Transcriptome analysis of genes involved in the pathogenesis mechanism of potato virus Y in potato cultivar YouJin

Tianqi Yang; Xingyue Zhao; Jinjiang Bai; Wenxia Lv; Qi Chen; Jun Hu; Guangjing Liu; Yuanzheng Zhao; Hongyou Zhou; Mingmin Zhao; Hongli Zheng

doi:10.3389/fmicb.2024.1353814

Transcriptome analysis of genes involved in the pathogenesis mechanism of potato virus Y in potato cultivar YouJin

Front Microbiol. 2024 Mar 6:15:1353814. doi: 10.3389/fmicb.2024.1353814. eCollection 2024.

Authors

Tianqi Yang^#¹, Xingyue Zhao^#¹, Jinjiang Bai¹, Wenxia Lv², Qi Chen³, Jun Hu², Guangjing Liu², Yuanzheng Zhao⁴, Hongyou Zhou^{1

5}, Mingmin Zhao^{1

5}, Hongli Zheng¹

Affiliations

¹ College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China.
² Inner Mongolia Zhongjia Agricultural Biotechnology Co., Siziwang Banner, China.
³ Siziwang Banner Agricultural and Livestock Products Quality and Safety Inspection and Testing Station, Siziwang Banner, China.
⁴ Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
⁵ Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China.

^# Contributed equally.

Abstract

Introduction: Potatoes (Solanum tuberosum L.) can be infected by various viruses, but out of all of viruses, the potato virus Y (PVY) is the most detrimental. Research shows that the potato cultivar YouJin is especially vulnerable to PVY and displays severe symptoms, including leaf vein chlorosis, curled leaf margins, large necrotic spots on the leaf blades, and the growth of small new leaves.

Methods: PVY infection in potato cultivar YouJin was confirmed through symptom observation, RT-PCR, and Western blot analysis. Transcriptome sequencing was used to analyze the genes associated with PVY pathogenesis in this cultivar.

Result: Transcriptome analysis of differential genes was conducted in this study to examine the pathogenesis of PVY on YouJin. The results showed that 1,949 genes were differentially regulated, including 853 upregulated genes and 1,096 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that carbohydrate synthesis and metabolism pathways were suppressed, and electron transferase and hydrolase activities were reduced. Moreover, there were increased expression levels of protein kinase genes. By focusing on plant-pathogen interaction pathways, six core genes all upregulating the WARK family of transcription factors were obtained. Additionally, a constructed PPI network revealed the identification of key modular differential genes, such as downregulated photosynthesis-related protein genes and upregulated AP2/ERF-ERF transcription factors. Functional network enrichment analysis revealed that PVY infection limited RNA metabolism, glutathionylation, and peroxiredoxin activity while triggering the expression of associated defense genes in YouJin. After analyzing the above, 26 DEGs were screened and 12 DEGs were confirmed via RT-qPCR.

Conclusion: These results establish a hypothetical framework for clarifying the pathogenesis of PVY in the YouJin variety of potatoes, which will help design the disease resistance of YouJin.

Keywords: RNA-Seq; candidate genes; functional analysis; potato cultivar YouJin; potato virus Y.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by grants for the major project of the Nature Science Foundation of Inner Mongolia of China (grant no. 2021ZD06) to MZ, the potato revealed as the most important project of Inner Mongolia of China (2022JBGS0037) to HYZ, and the China Agriculture Research System of MOF and MARA (grant no. CARS-07-C-3) to HYZ.