Comparative transcriptome analysis revealed the molecular mechanism response to salt stress at the seedling stage in hexaploid triticale (× Triticosecale Wittmack)

Hexaploid triticale (×Triticosecale Wittmack), a grain-forage crop, exhibits outstanding stress tolerance and adapts well to the saline soils of the Qaidam Basin in Qinghai Province, China. In this study, we conducted comparative analyses of transcriptomic, phenotypic, and biochemical responses in a salt-tolerant (ST) accession ‘QSM2’ and a salt-sensitive (SS) accession ‘PI429196’, following salt stress treatments for 12, 24, 48 h, and 7 d. The ST accession displayed greater tolerance based on root length, seedling height, and antioxidant enzyme activities. The number of DEGs and overlapping DEGs in ST was more than that in SS at three time points (12, 24, and 48 h). Gene co-expression networks were constructed in response to salt stress, and the brown module correlated significantly with ST under salt stress. A total of 25 core genes responsive to salt stress, showed up-regulated expression level in ST but down-regulated expression in SS. Two candidate genes (TsABCF1 and TsLEA14), encoding ABC transporter F and late-embryogenesis abundant (LEA) protein, were obtained based on the conjoint analysis of the transcriptome and genome-wide associated studies. These findings provide valuable insights for the fine-mapping and cloning of salt-tolerant genes and facilitate the development of salt-tolerance triticale cultivars.