Meta-analysis of transcriptomic responses to cold stress in plants
Chiara Vergata A # , Sanaz Yousefi B # , Matteo Buti C * , Federica Vestrucci
A , Mansour Gholami B , Hassan Sarikhani B , Seyed Alireza Salami D and Federico Martinelli A *
+ Author Affiliations
- Author Affiliations
A Department of Biology, University of Florence, Firenze, Italy.
B Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran.
C Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Firenze, Italy.
D Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Tehran, Tehran, Iran.
* Correspondence to: matteo.buti@unifi.it, federico.martinelli@unifi.it
# These authors contributed equally to this paper
Handling Editor: Thomas Roberts
Functional Plant Biology 49(8) 704-724 https://doi.org/10.1071/FP21230
Submitted: 6 August 2021 Accepted: 10 March 2022 Published: 5 April 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Transcriptomic analyses are needful tools to gain insight into the molecular mechanisms underlying plant responses to abiotic stresses. The aim of this study was to identify key genes differentially regulated in response to chilling stress in various plant species with different levels of tolerance to low temperatures. A meta-analysis was performed using the RNA-Seq data of published studies whose experimental conditions were comparable. The results confirmed the importance of ethylene in the hormonal cross-talk modulating the defensive responses against chilling stress, especially in sensitive species. The transcriptomic activity of five Ethylene Response Factors genes and a REDOX Responsive Transcription Factor 1 involved in hormone-related pathways belonging to ethylene metabolism and signal transduction were induced. Transcription activity of two genes encoding for heat shock factors was enhanced, together with various genes associated with developmental processes. Several transcription factor families showed to be commonly induced between different plant species. Protein–protein interaction networks highlighted the role of the photosystems I and II, as well as genes encoding for HSF and WRKY transcription factors. A model of gene regulatory network underlying plant responses to chilling stress was developed, allowing the delivery of new candidate genes for genetic improvement of crops towards low temperatures tolerance.
Keywords: abiotic stress, chilling stress, ethylene, meta-analysis, plant, RNA-seq, temperature, transcription factors.
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