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

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Abstract

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.

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey

    I. Koc

  2. Department of Biology, Faculty of Science and Arts, Marmara University, 34722, Goztepe, Istanbul, Turkey

    R. Vatansever & I. I. Ozyigit

  3. Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750, Cilimli, Duzce, Turkey

    E. Filiz

  4. Crop Science, University of Illinois at Urbana-Champaign, Champaign, USA

    I. Koc

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Koc, I., Vatansever, R., Ozyigit, I.I. et al. Identification of Differentially Expressed Genes in Chilling-Induced Potato (Solanum tuberosum L.); a Data Analysis Study. Appl Biochem Biotechnol 177, 792–811 (2015). https://doi.org/10.1007/s12010-015-1778-9

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