Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress

Wei Wang,Lianjia Zhao,Guorong Yan,Yushan Li,Chaohong Deng,Abudukeyoumu Abudurezike,Ning Liu,Zhibin Zhang,Fan Wang,Shubing Shi

doi:10.1038/s41598-020-77686-8

Abstract

Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress. However, the molecular regulatory mechanism of triticale seedlings under salt stress conditions is still unclear so far. In this study, a salt-responsive transcriptome analysis was conducted to identify candidate genes or transcription factors related to salt tolerance in triticale. The root of salt-tolerant triticale cultivars TW004 with salt-treated and non-salt stress at different time points were sampled and subjected to de novo transcriptome sequencing. Total 877,858 uniquely assembled transcripts were identified and most contigs were annotated in public databases including nr, GO, KEGG, eggNOG, Swiss-Prot and Pfam. 59,280, 49,345, and 85,922 differentially expressed uniquely assembled transcripts between salt treated and control triticale root samples at three different time points (C12_vs_T12, C24_vs_T24, and C48_vs_T48) were identified, respectively. Expression profile and functional enrichment analysis of DEGs found that some DEGs were significantly enriched in metabolic pathways related to salt tolerance, such as reduction–oxidation pathways, starch and sucrose metabolism. In addition, several transcription factor families that may be associated with salt tolerance were also identified, including AP2/ERF, NAC, bHLH, WRKY and MYB. Furthermore, 14 DEGs were selected to validate the transcriptome profiles via quantitative RT-PCR. In conclusion, these results provide a foundation for further researches on the regulatory mechanism of triticale seedlings adaptation to salt stress in the future.

Highlights

Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress
We identified some candidate genes and transcription factors involved in key metabolic pathway that association with salt stress responses in triticale by salt-responsive transcriptome analysis, which will provide a valuable resource for elucidating the molecular mechanisms of triticale salt tolerance
Sequence annotation indicated that 41.71% (366,168), 21.05% (184,767), 21.76% (190,980), 22.19% (194,791), 36.39% (319,455), and 33.72% (296,000) of the uniquely assembled transcripts were annotated to the nr, Gene Ontology (GO), Kyoto Encyclopedia of Gene and Genome (KEGG), Pfam, eggNog, and Swissport databases, respectively

Summary

Introduction

Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress. Numerous genetic improvement investigations into crop plants have been conducted to elucidate changes in the transcriptome-level of species in response to salt stress, such as Arabidopsis5, rice6, peanut[7], sugar b eet8, cotton9, citrus[10], Clerodendrum inerme (L.)[11], Microalgae Dunaliella12, kenaf[13], and wild b arley[14]. There were few studies focusing on identifying important regulatory factors related to salt stress in triticale using bioinformatics methods nowadays as the lack of a reference genome sequence[19,20,21] These studies only focused on their role in the adaptation process after long-term stress, did not provide a global view of the transcriptome at salt-response stage. The cultivation of triticale with high salt tolerance is of great practical benefit for the effective use of saline-alkali land to improve grain yield

Methods

Results

Discussion

Conclusion