Transcriptome resequencing analysis of the responses of Ty-5-Mediated resistance to TYLCV via in resistant vs. susceptible tomato cultivars
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Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomato in both tropical and subtropical regions. Five major genes (Ty-1, Ty-2, Ty-3, Ty-4 and Ty-5) from wild tomato species have been associated with resistance to TYLCV. Researchers have recently attempted to determine the functions of these resistance genes, but molecular mechanisms underlying the observed resistance remain unclear. Here, resistant (cv. CLN3212A-23, carrying Ty-5) and susceptible (cv. Moneymaker) plants were either left untreated (R and S, respectively) or artificially inoculated with TYLCV via Agrobacterium-mediated transformation (RT and ST, respectively). The transcriptomes of the plants in the four groups were then analyzed by RNA-Seq, and the results identified 8,639 differentially expressed genes (DEGs) between the R and RT groups, 2,818 DEGs between the RT and ST groups, 8,899 DEGs between the S and ST groups, and 707 DEGs between the R and S groups. The gene expression profiles in both the resistant and susceptible tomato cultivars appeared to undergo notable changes after viral inoculation, and functional classification revealed that most DEGs were associated with 18 GO terms. Moreover, the functional classification of the response of Ty-5-carrying tomato plants to TYLCV infection identified the importance of the GO term “response to stimulus” in the BP category, which is related to disease resistance. In addition, 28 genes were significantly enriched in the “Plant hormone signal transduction”, “Carbon metabolism”, “ Carbon fixation in photosynthetic organisms ” and “ Glutathione metabolism ” pathways. The differential expression levels of 12 select genes were confirmed by quantitative real-time PCR. The present study indicates that the Ty-5 gene activates the expression of multiple genes involved in the resistance process and will aid a more in-depth understanding of the effects of the Ty-5 gene on resistance based on its molecular mechanism with the aim of improving TYLCV disease management in tomato.
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2018. Transcriptome resequencing analysis of the responses of Ty-5-Mediated resistance to TYLCV via in resistant vs. susceptible tomato cultivars. PeerJ Preprints 6:e26578v1 https://doi.org/10.7287/peerj.preprints.26578v1Author comment
This is a submission to PeerJ for review.
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Supplemental Information
Gene Ontology and enrichment of DEGs in different group comparisons, including RT-VS-ST, R-VS-RT, R-VS-S and S-VS-ST
GO enrichment of DEGs for the biological process category
GO enrichment of DEGs for cellular component category in RT-VS-ST, R-VS-RT and S-VS-ST
GO enrichment of DEGs for molecular function category in RT-VS-ST, R-VS-RT and S-VS-ST
DEGs identified in the S-VS-ST comparison by DEseq2 methods
DEGs identified in the RT-VS-ST comparison by DEseq2 methods
DEGs identified in the R-VS-RT comparison by DEseq2 methods
DEGs identified in the R-VS-S comparison by DEseq2 methods
Expression values of 12 genes in the S, R, RT and ST groups obtained by RNA-Seq and RT-qPCR analysis
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Qingqi Chen conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Xiangyang Xu authored or reviewed drafts of the paper.
Jingbin Jiang conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper.
Jingfu Li conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
Field experiments were approved by Northeast Agricultural University.
Data Deposition
The following information was supplied regarding data availability:
The raw data are provided as Supplemental Files.
Funding
This research was supported by the National 13th Five Year Plan Key Research Project (2016YFD0101703). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
