title: Identification of Differentially Expressed Genes in Chilling-Induced Potato (Solanum tuberosum L.); a Data Analysis Study.
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.
authors.affiliation: Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey.|Crop Science, University of Illinois at Urbana-Champaign, Champaign, USA.
authors.forename: I
authors.initials: I
authors.lastname: Koc
authors.affiliation: Department of Biology, Faculty of Science and Arts, Marmara University, 34722, Goztepe, Istanbul, Turkey.
authors.forename: R
authors.initials: R
authors.lastname: Vatansever
authors.affiliation: Department of Biology, Faculty of Science and Arts, Marmara University, 34722, Goztepe, Istanbul, Turkey.
authors.forename: I I
authors.initials: II
authors.lastname: Ozyigit
authors.affiliation: Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750, Cilimli, Duzce, Turkey. ertugrulfiliz@gmail.com.
authors.forename: E
authors.initials: E
authors.lastname: Filiz
mesh_terms: D058639:Cold-Shock Response / Q000235:genetics*; D020869:Gene Expression Profiling; D050356:Lipid Metabolism / Q000235:genetics; D058977:Molecular Sequence Annotation; D010788:Photosynthesis / Q000235:genetics; D010937:Plant Growth Regulators / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics; D011198:Solanum tuberosum / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics
chemical_list: D010937:Plant Growth Regulators; D014157:Transcription Factors
keywords: COR genes; Cold acclimation; Microarray; Phytohormone; Signal transduction