Identification of Differentially Expressed Genes in Chilling-Induced Potato (Solanum tuberosum L.); a Data Analysis Study

• Published in: Applied biochemistry and biotechnology Vol. 177; no. 4; pp. 792 - 811
• Main Authors: Koc, I, Vatansever, R, Ozyigit, I. I, Filiz, E
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.10.2015; Springer Nature B.V
• Subjects: acclimation; Analysis; Biochemistry; Biotechnology; calcium; Chemistry; Chemistry and Materials Science; Cold; cold stress; cold tolerance; cold treatment; Cold-Shock Response - genetics; enzyme activity; gene expression; Gene Expression Profiling; gene expression regulation; Genes; lipid metabolism; Lipid Metabolism - genetics; Molecular Sequence Annotation; photosynthesis; Photosynthesis - genetics; Plant Growth Regulators - genetics; plant hormones; Potatoes; protein kinases; signal transduction; Signal Transduction - genetics; Solanum; Solanum tuberosum; Solanum tuberosum - cytology; Solanum tuberosum - genetics; Solanum tuberosum - metabolism; Solanum tuberosum - physiology; Studies; Time Factors; transcription factors; Transcription Factors - genetics; Signal transduction; Phytohormone; Microarray; genes; Cold acclimation; COR genes
• DOI: 10.1007/s12010-015-1778-9
• ISSN: 0273-2289

Cold stress, as chilling (<20 °C) or freezing (<0 °C), is one of the frequently exposed stresses in cultivated plants like potato. Under cold stress, plants differentially modulate their gene expression to develop a cold tolerance/acclimation. In the present study, we aimed to identify the overall gene expression profile of chilling-stressed (+4 °C) potato at four time points (4, 8, 12, and 48 h), with a particular emphasis on the genes related with transcription factors (TFs), phytohormones, lipid metabolism, signaling pathway, and photosynthesis. A total of 3504 differentially expressed genes (DEGs) were identified at four time points of chilling-induced potato, of which 1397 were found to be up-regulated while 2107 were down-regulated. Heatmap showed that genes were mainly up-regulated at 4-, 8-, and 12-h time points; however, at 48-h time point, they inclined to down-regulate. Seventy five up-regulated TF genes were identified from 37 different families/groups, including mainly from bHLH, WRKY, CCAAT-binding, HAP3, and bZIP families. Protein kinases and calcium were major signaling molecules in cold-induced signaling pathway. A collaborated regulation of phytohormones was observed in chilling-stressed potato. Lipid metabolisms were regulated in a way, highly probably, to change membrane composition to avoid cold damage and render in signaling. A down-regulated gene expression profile was observed in photosynthesis pathway, probably resulting from chilling-induced reduced enzyme activity or light-triggered ROSs damage. The findings of this study will be a valuable theoretical knowledge in terms of understanding the chilling-induced tolerance mechanisms in cultivated potato plants as well as in other Solanum species.