semi-arid regions. Results: In this study, we selected the salt-tolerant wheat (Triticum aestivum) strain ST9644 as a model to study differences in expression patterns between salt-tolerant and salt-sensitive strains. High-throughput RNA sequencing resulted in more than 359.10 Gb of clean data from 54 samples, with an average of 6.65 Gb per sample. Compared to the IWGSC reference annotation, we identified 50,096 new genes, 32,923 of which have functional annotations. Comparisons of abundances between salt-tolerant and salt-sensitive strains revealed 3,755, 5,504, and 4,344 genes that were differentially expressed at 0, 6, and 24 h, respectively, in root tissue under salt stress. KEGG pathway analysis of these genes showed that they were enriched for phenylpropanoid biosynthesis (ko00940), cysteine and methionine metabolism (ko00270), and glutathione metabolism (ko00480). We also applied weighted gene co-expression network analysis (WGCNA) analysis to determine the time course of root tissue response to salt stress and found that the acute response lasts >6 h and ends before 12 h. We also identified key alternative splicing factors showing different splicing patterns in salt-sensitive and salt-tolerant strains; however, only few of them were differentially expressed in the two groups. Conclusion: Our results offer a better understanding of wheat salt tolerance and improve wheat breeding.