Abstract
Plants tolerate cold stress by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. Identifying TFs related to cold tolerance contributes to cold-tolerant crop breeding. In this study, a comparative transcriptome analysis was carried out to investigate global gene expression of entire TFs in two peanut varieties with different cold-tolerant abilities. A total of 87 TF families including 2328 TF genes were identified. Among them, 445 TF genes were significantly differentially expressed in two peanut varieties under cold stress. The TF families represented by the largest numbers of differentially expressed members were bHLH (basic helix—loop—helix protein), C2H2 (Cys2/His2 zinc finger protein), ERF (ethylene-responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), NAC (NAM, ATAF1/2, CUC2) and WRKY TFs. Phylogenetic evolutionary analysis, temporal expression profiling, protein–protein interaction (PPI) network, and functional enrichment of differentially expressed TFs revealed the importance of plant hormone signal transduction and plant-pathogen interaction pathways and their possible mechanism in peanut cold tolerance. This study contributes to a better understanding of the complex mechanism of TFs in response to cold stress in peanut and provides valuable resources for the investigation of evolutionary history and biological functions of peanut TFs genes involved in cold tolerance.
Highlights
Peanut (Arachis hypogaea L.), one of the most important grain legumes as the source of edible oils and proteins, is cultivated in the tropical and subtropical regions of the world [1]
A large number of Transcription factor (TF) that were differentially expressed was not surprising as cold stress array of plant developmental and biochemical and physiological processes [44], which proved the vital position of TFs in peanut cold tolerance
These results indicated ICE1, MYC2, and MYC4 in Basic helix—loop—helix protein (bHLH) family played an important role in peanut cold tolerance, which were positively regulated by jasmonic acid (JA) signaling pathway
Summary
Peanut (Arachis hypogaea L.), one of the most important grain legumes as the source of edible oils and proteins, is cultivated in the tropical and subtropical regions of the world [1]. Transcriptomic studies in model species under controlled conditions have indicated that the transcript abundances of hundreds of genes are altered under the imposition of cold stress [6,7] These transcriptome changes are regulated by a complex network of transcription factors (TFs) and other regulatory proteins and RNAs. TFs act as transcriptional activators or repressors and play a central role in the regulation of development, metabolic processes, and biotic and abiotic stresses [8]. CBFs are reported to play a central role in cold-responsive network by directly regulating the expression levels of cold-responsive (COR) genes, improving cold tolerance in many plant species [15,16,17]. A set of TF genes in response to cold stress were identified in peanut and were classified into various families based on their homology and. Tehxeprqeusasinotnitaletviveelsrbeayl-thtiemveaPluCeRs o(qf RfrTa-gPmCeRn)tsanpaelryksielsobwaesreeopfetrrfaonrsmcreipdtopnertemnidlliiffonerfernatgimalleynetsxmpraepsspeedd g(eFnPeKsMan).dTthhee qreuliaanbtiiltiatytivoef RreNalA-t-ismeqe dPaCtRa v(aqlRidTa-PteCdR()FiagnuarleysSe1s).were performed on ten differentially expressed genes and the reliability of RNA-seq data validated (Figure S1)
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