Coexpression gene network analysis of cold-tolerant Solanum commersonii reveals new insights in response to low temperatures

Salvatore Esposito, Riccardo Aversano, James Bradeen, Vincenzo D'Amelia, Clizia Villano, Domenico Carputo

Research output: Contribution to journalArticlepeer-review

Abstract

Among abiotic stressors, cold is one of the most harmful for the cultivated potato (Solanum tuberosum L.), a frost-sensitive crop. RNA sequencing (RNA-seq) profiling of two different clones of wild potato (S. commersonii Dun.) contrasting in their capacity to withstand low temperatures revealed a higher number of differentially expressed genes (DEGs) under nonacclimated conditions (NAC) in tolerant clone cmm1T vs. the susceptible cmm6-6 (1,002 and 8,055 DEGs, respectively). By contrast, the number of DEGs was much more comparable when both genotypes were under acclimated conditions (AC). Indeed, a total of 5,650 and 8,936 DEGs were detected in the tolerant genotype vs. the susceptible. Gene ontology (GO) classification under NAC showed a significant role for transcription regulation, lignin catabolic genes, and regulation of plant type secondary cell wall in the cold-tolerant genotypes, suggesting an important role in conferring tolerance response. By contrast, response to stress and response to stimuli were enriched GO categories in both clones under AC. Unsigned weighted correlation networks analysis (WGCNA) allowed identification of coexpressed hub genes with possible main regulatory functions and major impacts on the phenotype. Among those identified, we clarified the role of CBF4. This gene showed contrasting expression profiles in the two clones under NAC, being induced in cold-tolerant cmm1T but suppressed in susceptible cmm6-6. By contrast, under AC, CBF4 was upregulated in both clones. Our study provides a global understanding of mechanisms involved following exposure to NAC and AC in S. commersonii. The mechanisms described here will inform future investigations for detailed validation in studies regarding cold tolerance in plants.

Original languageEnglish (US)
Pages (from-to)3538-3550
Number of pages13
JournalCrop Science
Volume61
Issue number5
DOIs
StatePublished - Feb 22 2021

Bibliographical note

Funding Information:
This work was carried out within the project ‘Development of potato genetic resources for sustainable agriculture’ (PORES) funded by the University of Naples Federico II.

Publisher Copyright:
© 2021 The Authors. Crop Science published by Wiley Periodicals LLC on behalf of Crop Science Society of America

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