Identifying conserved genes involved in crop tolerance to cold stress
Sanaz Yousefi A # , Annalisa Marchese B , Seyed Alireza Salami C , Jubina Benny
B , Antonio Giovino D , Anna Perrone E , Tiziano Caruso B , Mansour Gholami A , Hassan Sarikhani A , Matteo Buti F and Federico Martinelli G H # *
+ Author Affiliations
- Author Affiliations
A Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
B Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze — Ed. 4, 90128 Palermo, Italy.
C Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj 31587-77871, Iran.
D Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), 90011 Bagheria, Italy.
E Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo 90128, Italy.
F Department of Agriculture, Food, Environment and Forestry, University of Florence, Firenze, Italy.
G Department of Biology, University of Florence, Firenze, Italy.
H Istituto di Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Rome, Italy.
* Correspondence to: federico.martinelli@unifi.it
# These authors contributed equally to this paper
Handling Editor: Manuela Chaves
Functional Plant Biology 49(10) 861-873 https://doi.org/10.1071/FP21290
Submitted: 8 December 2021 Accepted: 6 June 2022 Published: 5 July 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Low temperature is a limiting factor for crop productivity in tropical and subtropical climates. Cold stress response in plants involves perceiving and relaying the signal through a transcriptional cascade composed of different transduction components, resulting in altered gene activity. We performed a meta-analysis of four previously published datasets of cold-tolerant and cold-sensitive crops to better understand the gene regulatory networks and identify key genes involved in cold stress tolerance conserved across phylogenetically distant species. Re-analysing the raw data with the same bioinformatics pipeline, we identified common cold tolerance-related genes. We found 236 and 242 commonly regulated genes in sensitive and tolerant genotypes, respectively. Gene enrichment analysis showed that protein modifications, hormone metabolism, cell wall, and secondary metabolism are the most conserved pathways involved in cold tolerance. Upregulation of the abiotic stress (heat and drought/salt) related genes [heat shock N-terminal domain-containing protein, 15.7 kDa class I-related small heat shock protein-like, DNAJ heat shock N-terminal domain-containing protein, and HYP1 (HYPOTHETICAL PROTEIN 1)] in sensitive genotypes and downregulation of the abiotic stress (heat and drought/salt) related genes (zinc ion binding and pollen Ole e 1 allergen and extensin family protein) in tolerant genotypes was observed across the species. Almost all development-related genes were upregulated in tolerant and downregulated in sensitive genotypes. Moreover, protein–protein network analysis identified highly interacting proteins linked to cold tolerance. Mapping of abiotic stress-related genes on analysed species genomes provided information that could be essential to developing molecular markers for breeding and building up genetic improvement strategies using CRISPR/Cas9 technologies.
Keywords: abiotic stress, chilling and freezing stresses, crops, differentially expressed genes, heat shock proteins, meta-analysis, RNA-seq, transcriptomics.
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