The genome sequences of Arabidopsis and P. trichocarpa were downloaded from TAIR10 (Huala et al., 2001) and Phytozome v13.1 (Goodstein et al., 2012), respectively. To obtain TCP homologs in P. trichocarpa, we first used the 24 Arabidopsis TCP proteins that have been genome-wide identified (Martín-Trillo and Cubas, 2010) as query sequences to perform BLASTP against P. trichocarpa proteome sequences (P. trichocarpa v3.1), and those genes with E-value < 1e-10 were selected as candidate PtrTCP proteins. In addition, we also downloaded the predicted P. trichocarpa TCP proteins from the Plant Transcription Factor Database (PlantTFDB 5.0) (Tian et al., 2020). Based on the above sequences, we further confirmed TCP domain containing proteins using hmmsearch¹ using the Hidden Markov Model (HMM) profile of TCP domain (PF03634) (Finn et al., 2014, 2016). Accordingly, we obtained a total of 36 PtrTCP genes in P. trichocarpa.

The TCP proteins of P. trichocarpa and Arabidopsis were aligned by MUSCLE program (Edgar, 2004). The phylogenetic tree was constructed using the maximum-likelihood (ML) method with the bootstrap of 1,000 implemented in IQ-TREE (Nguyen et al., 2015). Exon/intron information of TCP family genes was obtained from gene annotation files of P. trichocarpa and Arabidopsis. To investigate the conserved functional domain of PtrTCP proteins, we downloaded the HMMs of all protein domains from the Pfam database (Finn et al., 2016) and used hmmsearch (see text footnote 1) to search TCP proteins against the HMMs with an E-value < 1e-5. The locations of the conserved functional domains across the TCP proteins were further visualized using TBtools version 1.0971 (Chen et al., 2020).

To trace the expansion history of PtrTCP genes, MCScanX (Wang et al., 2012) was utilized to identify collinear gene blocks, some of which contained PtrTCP genes, and the synteny analysis result was visualized using the Circos software in TBtools version 1.0971 (Chen et al., 2020). In dating the expansion of PtrTCP family genes, the synonymous substitution (Ks) value of each pair of the collinear gene blocks was calculated using the YN method by KaKs_Calculator2.0 (Wang et al., 2010). Similarly, the average Ks of all the collinear gene blocks between P. trichocarpa and Arabidopsis was also calculated.

Gene ontology (GO) term assignment for P. trichocarpa genes was obtained using the eggnog-mapper version 2 tool, and GO term enrichment analysis of PtrTCP genes was performed using GOSeq (Young et al., 2010; Cantalapiedra et al., 2021). The GO terms with a value of p < 0.05 were considered to be significantly enriched. To identify potential cis-regulatory elements within the promoter sequences of PtrTCP genes, we searched 1-kb sequence upstream of the translation initiation site (TIS) of PtrTCP genes in PlantCARE (Rombauts et al., 1999; Lescot et al., 2002) and visualized the distribution of the enriched elements using TBtools version 1.0971 (Chen et al., 2020).

Transcriptome data of P. trichocarpa under abiotic stresses were downloaded from the NCBI BioProject (accession ID: PRJEB19784) (Filichkin et al., 2018). Trimmomatic software was utilized to remove the Illumina adapter contamination and filter the low-quality bases (Bolger et al., 2014), and then, the obtained clean reads were mapped to P. trichocarpa genome (version 3.1) by HISAT2 (Pertea et al., 2016). StringTie was further utilized to calculate the Transcripts Per Kilobase Million (TPM) value for each gene in the genome (Pertea et al., 2016). According to the gene expression, we calculated Pearson correlation coefficients of the leaf, stem, and root samples under cold, heat, salt, and drought stresses using R programming and visualized the expression patterns of PtrTCP genes using TBtools v1.0971 (Chen et al., 2020). The differentially expressed genes (DEGs) between two groups were obtained using edgeR, DESeq2, and Ballgown (Robinson et al., 2010; Trapnell et al., 2013; Love et al., 2014; Frazee et al., 2015). Those genes that had an adjusted p < 0.05 and an absolute value of fold change ≥2 from at least two of the methods were considered to be DEGs. Finally, we obtained the DEGs of PtrTCP genes in P. trichocarpa leaf, stem, and root samples under cold, heat, salt, and drought stresses.

Populus trichocarpa seedlings were cultured in an artificial climate chamber with 25°C at a photoperiod of 16/8 h light/dark cycle, and the 2-month-old P. trichocarpa seedlings with a similar growth status were utilized for abiotic stress treatments, including cold (4°C), heat (39°C), salt (200 mM NaCl), and drought (20% PEG6000). The fourth expanded leaves of P. trichocarpa seedlings were separately collected after short period (24 h for cold, salt, and drought, while 12 h for heat) and long period (7 days) of the corresponding abiotic stress treatments. Total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, United States) following the manufacturer’s procedure, and cDNA was synthesized by the PrimeScript RT™ Reagent Kit with gDNA Eraser (TaKaRa, Japan). Quantitative Real-time PCR (qRT-PCR) was performed using a CFX96 real-time PCR system with ChamQ SYBR qPCR Master Mix (Vazyme, Nanjing, China), and PCR reaction was performed under the following conditions: 95°C for 10 min, 45 cycles of 95°C for 30 s, and 60°C for 10 s. Relative expression level of each gene was normalized to PtrHIS (Potri.005G072300), Ptr60S (Potri.007G093700), PtrACTIN (Potri.019G010400), and PtrACTIN2 (Potri.001G309500), and the achieved data were analyzed using the 2^–ΔΔCT method (Livak and Schmittgen, 2001).

Based on the above RNA-seq analysis of P. trichocarpa under abiotic stresses, R package WGCNA was utilized to identify modules of highly correlated genes that were associated with each abiotic stress treatment (Langfelder and Horvath, 2008). First, Pearson’s correlation coefficients were calculated for all pair-wise genes, and soft threshold was then obtained to construct an adjacency matrix. Subsequently, the topological overlap matrix (TOM) was calculated from the resulting adjacency matrix, and the genes were hierarchically clustered based on TOMsimilarity. Finally, the dynamic tree cut algorithm was utilized to cut the hierarchal clustering tree into gene modules (minModuleSize = 10 and cutHeight = 0.2), and the Pearson’s correlation coefficients between modules and abiotic stresses were calculated.

The full length of PtrTCP10 coding sequence (CDS) without the stop codon was amplified from the wild-type P. trichocarpa cDNA using the PtrTCP10 specific primers designed with KpnI and SalI sites, and then, the purified PCR product was inserted into the pCAMBIA1300-sGFP vector under the control of CaMV35S promoter. After transferring pCAMBIA1300-PtrTCP10-sGFP plasmid into Agrobacterium tumefaciens EHA105 competent cells, transformation of PtrTCP10 into Arabidopsis was further performed using the floral dip method. Finally, the positive seedlings screened on the hygromycin-resistant plates were selected as candidate 35S::PtrTCP10 overexpression (OE) lines, and each of the candidate 35S::PtrTCP10 OE lines was verified by PCR and qRT-PCR.

For freezing tolerance assay, 3-week-old plotted cultivation 35S::PtrTCP10 OE lines and wild-type plant (Col-0) that were cultured under a 12/12 h light/dark photoperiod were treated with or without cold acclimation (4°C for 3 days), and then, freezing tolerance assays were performed as described by Jia et al. (2016). In brief, the program was set at 4°C for 10 min and 0°C for 20 min and dropped 1°C/h to the desired temperatures. After freezing treatment, the plants were grown at 4°C in dark for 12 h and then were transferred to 22°C for additional 3 days. Freezing tolerance phenotype of each line was observed, and the survival rate of each line was also calculated.

For salt stress assay, seeds of the 35S::PtrTCP10 OE lines and wild-type plant (Col-0) were cultured on the 1/2 MS media containing different concentrations of NaCl (0, 100, 125, and 150 mM). After being treated at 4°C for 2 days, seeds were cultured in a light incubator with 23°C at a photoperiod of 12/12 h light/dark cycle. The number of the germinated seeds of each line under different salt stress treatments was counted every day, and the germination rate of each line was finally calculated. In addition, we also measured root length and fresh weight of the salt-treated seedlings.

The Pearson correlation coefficient (PCC) between PtrTCP10 and other genes was calculated by using the above transcriptome data of P. trichocarpa under cold and salt stresses, and the genes with |PCC| > 0.7 and p < 0.0001 were identified as PtrTCP10 co-expressed genes. GO enrichment analysis of the co-expressed genes was performed and visualized by ClueGO (Bindea et al., 2009). To further predict the putative target genes of PtrTCP10, 1-kb sequence upstream of the TIS of PtrTCP10 co-expressed genes was utilized to search for PtrTCP10 binding site with at most one-mismatch across the consensus sequence GTGGNCCC. Accordingly, a regulatory network centrally mediated by PtrTCP10 was constructed based on PtrTCP10 and its putative co-expressed target genes that contained at least two TCP binding sites. In addition, the well-known cold- and salt-relevant genes (e.g., ZAT10, GolS2, HY5, CBL1, and SOS1) that contained one TCP binding site were also included in this regulatory network (Wu et al., 1996; Cheong et al., 2003; Sakamoto et al., 2004; Nishizawa et al., 2008; Zhang et al., 2020).

Based on a homolog search in combination with previous reported PtrTCP genes (Ma et al., 2016), we gave an updated list of the family, designating PtrTCP1 to PtrTCP12 and PtrTCP14 to PtrTCP37. As a total, we obtained 36 PtrTCP genes (Supplementary Table 1), which showed 50% more than that in Arabidopsis (Danisman et al., 2013). Among them, PtrTCP37 (Potri.006G207700) was a newly identified member that had not been reported previously, and a 41-amino acid length protein identified as PtrTCP13 (Potri.005G140600) by Ma et al. (2016) was excluded. To elucidate phylogenetic relations of PtrTCP family, we constructed a phylogenetic tree by including Arabidopsis TCP genes as references (Figure 1A). The tree showed that PtrTCP genes can be classified into two major groups (i.e., class I and class II), and the members within class II were further divided into two lineages (i.e., CIN and CYC), supporting the previous results from other plants (Kosugi and Ohashi, 2002; Navaud et al., 2007; Li, 2015).

As the gene structure is considered to provide important clues for the conservation and evolution of homologous genes (Xu et al., 2017), we analyzed the gene structures of PtrTCP genes (Figure 1B). PtrTCP genes were likely to have relatively simple exon/intron structures, with the exon number from one to five, and most of the PtrTCP genes within the same subfamily shared similar gene structures. Approximately, 86% of PtrTCP genes contained one or two exons, while only two genes (i.e., PtrTCP29 and PtrTCP37) contained five exons. In addition, we also detected the conserved domains or motifs of PtrTCP proteins, and a total of seven conserved motifs were identified (Figure 1C and Supplementary Figure 1). Of the motifs, motifs 1 and 2 constituted the TCP domain. Interestingly, PtrTCP29 and PtrTCP37 have an order of motif 1 followed by motif 2 in contrast to all of the other PtrTCP proteins sharing an order of motifs 2 and 1, demonstrating that PtrTCP29 and PtrTCP37 underwent an evolution of reverse positions of motifs 1 and 2. Except for the two motifs, it is worthy to note that motif 4 with an enrichment of Gln (Q) is the most widely distributed in the PtrTCP proteins (Figure 1C and Supplementary Figure 1). Together, PtrTCP genes have a similar composition of exon/intron structures and protein domains but also some divergences especially between the subfamilies.

As described above, P. trichocarpa has 50% more TCP genes than Arabidopsis. To investigate the innovation of PtrTCP family genes, we detected their chromosomal distribution and gene duplication events. PtrTCP genes were distributed unequally on P. trichocarpa chromosomes, with 34 genes on 17 chromosomes and two genes on the unmapped scaffolds (Figure 2A). Intra-specie genomic comparison generated hundreds of collinear gene blocks; Of which, 30 blocks were identified to contain 32 PtrTCP genes (Figure 2A, gene block pairs connected by color lines). Accordingly, WGD is the major duplication mechanism to generate PtrTCP genes in P. trichocarpa (Figure 2B).

To further estimate the time of WGD-expanded PtrTCP genes, we calculated the synonymous substitutions per synonymous site (Ks) of collinear gene blocks (Supplementary Table 2). We found that the gene blocks could be mainly classified into three categories (Figure 2C). The first category included nine pairs of PtrTCP genes (shown in blue) with Ks value ranging from 3.43 to 4.66, which were derived from the ancient angiosperm-wide or seed plant-wide WGD (Jiao et al., 2011). The second category included seven pairs of PtrTCP genes (shown in green) that were derived from the γ whole-genome triplication (γ-WGT) shared by core eudicots (Tang et al., 2008). The third category included 14 pairs of PtrTCP genes (shown in red) with Ks value ranging from 0.17 to 0.31, suggesting that these genes blocks were originated from the most recent WGD (rWGD) in Populus lineage after its divergence from Arabidopsis, which explained well 50% more PtrTCP genes in P. trichocarpa than that in Arabidopsis. The findings demonstrated that the three WGD events are the dominant underlying mechanism for expanding PtrTCP family genes, and rWGD is the main event to lead the innovation of PtrTCP family genes in contrast to Arabidopsis.

Interestingly, the rWGD event occurred around K-Pg extinction event ∼66 million years ago, which was followed by the Cenozoic global cooling (Wu et al., 2020). Those rWGD-duplicated PtTCP genes might have undergone subfunctionalization or neofunctionalization, which contributed to their retention and plant adaptation during the cooling stress. Then, we investigated the functional enrichments of PtTCP genes and their regulation under abiotic stresses, especially cold stress.

To investigate the biological pathways that PtrTCP genes might participate in, GO term enrichment analysis of PtrTCP genes was performed (Figure 3A). We found that the GO terms related to the regulation of various developmental processes were significantly enriched, such as shoot system development, morphogenesis of a branching structure, timing of transition from vegetative to reproductive phase, inflorescence development, seed germination, and embryonic morphogenesis, which were consistent with previous studies (Takeda et al., 2006; Tatematsu et al., 2008; Sarvepalli and Nath, 2011; Rueda-Romero et al., 2012; Aguilar-Martínez and Sinha, 2013; Manassero et al., 2013). In addition, GO terms related to the regulation of response to hormone and environmental stresses were also enriched, such as response to gibberellin, response to cytokinin, regulation of response to stress, and regulation of response to stimulus. These results indicated that PtrTCP genes may not only be involved in plant growth and development but also participate in response to hormones and environmental stresses.

Cis-regulatory elements in promoters are essential for regulating gene expression (Lescot et al., 2002). We predicted potential cis-regulatory elements in the 1-kb sequence upstream of TIS of PtrTCP genes using PlantCARE (Rombauts et al., 1999). In addition to the common cis-regulatory elements (e.g., TATA-box and CAAT-box), we found cis-regulatory elements in relation to plant growth and development (e.g., endosperm expression, meristem expression, and circadian control), and in response to environmental stresses (e.g., low-temperature, drought, and light) and hormone responses (e.g., abscisic acid, salicylic acid, MeJA, gibberellin, and auxin) (Figure 3B). This suggested that the expression of PtrTCP genes might be dynamically regulated in plant growth and development under normal and/or environmental stresses. Then, we investigated the expression profiles of PtrTCP genes in leaf, stem, and root tissues under normal and stress conditions (e.g., cold, heat, salt, and drought).

Correlation analysis on transcriptome-scale gene expression from P. trichocarpa samples showed three clusters, which were classified by leaf, stem, and root tissues rather than by abiotic stresses (Figure 4A). This demonstrated that the tissue type was the main factor to classify the samples, and meanwhile, the genes in these tissues were likely to be elaborately controlled in response to abiotic stresses. Inspecting the expression profiles of PtrTCP genes in the tissues under abiotic stresses (Figure 4B), we found that most of the class I genes were highly expressed, while the genes in CYC lineage were lowly expressed in the three tissues despite all of the abiotic stresses. However, PtrTCP genes in CIN lineage showed diversified expression profiles. In detail, 50% of CIN lineage genes including PtrTCP24, PtrTCP34, PtrTCP4, PtrTCP9, and PtrTCP19 were highly, moderately, and lowly expressed, respectively, in leaf, root, and stem, and some CIN lineage genes (e.g., PtrTCP10, PtrTCP36, PtrTCP31, and PtrTCP27) were especially expressed in leaf tissue, suggesting an important role of CIN lineage in leaves. Moreover, PtrTCP genes were likely to be elaborately regulated in response to abiotic stresses (Figure 4B). For example, PtrTCP10, PtrTCP36, PtrTCP35, and PtrTCP5 were obviously upregulated in leaves after cold stress. Then, we investigated the abiotic stress-affected PtrTCP genes in detail.

We compared the expression changes of PtrTCP genes in the tissues between abiotic stresses and normal condition (Figure 5 and Supplementary Table 3). In the aspect of PtrTCP genes under each of the four abiotic stresses, there were 19, 21, 18, and 13 differentially expressed (DE) ones, respectively, in response to cold, heat, salt, and drought stresses. Under the same stress, different tissues showed an overlap but also a great divergence of DE PtrTCP genes (Figure 5A). For cold, heat, and salt stresses, most of the DE PtrTCP genes were determined in leaf, while for drought, the counterpart was determined in the root. In addition, some of those PtrTCP genes could be induced by multiple abiotic stresses. For example, 22 genes could respond to at least two of the stresses, and in particular, five genes were differentially regulated by all the four abiotic stresses (Figure 5B). In the aspect of PtrTCP genes in each of the tissues, 23, 17, and 20 genes were differentially regulated by at least one of the four abiotic stresses, respectively, in leaf, root, and stem (Figure 5C). Of them, 11 DE PtrTCP genes could respond to abiotic stresses in the three tissues (Figure 5D). In leaf, 13, 14, 15, and 5 PtrTCP genes were DE under the treatment of cold, heat, drought, and salt, respectively (Figure 5E). In addition to the overlaps of DE PtrTCP genes between the abiotic stresses, some PtrTCP genes could uniquely respond to one of cold, heat, and salt in leaf (Figure 5F). Moreover, of the DE PtrTCP genes, some showed different expression patterns in response to short periods and/or long periods of abiotic stresses (Figure 5G and Supplementary Table 3). Likewise, in stem and root, we also observed similar patterns of DE PtrTCP genes in response to abiotic stresses of cold, heat, salt, and drought at different time points (Figures 5H–M).

To further validate the expression of PtrTCP genes in response to abiotic stresses, 16 DE PtrTCP genes that could be induced or repressed by at least one of the abiotic stresses were selected to be for experimentally qRT-PCR confirmation in leaf (Supplementary Table 4). Except for PtrTCP33, the selected PtrTCP genes could respond to at least one of the abiotic stresses, showing similar expression trends under abiotic stresses with those detected by RNA-seq (Figure 6 and Supplementary Table 3). For example, PtrTCP5, PtrTCP10, and PtrTCP35 were significantly upregulated by cold treatments at 24 h and 7 days, while PtrTCP34 was downregulated. PtrTCP1, PtrTCP4, PtrTCP2, PtrTCP7, PtrTCP8, PtrTCP11, and PtrTCP35 responded to both the short period and the long period of heat treatments. PtrTCP1, PtrTCP7, PtrTCP10, PtrTCP26, and PtrTCP35 were significantly induced by salt stress, and in contrast, PtrTCP4, PtrTCP11, PtrTCP18, PtrTCP20, PtrTCP24, and PtrTCP34 were repressed. These findings suggested that at least half of the PtrTCP genes could respond to abiotic stresses, and they might be involved in regulating abiotic stress tolerance. Then, we sought to explore the potential hub PtrTCP genes in an abiotic process using the gene co-expression network.

Based on the expressed genes including PtrT in leaf, root, and stem under abiotic stresses, we constructed a co-expression network (Figure 7A) using weighted correlation network analysis (WGCNA; Langfelder and Horvath, 2008). In the network, 28 modules were obtained, and some modules were significantly correlated with the tissue traits (Figure 7B). For example, the module MElavenderblush3 was significantly positively correlated with the trait (Leaf_cold_24h), which indicated that the genes in MElavenderblush3 were especially upregulated in the same orientation in leaf under cold stress at 24 h. In the case of PtrTCP family genes, 30 members were clustered into six modules, e.g., ten in MEblue, six in MEbrown, six in MEdarkolivegreen, four in MEgrey, three in MElavenderblush3, and one in MEgrey60 (Figure 7B and Supplementary Table 5). However, of the six modules, only two modules (i.e., MEgrey60 and MElavenderblush3) including four PtrTCP genes were significantly correlated with abiotic stress treatments. Although PtrTCP12 in MEgrey60 was correlated with Root_salt_24h, the gene was not significantly upregulated (<2 fold change) by salt treatment at 24 h (Supplementary Table 3). In contrast, PtrTCP10, PtrTCP31, and PtrTCP36 in MElavenderblush3 were correlated and significantly upregulated in leaf under cold stress at 24 h (Leaf_cold_24h), demonstrating a potential role of the genes in MElavenderblush3 under cold stress.

Notably, PtrTCP10, PtrTCP31, and PtrTCP36 genes were P. trichocarpa inparalogs related to other dicot orthologs including Arabidopsis singular ortholog AtTCP5 and Glycine five co-orthologs (the left panel in Figure 7C). This demonstrated the three genes evolved from gene duplications within P. trichocarpa lineage after the divergence from other dicot lineages, which was consistent with the above WGD analysis (Figure 2). Further expression analysis of those genes showed that PtrTCP10 and PtrTCP36 were significantly upregulated (>5-fold change) by cold stress, whereas the corresponding co-orthologs in other close dicots (e.g., Arabidopsis, Cucumis sativus, Carya illinoinensis, Betula pendula, and Glycine max) were not or less affected (the right panel in Figure 7C and Supplementary Table 6). Based on the expansion history of PtrTCP genes (Figure 2), PtrTCP36 was mapped on a scaffold and predicated to be produced by dispersed duplication from PtrTCP10, whereas PtrTCP10 was mapped on Chr4 and duplicated from PtrTCP31 by rWGD ∼66 million years ago (Figure 7D). After rWGD, the Cenozoic global cooling and other environmental factors might have driven subfunctionalization and/or neofunctionalization of these TCP genes in regulation and function, and of those TCP orthologs in the six plants, only PtrTCP10 and PtrTCP36 acquired a strong capability of cold induction. We questioned whether the acquirement of cold-induced capability in PtrTCP10 and PtrTCP36 contributed to the cold adaptation of the plants. Then, we selected the WGD-duplicated PtrTCP10 for OE in Arabidopsis to investigate its potential role in cold stress.

To further investigate the role of PtrTCP10 under cold stress, we generated 35S::PtrTCP10 OE lines in Arabidopsis. The candidate positive seedlings screened on the hygromycin-resistant plates were verified by PCR and qRT-PCR (Supplementary Figure 2), and three independent 35S::PtrTCP10 OE lines (i.e., OE1, OE3, and OE6) with high expression levels of PtrTCP10 were selected for further study. Under normal condition, we found that the OE lines showed a similar growth as the wild-type (Col-0), and in contrast, under freezing condition, they exhibited freezing tolerance phenotypes with or without cold acclimation (Figure 8A). Statistically, their survival rates were significantly higher than the wild type (Figure 8B). Given that PtrTCP10 could also be significantly induced by salt treatment at 7 days (Figures 4, 6), we examined the phenotypes of 35S::PtrTCP10 OE lines under salt treatments. Compared with the wild type, the OE lines were more sensitive to salt stress (Figure 9). Their germination rate, root length, and fresh weight were significantly lower than the wild type. The findings suggested that PtrTCP10 was positively involved in plant resistance to cold stress but also might be a negative regulator involved in salt stress. Then, we elucidated the regulatory molecular mechanism of PtrTCP10 in response to cold and salt stresses.

First, we identified a total of 813 significantly co-expressed genes of PtrTCP10 from the above transcriptome data under cold and salt stresses. The co-expressed genes were significantly enriched in the GO terms related to environmental stresses, such as response to cold, response to salt stress, response to osmotic stress, regulation of cell death, potassium ion transmembrane transport, and leaf senescence (Figure 10A). TCP transcription factors have been shown to recognize GC-rich cis-acting regulatory elements, and the class II TCP proteins show a preference binding for the motif GTGGNCCC (Kosugi and Ohashi, 2002; Viola et al., 2011; Manassero et al., 2013). To predict the putative target genes of PtrTCP10, we searched for the motif allowing a degenerate mutation against the promoters (1-kb upstream of TIS) of the 813 co-expressed genes. Approximately, 44% (359 out of 813) of the genes contained the motif, and of which, 118 genes contained at least two binding sites (Figure 10B). Based on the putative PtrTCP10 target genes (Supplementary Table 7), we constructed a regulatory network mediated by PtrTCP10. The network presented some well-acknowledged cold- and salt-responsive genes (e.g., ZAT10, GolS2, HY5, CBL1, SOS1, RCI2A, and SnRK3.9) directly regulated by PtrTCP10, which suggested that PtrTCP10 might be involved in response to cold and salt stresses by regulating those stress-related genes (Figure 10C; Wu et al., 1996; Capel et al., 1997; Guo et al., 2001; Cheong et al., 2003; Sakamoto et al., 2004; Nishizawa et al., 2008; Zhang et al., 2020).