Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

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.

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

“…In this study, 147 TFs belonging to 32 TF families, including AP2/ERF (27), MYB (19), bHLH (13), WRKY (21), C 2 H 2 (8), and NAC (13), were largely regulated by cold stress (Table 2, Figure 5). Similar to our findings, in previous studies, comparative transcriptome analysis of rice, Chinese jujube, and peanut under cold stress conditions identified the above TF families to be the most regulated gene members [60,61,71,72]. These TF genes in their respective families are divided into diverse subgroups based on their specific motif structures, showing that they may perform their specific biological activities under cold stress.…”

“…In previous studies, the expression of WRKY70 and TcWRKY53 was induced by cold stress in wheat and Thlaspi caerulescens, respectively [75,76]. Moreover, peanut cold stress tolerance was regulated by WRKY70 and WRKY53 via the plant-pathogen interaction pathway [72]. Moreover, MYB4 (Zm00001d041853), bHLH57 (Zm00001d027419), PIF4 (Zm00001d013130), PTF1 (Zm00001d045046), AGL22 (Zm00001d018142), GRF6 (Zm00001d000238), ATHB4 (Zm00001d002754), Scl7 (Zm00001d033834), BTB/POZ (Zm0000 1d023313, Zm00001d030864), and C 2 H 2 (Zm00001d024883) were all enhanced in the tolerant lines in this study (Tables S5 and S6).…”

“…In this study, the upregulation of the WRKY53 (Zm00001d023336) gene in the tolerant line increased the expression of 10 additional DEGs involved in signaling, amino acid phosphorylation, and transcription factors (Table S8). In a previous study, WRKY53 was highly increased in Arabidopsis thaliana under cold stress, where it interacted with hub genes, such as mitogenactivated protein kinase 3 (MPK3), WRKY33, and WRKY40, all of which are implicated in plant defense [72]. As a result, WRKY53 could have influenced maize cold tolerance via the plant-pathogen interaction route.…”

Use of Comparative Transcriptomic Analysis of Different Potato Varieties to Elucidate the Molecular Mechanism Underlying Differences in Cold Resistance

“…In addition to the CBF transcription factor family, such TFs as MYB, NAC, bZIP, and WRKY also play important roles in plant cold resistance [49][50][51][52][53][54][55][56][57][58][59][60][61]. The expression of WRKY TFs is induced by external environmental stimuli.…”

Comparative Transcriptomics for Pepper (Capsicum annuum L.) under Cold Stress and after Rewarming

“…At present, comparative transcriptomics has been widely used to illustrate the complex genes regulatory networks of many plants under cold stress. Comparative transcriptome analysis in two peanut varieties with different cold-tolerant abilities showed that 445 TF genes were significantly differentially expressed under cold and revealed some possible mechanism in peanut cold tolerance [17]. The comparison transcriptome of the tea plant under cold found that 978 differentially expressed genes (DEGs) owned by the tolerant and sensitive plants were enriched in pathways of photosynthesis and hormone signal transduction, among others, and considered that the different expression of Lhca2 and SNF1-related protein kinase 2 (SnRK2) are correlated with cold tolerance [18].…”