Skip to main content
Download PDF

Genome-wide identification and analysis of TCP family genes in Medicago sativa reveal their critical roles in Na+/K+ homeostasis

BMC Plant Biology volume 23, Article number: 301 (2023) Cite this article

Abstract

Background

Medicago sativa is the most important forage world widely, and is characterized by high quality and large biomass. While abiotic factors such as salt stress can negatively impact the growth and productivity of alfalfa. Maintaining Na+/K+ homeostasis in the cytoplasm helps reduce cell damage and nutritional deprivation, which increases a salt-tolerance of plant. Teosinte Branched1/ Cycloidea/ Proliferating cell factors (TCP) family genes, a group of plant-specific transcription factors (TFs), involved in regulating plant growth and development and abiotic stresses. Recent studies have shown TCPs control the Na+/K+ concentration of plants during salt stress. In order to improve alfalfa salt tolerance, it is important to identify alfalfa TCP genes and investigate if and how they regulate alfalfa Na+/K+ homeostasis.

Results

Seventy-one MsTCPs including 23 non-redundant TCP genes were identified in the database of alfalfa genome (C.V XinJiangDaYe), they were classified into class I PCF (37 members) and class II: CIN (28 members) and CYC/TB1 (9 members). Their distribution on chromosome were unequally. MsTCPs belonging to PCF were expressed specifically in different organs without regularity, which belonging to CIN class were mainly expressed in mature leaves. MsTCPs belongs to CYC/TB1 clade had the highest expression level at meristem. Cis-elements in the promoter of MsTCPs were also predicted, the results indicated that most of the MsTCPs will be induced by phytohormone and stress treatments, especially by ABA-related stimulus including salinity stress. We found 20 out of 23 MsTCPs were up-regulated in 200 mM NaCl treatment, and MsTCP3/14/15/18 were significantly induced by 10 μM KCl, a K+ deficiency treatment. Fourteen non-redundant MsTCPs contained miR319 target site, 11 of them were upregulated in MIM319 transgenic alfalfa, and among them four (MsTCP3/4/10A/B) genes were directly degraded by miR319. MIM319 transgene alfalfa plants showed a salt sensitive phenotype, which caused by a lower content of potassium in alfalfa at least partly. The expression of potassium transported related genes showed significantly higher expression in MIM319 plants.

Conclusions

We systematically analyzes the MsTCP gene family at a genome-wide level and reported that miR319-TCPs model played a function in K+ up-taking and/ or transportation especially in salt stress. The study provide valuable information for future study of TCP genes in alfalfa and supplies candidate genes for salt-tolerance alfalfa molecular-assisted breeding.

Peer Review reports

Introduction

Alfalfa is the important forage world widely, and is characterized by high quality, large biomass and strong stress tolerance. While abiotic stresses such as salinity stress can severely affect alfalfa development and production. Thus, it is crucial to breed alfalfa varieties with high abiotic tolerance. In 2020, the genome information of alfalfa was published [1], numerous genes have been identified that may act in response to abiotic stress. Some TFs in alfalfa have been reported responding to salinity, such as Q-type C2H2 zinc-finger protein (C2H2-ZFP) [2], MADS-box [3], and SPL family [4], which provide important genetic resources to breed salinity-resistant alfalfa varieties.

TCP (Teosinte Branched1/ Cycloidea/ Proliferating Cell Factors) gene family was firstly documented in 1999 [5], they are a group of plant-specific genes encoding TFs (transcription factors) with TCP domain. The TCP proteins are characterized with a 59-amino acid basic helix-loop-helix (bHLH) motif, and are considered to be involved in DNA binding, protein–protein interaction and nuclear targeting [6]. According to the amino acid sequences of the TCP domain, TCPs can be divided into two main classes: class I (also known as TCP-P class or PCF class) and class II (or TCP-C) [7]. TCPs belonging to Class II can be further subdivided into two clades, the CIN (CINCINNATA) and the CYC/TB1 (CYCLOIDEA/TEOSINTE BRANCHED 1) subclades [8]. Generally, the class I genes are mostly involved in promoting cell division and differentiation in diverse biological processes ranging from seed germination, leaf and floral organ development and senescence [9,10,11]. Class II TCP genes are mainly related to the development of lateral organs, part of them participate in plant stress resistance. TCP members belonging to CYC/TB1 clade mainly involved in regulating floral development, shoot branching and organ development [12,13,14]. It has been proved that the mRNAs of several CIN TCPs could be targeted and degraded by microRNA319 (miR319, one kind of small non-coding RNA) [15,16,17]. miR319-TCPs model is an essential genetic regulator in plants and play vital roles in plant development. Such as overexpressing miR319 or repressing its target TCPs both show abnormally wavy rosette leaves and serrated leaves [18], and miR319-TCP4 has been reported in regulating LOX2, which encode a key enzyme in jasmonate (JA) synthesis, and regulates plant leaf senescence [17, 19].

Recently, there has been an increasing interest in the role of the TCP family genes in plant salt stresses adaptation [20, 21]. For class I TCPs, over-expression of OsTCP19 enhanced salt tolerance through regulating ABA signal transduction [22]. For class II TCPs, the miR319-TCPs model also plays conserved positive roles in Medicago truncatula, switchgrass and creeping bentgrass salt tolerance [23,24,25]. And, it was interested that overexpression miR319 transgenic switchgrass and creeping bentgrass showed higher K+ content under normal condition [24, 25]. It also reported that OsPCF2 potentially activate the expression of OsNHX1, a K+-Na+/H+ antiporter gene induced by salinity [26]. Under salt stress condition, decreasing cytoplasmic Na+ concentration and increasing K+ concentration, a suitable K+/Na+ ratio in the cytoplasm can be obtained, thus preventing cell damage and nutrient deficiency [27]. However, it is largely unknown that whether, and how, TCPs regulate plant K+ content.

In this study, we want to give an insight on TCP family genes in alfalfa, and how they response to Na+-excess and K+-deficiency condition. And, we generated the MIM319 transgenic alfalfa, verified the miR319-MsTCP pathway could affect the salt tolerance of alfalfa by influence the K+ content through physiological experiment of salt stress, and analyzed the possible molecular mechanism.

Materials and methods

Identification of the MsTCP s in alfalfa

MsTCPs protein sequences in alfalfa were obtained from protein annotation file according to Medicago sativa Genome Database via InterProScan (v. 5.17–56.0) [28], and were confirmed in the Plant Transcriptional Regulatory Map (PlantRegMap) online (http://plantregmap.gao-lab.org/). The obtained MsTCPs’ sequences were applied to SMART (http://smart.embl-heidelberg.de/) to conduct domain analysis to confirm whether belongs to TCP family. The molecular weight (MW) and isoelectric point (PI) of each protein were calculated using ExPASy (http://web.expasy.org).

MsTCPs chromosomal distribution analysis

Information of chromosomal location of MsTCPs and the chromosomal length were obtained from tetraploid alfalfa genome database [1], and figure of the distribution of TCPs on chromosome was drawn via TBtools.

TCP Phylogenetic and domain analysis of MsTCP family

TCP protein sequences of M. sativa (MsTCPs) with A. thaliana (AtTCPs) [8] and M. truncatula (MtTCPs) [29] were used to construct an unrooted phylogenetic tree using MEGA5.0 (https://megasoftware.net). DNAMAN was used to conduct sequences alignment of MsTCPs. Multiple protein sequences alignment was carried out with Jalview software11 (http://www.jalview.org).

Gene structure and cis-element analysis of MsTCPs

The CDS and corresponding genomic DNA sequences of MsTCPs were obtained in the alfalfa genome database. The diagrams of exon, intron and conserved domains of MsTCPs genes were generated using TBtools software [28].

The upstream sequences (2 kb) of the MsTCPs coding region were retrieved from the alfalfa genomic database and submitted to PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html) to identify regulatory elements involved in hormone and stressed responses. Including abscisic acid (ABA)-responsive elements (ABRE), involved in ABA responsiveness; MBS, MYB binding site involved in drought-inducibility; TCA-elements and salicylic acid responsive elements (SARE), involved in salicylic acid responsive; P-box, TATC-box and GARE-motif, involved in gibberellin-responsive element; TGA-element and AuxRR-core, involved in auxin responsive; TGACG-motif and CGTCA-motif, involved in MeJA-responsiveness; low temperature responsive elements (LTR), involved in low-temperature response; and TC-rich repeats, involved in defense and stress response.

Detection of MsTCPs expression patterns in different organs

To detect the expression patterns of MsTCPs in different organs, total RNA from apical meristem (MS), young leaves (YL, top leaves), mature leaves (OL, the fourth leave form the top), young stems (YS, the first internode from the top), mature stems (MS, the fourth internode from the top) and root (R, 5 mm root tips) in alfalfa (Cultivar: Zhongmu NO.1) was extracted using Trizol reagent.

Salt and K+ deficiency treatment

Alfalfa plants were propagated via stem-cutting. 7-week-old plants were transferred into 1/4 Hoagland’s solution (containing 1 mM KCl, 0 mM NaCl) for cultivated for 48 h as preculture. After precultured, plants were transferred into 1/4 Hoagland’s solution containing 200 mM NaCl for 12 h as salt treatment, or 1/4 modified Hoagland’s solution containing 10 μM KCl for 24 h as K+ deficiency treatment. About ten roots (3 cm length from tip upward) were collected at 0, 1, 3, 6, 12 and 24 h (only K+ deficiency treatment) after salt or K+ deficiency treatment to extract RNA, each treatment had 3 biological replications.

Prediction and identification of miR319 targeted MsTCPs

miR319 target site prediction was performed using CDS of candidate MsTCPs via psRNATarget (http://plantgrn.noble.org/psRNATarget). 5' RLM-RACE was used to validate predicted miR319 cleavage sites in MsTCPs experimentally, primers used in this experiment were listed in Table S2. In brief: total RNA was extracted and ligated with the 5’ adaptor ligation RNA (Sangon Biotech, Shanghai, China) by T4 RNA ligase. The ligated product was reverse‐transcribed into the first-strand cDNA using primer complementary to the 5’ adaptor ligation RNA. The cDNA was subsequently PCR‐amplified using GeneRacer 5’primer and MsTCP_GSP_R primer pairs. The PCR products were purified, ligated into the pMD19-T vector and sequenced. Finally, the sequencing results were analyzed to verify the miR319 cleavage site in MsTCPs [24].

Obtain and identification of transgenic alfalfa plants

The miR319 precursor genes of Arabidopsis, Medicago truncatula and rice were obtained from miRBase database (http://www.mirbase.org/), and were used as templates to blast in genome of alfalfa (https://www.alfalfatoolbox) to obtain MsMIR319 precursor genes. And the miRBase database was used to predict the mature miR319 sequence produced by MsMIR319s. To blocking miR319 expression, we transferred pZh01:MIM319B plasmid into alfalfa by Agrobacterium-mediated transformation as our previous report [30]. Transgenic alfalfa plants were obtained and identified by stem-loop qRT-PCR.

Salt treatment of MIM319 alfalfa

MIM319 transgenic plants and WT plants were propagated by stem-cutting. Two-month old plants were cultured in 1/4 Hoagland’s solution containing 250 mM NaCl for 3 d. Leaves and roots of WT and transgenic plants were collected respectively to measure the concentration of K+ and Na+. Briefly, dried samples were grinded, then about 50 mg of powder was taken into a 15 ml glass test tube with cover, 10 ml of deionized water was added in a boiling water bath and extract for 2 h, fix the volume into a 50 ml volumetric flask, filter and then determine the concentration of Na+ and K+ in the filtrate with flame spectrophotometer. Each treatment had three replications.

MIM319 plants under different level of salt stress

Seedlings grown for 4 weeks via stem-cutting were cleaned and transferred to 100 mL brown bottles, containing 100 mL of the following reagents: NaCl concentrations of 0, 140, 160, 180, 200 mM solution (1/4 Hoagland nutrient solution), then were treated for 48 h (photoperiod 14 h light/8 h dark; temperature 25 °C; humidity 50%).

Prediction of TCP s binding sites

According to the annotation file of alfalfa genome, genes related to K+ up-taking and transportation were selected. The promoters of these genes were analyzed on JASPAR (https://jaspar.genereg.net/) to predict the presence of TCPs binding site. Genes containing TCP binding sites were named after the blast result on NCBI (https://blast.ncbi.nlm.nih.gov/).

RNA extraction and expression pattern detection

Total RNA was extracted using Trizol reagent. One microgram of total RNA was reverse transcription into cDNA following the protocol of a reagent kit (Takara RR047 A), the kit can remove the genomics contamination. For miR319 stem-loop qRT-PCR, One microgram of total RNA was reverse transcription using stem-loop PT primer (Table S1). Using cDNA as template, qRT-PCR reactions were performed using Starlighter SYBR Green qPCR Mix (Beijing Qihengxing Biotechnology Co., LTD, FS-Q1002 kit) with a qTOWER3G (analytik jena). The calculation of the relative expression levels following 2−ΔΔCT method [20]. MsActin was used as an internal control for normalizing. Primers used in qRT-PCR test were listed in Table S1.

Statistic analysis

All statistical analyses were performed with the IBM SPSS Statistics program (Version 24). Values are presented as the mean ± standard deviation (SD). For multi-group comparison, P values were derived from one-way ANOVA (continuous variables). For all comparisons, P < 0.05 was considered as statistically significant.

Results

Seventy-one MsTCP s genes were identified in alfalfa

Seventy-one MsTCPs genes which have intact TCP domains were obtained from alfalfa genome (Table 1). The validated TCP genes were named from MsTCP1 to MsTCP24 based on the phylogenetic relationship with AtTCPs and MtTCPs, and the lowercase a, b, c, or d were used to distinguish allele genes which located on homologous chromosome (Table 1).

Table 1 TCP gene family in Medicago sativa from the tetraploid alfalfa (Cultivar: XinJiangDaYe) genome database
Full size table

Gene characteristics, including length of CDS (Coding Sequence), length of amino acids, protein molecular weight, and theoretical isoelectric point (pI) were analyzed and listed in Table 1. Based on these data, the length of MsTCP proteins ranged from 107 (MsTCP23b) to 521 (MsTCP22a), and the molecular weight ranged from 11,418.15 kDa (MsTCP23b) to 55,105.21 (MsTCP22a). Furthermore, the MsTCPs were unevenly located on the chromosomes, as shown in Fig. S1. Most TCP genes were located on Chr1 and Chr8, with 6 (MsTCP7/8/11/19/12/21) and 5 (MsTCP6/15/18/4/19) genes, respectively.

Phylogenetic analysis and classification of MsTCPs in alfalfa

In order to elucidate the evolutionary relationship of the TCPs among species, complete protein sequence of 71 MsTCPs, 24 AtTCPs, and 21 MtTCPs were used to construct an unrooted phylogenetic tree. The results showed that 71 MsTCPs can be divided into two subfamilies, they were referred to as Class I and II according to the classification of MtTCPs and AtTCPs. Class I (PCF) contained 34 members, and 37 members were classified into Class II which can be further divided into two subclasses: the CIN (28 members) and CYC/TB1 (9 members) (Fig. 1a). Alignment analysis of MsTCPs’ protein sequences revealed that all the MsTCP proteins contained a conserved basic helix-loop-helix (bHLH) domain (TCP domain) (Fig. 1b). Only the CYC/TB1 subclass members (MsTCP12/1/2/18) include the R domain (Fig. 1b). The results suggested that MsTCPs are as evolutionary conservative as other species.

Fig. 1
figure 1

Phylogenetic analysis of TCP proteins and multiple sequence alignment of TCP transcription factors. a Phylogenetic analysis of TCP proteins of A. thaliana (At), M. truncatula (Mt) and M.sativa (Ms). An unrooted neighbor-joining (NJ) tree was constructed using MEGA5.0 (bootstrap value = 1,000). The different colors of branched lines in the subtrees indicate the different TCP subclasses and the corresponding names of subclasses are showed above the arc line. b Alignment of TCP domain and R domain of 23 TCP proteins in M. sativa. Amino acids that are conserved throughout are shaded in different colors. Conserved domains, including Basic, Helix I, Loop, and Helix II, are shown at the top

Full size image

Gene structure and cis-regulatory elements on MsTCPs’ promoters

To gain more insight to the evolution of MsTCPs gene family on structure, exon/ intron organization of MsTCPs genomic DNA and cis-elements on their promoters were analyzed (Fig. 2). Among non-redundant TCP genes, 17 out of 23 members had no introns. All the members among CYC/TB1 group contained one intron. Furthermore, MsTCP6 and MsTCP15 contained one intron, respectively (Fig. 2b). Exon/ intron organization within allele genes were also analyzed. Their structures were similar except for MsTCP6, MsTCP9 and MsTCP16 (Fig. S2). MsTCP6c/d had no intron, MsTCP9b and MsTCP16c had one intron, were different from the others which may due to the evolutionary changed.

Fig. 2
figure 2

Exon/ intron structure of MsTCPs in M.sativa and cis-elements analysis of MsTCPs’ promoter. a Phylogenetic analysis of non-redundant TCP proteins. b The exon/ intron organization of MsTCPs genes in M. sativa. Exons and introns of MsTCPs genes were indicated by green rectangles and black lines respectively. The CDS, TCP domain, and R domain are indicated green, yellow, and pink rectangles respectively. The scale was referred to the lengths of the genes. c Predicted cis-elements in MsTCPs’ promoters. Promoter sequences (− 2000 bp) of MsTCP genes are analyzed by PlantCARE. The upstream length to the translation start site can be inferred according to the scale at the bottom

Full size image

Cis-elements related to phytohormone and stress responses on TCPs’ promoters were also analyzed (Fig. 2c). The varieties and locations of cis-elements on TCPs were manifold, which implied MsTCPs functions in multiple metabolic processes. In a total, 95 cis-regulatory elements related to hormones, with 39 elements involved in the abscisic acid response (ABRE), 18 involved in salicylic acid response (17 TCA-elements and 1 SARE), 13 involved in gibberellin response (6 P-box, 2 TATC-box and 5 GARE-motif), 15 involved in auxin response (10 TGA-element,4 auxRR-core and 1 TGA-box) and 15 involved in the MeJA-response (TGACG-motif/ CGTCA-motif). Besides, there were 35 cis-regulatory elements involved in stress response, with 8 involved in low-temperature response (LTR elements), 9 involved in defense and stress response (9 TC-rich repeats) and 13 involved in drought-inducibility (MBS elements). Notably, 19 TCPs except MsTCP10A/11/22/24 contained ABRE (abscisic acid response element) and the total number reached at 39, which suggested that most of them responding to ABA treatment or abiotic stresses. Among the allele genes, obvious differences were observed on their promoters. Except for MsTCP24, none of them contained identical numbers or varieties of cis-elements on their promoters (Fig. S3), which implied the evolutionary changes in their promoters are widely existed.

MsTCPs of the same subfamily had similar expression patterns in different organs

Expression pattern of MsTCPs were detected by qRT-PCR at different organs in alfalfa, including meristem (MS), young leaf (YL), mature leaf (OL), young stem (YS), old stem (OS) and root tip (R) (Table S3). It should be noticed that due to the highly similarity in sequences between MsTCP1 and MsTCP2, MsTCP16 and MsTCP23, MsTCP10A and MsTCP10B, their expression level cannot be divided through qRT-PCR. As is shown in Fig. 3, each subclasses had their own characteristics in addition to individual genes. MsTCPs of CIN clade were predominantly expressed in mature leaves except for MsTCP23 which mainly expressed in young leaves and young stems, implying these genes may participate in leaf development. MsTCP4, MsTCP16 and MsTCP9 mainly expressed in meristem. MsTCP9, MsTCP16, MsTCP11 and MsTCP8 presented a relatively low expression level in roots. For CYC/TB1 class TCPs predominately expressed at meristems, suggesting they play similar roles in plant developmental processes. Meanwhile, MsTCP18 also had a relatively higher expression level at mature leaves. The TCPs belonging to PCF clade were found expressed specifically in different organs. Such as, MsTCP19, MsTCP22 and MsTCP14 mainly expressed at mature leaves, while MsTCP7, MsTCP21 and MsTCP15 showed relatively high expression level at young stems. Apart from those, MsTCP24 predominantly expressed at young leaves. These results implied that TCPs function in multiple plant development processes. However, divergent functions of MsTCPs in alfalfa are remaining uncovered, and further studies still to be needed to elucidate specific function on each MsTCP gene.

Fig. 3
figure 3

Exon/ intron structure of MsTCPs in M.sativa and cis-elements analysis of MsTCPs’ promoter. a Phylogenetic analysis of non-redundant TCP proteins. b The exon/ intron organization of MsTCP genes in M. sativa. Exons and introns of MsTCP genes were indicated by green rectangles and black lines respectively. The CDS, TCP domain, and R domain are indicated green, yellow, and pink rectangles respectively. The scale was referred to the lengths of the genes. c Predicted cis-elements in MsTCPs’ promoters. Promoter sequences (− 2000 bp) of MsTCP genes are analyzed by PlantCARE. The upstream length to the translation start site can be inferred according to the scale at the bottom

Full size image

MsTCP s showed different expression pattern after high Na+ treatments

Recent study has reported that TCPs response to salinity stress [22]. And root is the first organ to feel and response to salinity stress [31]. Thus, to decipher how MsTCPs respond to salinity stress, root expression profiles of 23 non-redundant MsTCPs under 200 mM NaCl for 0, 1, 3, 6 and 12 h were analyzed. As is shown in Fig. 4, 16 out of 23 MsTCPs were up-regulated under 200 mM NaCl treatment at first several hours then down-regulated, and reached their peaks within 3 h, except for MsTCP9/11/16/23 belonging to PCF family (Fig. 4a), MsTCP6/24 belonging to CIN family (Fig. 4b), and MsTCP1/2 of CYC/TB1 subclade (Fig. 4c). MsTCP1/2 had the same expression pattern as mentioned above, reached the peak after salt treatment for 12 h. MsTCP9 and MsTCP6 showed a consistent up-regulated pattern. Besides, the expression level of MsTCP11 and MsTCP21 did not change significantly. MsTCP3, MsTCP10A/B, and MsTCP24 showed significant decreased after salt treatment for 24 h. Their different expression patterns suggested that they may work at different stages in response to salinity stress.

Fig. 4
figure 4

The expression of MsTCPs in response to treatment with 200 mM NaCl for 0, 1, 3, 6 and 12 h in roots of alfalfa (7w after cuttage). Data are means with SD for the three replicates. a PCF family TCPs. b CIN family TCPs. c CYC/TB1 family TCPs. Values represent mean ± SD (n = 3); asterisks represent significant differences compared to “0 h”, and “*” was considered highly significant P < 0.05 (n = 3)

Full size image

Most of MsTCP genes response to K+ deficiency treatment

The wild type alfalfa were treated with 10 μM KCl, then the expression pattern of MsTCPs in roots was tested by qRT-PCR. As the result shown in Fig. 5, most MsTCPs were responded to 10 μM KCl treatment, except for MsTCP7 and MsTCP11 remained stable expression and showed no significant change, while expression pattern of the other MsTCPs were different. Most of them (MsTCP3/8/9/15/16/23/19/21/22) showed an increasing at first several hours then decreasing, and the time they reached their peaks were different (Fig. 5a-c). MsTCP8, MsTCP15 and MsTCP4 reached their peaks at 3 h post of treatment, however, MsTCP9, MsTCP16/23 and MsTCP19 reached the peak in 6 h. MsTCP10A/B had the highest expression level at both 6 and 24 h after treated with low K+ treatment. MsTCP14 and MsTCP6 showed a consistently increasing tendency. Besides, MsTCP5, MsTCP12 and MsTCP13 decreased firstly then increased after treatment in 3 h. MsTCP4 reached two peaks at 1 h and 6 h respectively. Besides, only MsTCP24 remained decreasing under 10 μM KCl treatment. Expression level of MsTCP3/14/15/18 were increased about 10 times after treatment with 10 μM KCl compared to their expression level before treatment. It should be noticed that MsTCP15/19/22 had similar expression pattern under salt treatment and K+ deficiency situation, while MsTCP16/23, MsTCP13 and MsTCP5 showed an opposite expression pattern under NaCl stress and low-concentration of K+ treatment, indicating these genes play dominant roles under stresses of high concentration of NaCl and low concentration of K+.

Fig. 5
figure 5

The expression of MsTCPs in response to treatment with 200 mM NaCl for 0, 1, 3, 6 and 12 h in roots of alfalfa (7 w after cuttage). Data are means with SD for the three replicates. a The expression patterns of PCF family MsTCPs, b CIN family MsTCPs, and c. CYC/TB1 family MsTCPs. Values represent mean ± SD (n = 3); asterisks represent significant differences compared to “0 h”, and “*” was considered highly significant P < 0.05 (n = 3)

Full size image

miR319 post-transcriptional cleaveaged MsTCP3/4/10A/B and repressed MsTCP1/2/5/13

Suppression of some TCPs by miR319 could be a conserved molecular connection among species [25]. To elucidate this relationship within alfalfa, the supposed MsMIR319 sequences in alfalfa genome database were selected that were highly homology with MtMIR319s, AtMIR319s and OsMIR319s, and predicted the mature miR319 sequences in miRBase software. We obtained eleven MsMIR319s and produced three kind of miR319 sequences (Fig. S4a). Non-redundant MsTCPs were searched for the miR319 target sites using psRNATarget, 14 TCPs were found containing a miR319 cleavage site. Ten of them belong to PCF class, three belong to CYC/TBI family, and 1 belongs to CIN family (Fig. S4c). 5′ RLM-RACE was then conducted to detect the miR319 cleavage site in vitro. The result showed the mRNAs of MsTCP10A/B, MsTCP3 and MsTCP4 were directly cleavaged by miR319 between the 10th and 11th bases of miR319 target site with the probabilities of 16/20, 18/20, 13/20 and 18/20, respectively (Fig. 6a). These results suggested that expression of MsTCP10A/B, MsTCP3, and MsTCP4 were post-transcriptionally regulated by miR319. To further illuminate the relationship of miR319 and MsTCPs, we overexpressed a MIM319 gene in alfalfa to blocking in vivo miR319. The stem-loop qRT-PCR results showed that the expression level of miR319 significant decreased in MIM319 transgenic plants (M4 and M6) compared that in WT (Fig. 6b, c). And the expression level of miR319 cleavaged MsTCPs (MsTCP3, 4, 10A/B) showed a significant increase in Ms than that in WT (Fig. 6d). We also found that the expression level of the other TCPs containing miR319 target site but don’t cleavage were changed in MIM319 transgenic plants (Fig. 6d). MsTCP1/2, MsTCP5 and MsTCP13 were up-regulated, while the expression level of MsTCP9 and MsTCP18 were decreased, which uncovered that their transcriptional level were regulated by miR319. The expression level of MsTCPs without miR319 complementary region showed no significant difference between WT and Ms plants (Table S4).

Fig. 6
figure 6

MIR319-target MsTCPs identification and the expreession pattern of MsTCPs in MIM319 transgenic plants. a Detection of the miR319 cleavage site of the mRNA of MsTCPs through 5’ RLM-RACE. Numbers: degradome 5′ ends at arrowhead/total within MsTCPs target region (blue). b Phenotype of WT plant and MIM319 plants (M4 and M6). Values represent as mean ± SD (n = 3). c The expression level of miR319 decreased in MIM319 plants. d The expression level of MsTCPs in MIM319 plants and WT. Values represent the mean of three biological replicates

Full size image

Blocking of miR319 decreased alfalfa resistance ability of salt shock due to lower K+ content in alfalfa

To test the effects of miR319-MsTCPs model on Na+/ K+ content regulation in alfalfa, four-week old seedlings were used to test the salt tolerance under different level of salt stress. As is shown in Fig. S5, MIM319 plants showed significant salt sensitivity compared to WT plants. Then, we analyzed the salt shock resistance of WT and Ms by soaking with 250 mM NaCl for 3 d. As is shown in Fig. 7, both WT and Ms alfalfa began to wilt, while the top leaves of WT plants were less damaged compared to those of MIM319 plants, after treated with 250 mM NaCl for 3 d (Fig. 7a-c). DAB staining assay revealed that more H2O2 was accumulated in MIM319 plants than WT plants. The concentration of K+ in roots of MIM319 plants was significantly lower than that in WT plants (P < 0.05), and gradually decreased with the prolong of salt treatment hours. Within this process, the concentration of K+ in MIM319 plants remained lower compared to WT plants (Fig. 7e). However, the concentration of K+ in WT leaves was stable during salt treatment (P < 0.05). Concentration of Na+ was gradually increased in both WT and MIM319 alfalfa, but no significant difference between WT and MIM319 plants (Fig. 7f). These results indicated that MIM319 plants reduced salt tolerance in alfalfa by the reduction of K+ concentration, which resulted a lower ratio of K+/ Na+ compared to WT plants.

Fig. 7
figure 7

Short-time high-level salt stress in wild-type and MIM319 transgenic plants (2-month-old plants). a Phenotypes of wild-type (WT) and overexpression MIM319 (M4 and M6) plants before salt stress treatment. b Phenotypes of WT and MIM319 plants after 250 mM NaCl treatment for 3 d. c morphology of top leaves of branches after salt treatment. d DAB staining of leaves after salt treatment. e Concentration of K+, Na+ and K+/Na+ ratio of roots at different stage of salt treatment. f Concentration of K+ and Na+, K+/Na.+ ratio of at top leaves at different stage of salt treatment. Values represent the mean ± SD of three biological replicates, “*”indicate significant differences (P < 0.05). g The expression pattern of potassium transported related genes in wild-type and MIM319 transgenic plants under normal condition. Values represent mean ± SD (n = 3); asterisks represent significant differences compared with “WT”, and “*” was considered highly significant P < 0.05 (n = 3)

Full size image

K+ transport genes were up-regulated in MIM319 transgenic plants

We detected the expression level of potassium-related iron transport genes which promoters contain TCP binding sites (Table S5). It can be observed that CNGCs (Cyclic Nucleotide-gated Channels), HAKs (High-affinity K+), and KEA (K+ efflux anti-porter) were up-regulated, which have been reported to be induced in K+ deficiency [32, 33]. CIPK23 (CBL-Interacting Protein Kinase) was also observed up-regulated in MIM319 plants, which can directly binds to the promoter of AKT1 (Arabidopsis K+ channel 1), and improve the influx of K+ [34]. These results elucidated that MIM319 showed a salt sensitivity characteristic due to the K+ deficiency. However, AKT2/3 (K+ channel 2/3) was induced at in MIM319 plants, which has been reported to be inhibited in K+ free solution [35], which may partly explain the K+ deficiency in MIM319 plants (Fig. 7g).

Discussion

The TCP transcription factors are widely exist in many monocotyledons and dicotyledons. While the number of them varies among species [8], for example, 23 and 22 TCP genes were identified in A. thaliana and O. sativa, respectively [36]. 21 MtTCPs were identified in M. truncatula [29], 42 PvTCPs were identified in switchgrass [37] and 19 FvTCPs were found in strawberry [38]. The genome of ‘Zhongmu No.1’ alfalfa assembled one set of the chromosomes, while the genome of ‘XinJiangDaYe’ assembled the whole four set of chromosomes. Considering that alfalfa is a tetraploid plant with self-incompatibility, there may be differences among genes located at homologous chromosomes, thus the genome sequence of ‘XinJiangDaYe’ was selected to perform the analysis. In alfalfa, 71 MsTCPs were identified from the genome of tetraploid (Cultivar: XinJiangDaYe), and there were 23 non-redundant MsTCPs. These TCPs anchor on chromosomes unevenly, which was also reported in MtTCPs [29]. The MsTCP gene family were phylogenetically divided into three clades, named as clade PCF, CYC/TB1, and CIN, as that in A. thaliana and M. truncatula [7, 29], which revealed that TCPs in alfalfa was evolutionary conserved. Exon/ intron arrangement of MsTCPs also revealed that the genes in the same class/ clade have similar extron/ intron structure.

TCP gene family can influence multiple pathways related to plant growth (such as leaf development, flower morphogenesis phytohormone biosynthesis, and lateral branching) and also evolved in abiotic stress [19, 26, 38, 39]. To predicted MsTCPs participate in which phytohormone metabolic pathways, cis-elements in MsTCPs’ promoters were analyzed, and hormone response elements and stress response were focused. Intriguingly, most of the MsTCPs’ (19 of 23 non-redundant TCPs) promoter had at least one abscisic acid responsive element (ABRE), which is responsible for ABA-mediated osmotic stresses signaling [40]. Suggested that abiotic stress such as salinity stress would change the expression level of MsTCPs. We also noticed that the cis-elements of allele genes’ promoter changed a lot, which implied the evolutionary changes in the promoters are widely, and resulted in their functional difference.

The expression pattern of MsTCPs at organs were analyzed, and different subclasses of TCPs have their unique expression pattern. CIN-like clade TCPs are involved in regulation of leaf mororphosis, and silencing these genes will lead to an increase of leaf area [18, 41]. Such as BpTCP7-overexpressing in Betula platyphylla resulted promoted ability of reactive oxygen species scavenging under salinity and drought conditions by integrating multiple hormone metabolic pathways [42]. TCPs of CIN clade in alfalfa were also predominantly expressed in mature leaves implying these genes may participate in leaf development. For CYC/TB1 clade, all of them showed high expression level in meristem, which implied their vital functions in floral development and branching process. In chrysanthemums, CYC/TB1 clade TCPs were associated with regulation of floral asymmetry [43]. In Arabidopsis, this clade genes are destabilized by phytoplasma SAP11 effector, resulting in the proliferation of axillary meristems [44]. Specifically, AtTCP1 plays an important role in the longitudinal elongation of petioles, rosettes and inflorescence stems [45]. In M. truncatula, MtTCP1A/1B/12 were specifically expressed in flowers, suggesting that they may have similar function. However, the molecular mechanism of these transcription factors on flower development are needed to be further investigated [29]. In cotton and Arabidopsis, both of TCP12 and TCP18 (also known as BRANCHED1 (BRC1)) are related to branching and axillary bud growth [46, 47], and is also a response factor for spring bud recovery in perennial plants [48], and can directly bind to a HD-ZIP gene then improve its transcription level, resulting in enhancing the expression of NCED3, and inhibiting bud development [49]. By directly inhibiting the expression of CsPIN3, CsBRC1 inhibit auxin accumulation in axillary buds and inhibit lateral buds growing in cucumber [50]. For CYC/TB1 class TCPs in alfalfa predominately expressed at meristem, suggesting they play similar roles in plant developmental processes, as their functions in other species. Compared with other two types of TCP transcription factors, PCF class showed less tissue-/organ-specific expression patterns, and widely expressed in various tissues, suggesting that PCF class members play various regulatory roles at multiple developmental stages in both Medicago truncula [29]and Medicago sativa.

The expression level of MsTCPs in roots after treated with 200 mM NaCl and 10 μM KCl were tested respectively, to elucidate whether MsTCPs response to salt stress. We noticed that MsTCP9, MsTCP15 and MsTCP22 were significantly induced by 200 mM NaCl treatment, besides, MsTCP3, MsTCP14, MsTCP15 and MsTCP18 were significantly induced by K+ deficiency. The results implied that these MsTCPs may participate in salt stress through K+ up-taking or transportation. It was well known that TCP genes can be post-transcriptionally regulated by miR319 [25]. Recent research has reported that this miR319-TCP model affect multiple development and metabolic pathways. In A. thaliana, miR319 affects leaf development and photosynthesis through TCPs [15]. Besides it also regulates leaf growth and leaf aging through JA synthesis pathway [17, 51]. MIR319 was also found influence the elongation of internodes, which leads to the decreasing of plant height. Besides, miR319-TCPs significantly induced ethylene synthesis and downstream signaling in switchgrass [24]. And under K+ deficiency condition, ethylene stimulates the up-regulation of the low potassium ion marker gene AtHAK5 and improves plant perception of low K+ concentration [24].

It has been reported miR319-TCPs model functions in salt stress in many species such as Medicago truncula, Panicum virgatum and Solanum lycopersicum [23, 37, 52]. In this study, we identified four MsTCP genes (MsTCP3/4/10A/10B) can be degraded by miR319, and MsTCP3 significantly induced by K+ deficiency. Which we considered as a candidate gene that will regulate the tolerance of alfalfa via influencing the iron balance. Furthermore, MIM319 plants were conducted, and it turned out that salt tolerance was reduced in MIM319 plants compared to wild type alfalfa, which could be caused by the lower content of K+ in root and shoot. We also noticed that K+-deficiency induced genes were upregulated in MIM319 compared to wild-type (WT) plants, such as CNGCs, KEA5, HAKs and CIPK23. Interesting, a K+-efflux channel MsAKT2/3 was up-regulated in MIM319 plants, which has been reported as a down-regulated gene under K+ deficiency. Which may be part of explanation that salt sensitivity and K+ deficiency in MIM319 plants. Therefore, it is possible that miR319-MsTCPs module play a significant role in salt-tolerance by regulating the K+ up-taking and transportation pathway.

Conclusion

In conclusion, we identified 71 (23 non-redundant) MsTCPs in tetraploid alfalfa genome, which located on different chromosome and belong to PCF (37 members), CIN (28 members) and CYC/TB1 (9 members) subfamily. And, MsTCPs of the same subfamily had similar expression patterns in different organs, but with different expression pattern under Na+-excess and K+-deficiency situation, suggesting that MsTCP genes involved in growth and development regulation and keeping the homeostasis of iron under salt tolerance with function redundancy and specificity. Four MsTCPs (MsTCP3/4/10A/10B) were targeted and degraded by miR319 at the post-transcriptional level, and the expression levels of MsTCP1/2, MsTCP5 and MsTCP13 (containing miR319 target site but do not degraded by miR319) were also up-regulated in MIM319 plants. MIM319 plants showed a sensitive to salt stress, and low concentration of K+ in roots and leaves, demonstrating that miR319-TCPs module involved in the regulation of salt stress via K+ up-taking and/ or transportation, at least partly. And, the expression of potassium transported related genes showed higher expression level in MIM319 transgenic plants than that in WT. The study provide valuable information for future study of TCP genes in alfalfa and supplies candidate genes for salt-tolerance alfalfa molecular-assisted breeding.

Availability of data and materials

All data generated or analyzed during this study are included in this published article and its supplementary information files. The datasets analysed during the current study are available in Medicago Analysis Portal (https://v1.legumefederation.org/data/v2/Medicago/sativa/genomes/).

Abbreviations

TCP:

Teosinte Branched1/ Cycloidea/ Proliferating cell factors

TFs:

Transcription factors

CIN:

CINCINNATA

CYC/TB1:

CYCLOIDEA/TEOSINTE BRANCHED 1

MBS:

MYB binding site involved in drought-inducibility

JA:

Jasmonate

ABA:

Abscisic acid

ABRE:

Abscisic acid (ABA)-responsive elements

SARE:

Salicylic acid responsive elements

LTR:

Low temperature responsive elements

MS:

Apical meristem

YL:

Young leaves

OL:

Mature leaves

YS:

Young stems

MS:

Mature stems

R:

Root tip

PCR:

Polymerase Chain Reaction

qRT-PCR:

Quantitative Real-time Polymerase Chain Reaction

CNGCs:

Cyclic Nucleotide-gated Channels

HAKs:

High-affinity K + 

KEA:

K+ efflux anti-porter

CIPK23:

CBL-Interacting Protein Kinase 23

AKT:

Arabidopsis K+ channel

CDS:

Coding sequence

aa:

Amino acids

kDa:

Kilo Dalton

pI:

Protein isoelectric point

References

  1. Chen HT, Zeng Y, Yang YZ, Huang LL, Tang BL, Zhang H, et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat Commun. 2020;11(1):2494. https://doi.org/10.1038/s41467-020-16338-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Pu J, Li MY, Mao P, Zhou Q, Liu WX, Liu ZP. Genome-wide identification of the Q-type C2H2 transcription factor family in alfalfa (Medicago sativa) and expression analysis under different abiotic stresses. Genes (Basel). 2021;12(12):1906. https://doi.org/10.3390/genes12121906.

    Article  CAS  PubMed  Google Scholar 

  3. Dong XM, Deng H, Ma WX, Zhou Q, Liu ZP. Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress. BMC Genomics. 2021;22(1):603. https://doi.org/10.1186/s12864-021-07911-9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ma L, Liu XQ, Liu WH, Wen HY, Zhang YC, Pang YZ, et al. Characterization of squamosa-promoter binding protein-box family genes reveals the critical role of MsSPL20 in alfalfa flowering time regulation. Front Plant Sci. 2022;12:775690.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Cubas P, Lauter N, Doebley J, Coen E. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 1999;18(2):215–22. https://doi.org/10.1046/j.1365-313X.1999.00444.x.

    Article  CAS  PubMed  Google Scholar 

  6. Kosugi S, Ohashi Y. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 2002;30(3):337–48. https://doi.org/10.1046/j.1365-313X.2002.01294.x.

    Article  CAS  PubMed  Google Scholar 

  7. Navaud O, Dabos P, Carnus E, Tremousaygue D, Hervé C. TCP transcription factors predate the emergence of land plants. J Mol Evol. 2007;65(1):23–33. https://doi.org/10.1007/s00239-006-0174-z.

    Article  CAS  PubMed  Google Scholar 

  8. Martín-Trillo M, Cubas P. TCP genes: a family snapshot ten years later. Trends Plant Sci. 2010;15(1):31–9. https://doi.org/10.1016/j.tplants.2009.11.003.

    Article  CAS  PubMed  Google Scholar 

  9. Danisman S, van der Wal F, Dhondt S, Waites R, de Folter F, Bimbo A, et al. Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically. Plant Physiol. 2012;159(4):1511–23. https://doi.org/10.1104/pp.112.200303.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Li S. The Arabidopsis thaliana TCP transcription factors: a broadening horizon beyond development. Plant Signal Behav. 2015;10(7):e1044192–e1044192. https://doi.org/10.1080/15592324.2015.1044192.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Resentini F, Felipo-Benavent A, Colombo L, Blázquez MA, Alabadi D, Masiero S. TCP14 and TCP15 mediate the promotion of seed germination by gibberellins in Arabidopsis thaliana. Mol Plant. 2015;14(10):1771. https://doi.org/10.1016/j.molp.2014.11.018.

    Article  CAS  Google Scholar 

  12. Dhaka N, Bhardwaj V, Sharma MK, Sharma R. Evolving tale of TCPs: new paradigms and old lacunae. Front Plant Sci. 2017;8:479. https://doi.org/10.3389/fpls.2017.00479.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Koyama T, Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M. TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell. 2010;22(11):3574–88. https://doi.org/10.1105/tpc.110.075598.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Xu SL, Luo YH, Cai ZG, Cao XL, Hu XH, Yang J, et al. Functional diversity of CYCLOIDEA-like TCP genes in the control of zygomorphic flower development in Lotus japonicus. J Integr Plant Biol. 2013;55(3):221–31. https://doi.org/10.1111/j.1744-7909.2012.01169.x.

    Article  CAS  PubMed  Google Scholar 

  15. Bresso EG, Chorostecki U, Rodriguez RE, Palatnik JF. Spatial control of gene expression by miR319-regulated TCP transcription factors in leaf development. Plant Physiol. 2018;176(2):1694–708. https://doi.org/10.1104/pp.17.00823.

    Article  CAS  PubMed  Google Scholar 

  16. Palatnik JF, Allen E, Wu XL, Schommer C, Schwab R, Carrington JC, et al. Control of leaf morphogenesis by microRNAs. Nature. 2003;425(6955):257–63. https://doi.org/10.1038/nature01958.

    Article  CAS  PubMed  Google Scholar 

  17. Schommer C, Palatnik JF, Aggarwal P, Chételat A, Cubas P, Famer EE, et al. Control of jasmonate biosynthesis and senescence by miR319 targets. Plos Biol. 2008;6(9):e230. https://doi.org/10.1371/journal.pbio.0060230.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Koyama T, Furutani M, Tasaka M, Ohme-Takagi M. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell. 2007;19(2):473–84. https://doi.org/10.1105/tpc.106.044792.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Koyama T, Sato F, Ohme-Takagi M. Roles of miR319 and TCP transcription factors in leaf development. Plant Physiol. 2017;175(2):874–85. https://doi.org/10.1104/pp.17.00732.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Method San Diego Calif. 2001;25(4):402–8. https://doi.org/10.1006/meth.2001.1262.

    Article  CAS  Google Scholar 

  21. Yin ZJ, Li Y, Zhu WD, Fu XQ, Han XL, Wang JJ, et al. Identification, characterization, and expression patterns of TCP genes and microRNA319 in cotton. Int J Mol Sci. 2018;19(11):3655. https://doi.org/10.3390/ijms19113655.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Mukhopadhyay P, Tyagi AK. OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci Rep. 2015;5:9998. https://doi.org/10.1038/srep09998.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Cao CY, Long RC, Zhang TJ, Kang JM, Zheng W, Wang PQ, et al. Genome-wide identification of microRNAs in response to salt/alkali stress in Medicago truncatula through high throughput sequencing. Int J Mol Sci. 2018;19(12):4076. https://doi.org/10.3390/ijms19124076.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Liu YR, Li DY, Yan JP, Wang KX, Luo H, Zhang WJ. MiR319-mediated ethylene biosynthesis, signalling and salt stress response in switchgrass. Plant Biotechnol J. 2019;17(12):2370–83. https://doi.org/10.1111/pbi.13154.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zhou M, Li DY, Li ZG, Hu Q, Yang CH, Zhu LH, et al. Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol. 2013;161(3):1375–91. https://doi.org/10.1104/pp.112.208702.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Almeida DM, Gregorio GB, Oliveira MM. Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype. Plant Mol Biol. 2017;93(1–2):61–77. https://doi.org/10.1007/s11103-016-0547-7.

    Article  CAS  PubMed  Google Scholar 

  27. Niu X, Bressan RA, Hasegawa PM, Pardo JM. Ion homeostasis in NaCl stress environments. Plant physiol. 1995;109(3):735–42. https://doi.org/10.1104/pp.109.3.735.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Chen CJ, Chen H, Zhang Y, Thomas RH, Frang MH, He YH, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202. https://doi.org/10.1016/j.molp.2020.06.009.

    Article  CAS  PubMed  Google Scholar 

  29. Wang HF, Wang HW, Liu R, Xu YT, Lu ZC, Zhou CE. Genome-wide identification of TCP family transcription factors in Medicago truncatula reveals significant roles of miR319-targeted TCPs in nodule development. Front Plant Sci. 2018;9:774. https://doi.org/10.3389/fpls.2018.00774.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang WJ, Wang T. Enhanced salt tolerance of alfalfa (Medicago sativa) by rstB gene transformation. Plant Sci. 2015;234:110–8. https://doi.org/10.1016/j.plantsci.2014.11.016.

    Article  CAS  PubMed  Google Scholar 

  31. Julkowska MM, Hoefsloot HC, Mol S, Feron R, de Boer GJ, Haring MA, et al. Capturing Arabidopsis root architecture dynamics with ROOT-FIT reveals diversity in responses to salinity. Plant Physiol. 2014;166(3):1387–402. https://doi.org/10.1104/pp.114.248963.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Gierth M, Mäser P. Potassium transporters in plants–involvement in K+ acquisition, redistribution and homeostasis. FEBS Lett. 2007;581(12):2348–56. https://doi.org/10.1016/j.febslet.2007.03.035.

    Article  CAS  PubMed  Google Scholar 

  33. Hetherington AM, Brownlee C. The generation of Ca(2+) signals in plants. Annu Rev Plant Biol. 2004;55:401–27. https://doi.org/10.1146/annurev.arplant.55.031903.141624.

    Article  CAS  PubMed  Google Scholar 

  34. Li J, Wu WH, Wang Y. Potassium channel AKT1 is involved in the auxin-mediated root growth inhibition in Arabidopsis response to low K+ stress. J Integr Plant Biol. 2017;59:895–909. https://doi.org/10.1111/jipb.12575.

    Article  CAS  PubMed  Google Scholar 

  35. Geiger D, Becker D, Lacombe B, Hedrich R. Outer pore residues control the H+ and K+ sensitivity of the Arabidopsis potassium channel AKT3. Plant Cell. 2002;14(8):1859–68. https://doi.org/10.1105/tpc.003244.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Yao X, Ma H, Wang J, Zhang DB. Genome-wide comparative analysis and expression pattern of TCP gene families in Arabidopsis thaliana and Oryza sativa. J Integr Plant Biol. 2007;49(6):885–97. https://doi.org/10.1111/j.1744-7909.2007.00509.x.

    Article  CAS  Google Scholar 

  37. Huo YZ, Xiong WD, Su KL, Li Y, Yang YW, Fu CX, et al. Genome-wide analysis of the TCP gene family in switchgrass (Panicum virgatum L.). Int J Genomics. 2019;8514928. https://doi.org/10.1155/2019/8514928.

  38. Wei W, Hu Y, Cui MY, Han YT, Gao K, Feng JY. Identification and transcript analysis of the TCP transcription factors in the diploid woodland strawberry Fragaria vesca. Front Plant Sci. 2016;7:1937. https://doi.org/10.3389/fpls.2016.01937.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Uberti-Manassero NG, Coscueta ER, Gonzalez DH. Expression of a repressor form of the Arabidopsis thaliana transcription factor TCP16 induces the formation of ectopic meristems. Plant Physiol Biochem. 2016;108:57–62. https://doi.org/10.1016/j.plaphy.2016.06.031.

    Article  CAS  PubMed  Google Scholar 

  40. Kim JS, Mizoi J, Yoshida T, Fujita Y, Nakajima J, Ohori T, et al. An ABRE promoter sequence is involved in osmotic stress-responsive expression of the DREB2A gene, which encodes a transcription factor regulating drought-inducible genes in Arabidopsis. Plant Cell Physiol. 2011;52:2136–46. https://doi.org/10.1093/pcp/pcr143.

    Article  CAS  PubMed  Google Scholar 

  41. Méndez-Vigo B, de Andrés MT, Ramiro M, Martínez-Zapater JM, Alonso-Blanco C. Temporal analysis of natural variation for the rate of leaf production and its relationship with flowering initiation in Arabidopsis thaliana. J Integr Plant Biol. 2010;61(6):1611–23. https://doi.org/10.1093/jxb/erq032.

    Article  CAS  Google Scholar 

  42. Li HY, Yuan HM, Liu FM, Luan JY, Yang Y, Ren L, et al. BpTCP7 gene from Betula platyphylla regulates tolerance to salt and drought stress through multiple hormone pathways. Plant Cell Tissue Organ Cult. 2020;141(1):17–30. https://doi.org/10.1007/s11240-019-01748-7.

    Article  CAS  Google Scholar 

  43. Yuan CQ, Huang D, Yang Y, Sun M, Cheng T, Wang J, et al. CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium. Plant Mol Biol. 2020;103(1–2):159–71. https://doi.org/10.1007/s11103-020-00981-5.

    Article  CAS  PubMed  Google Scholar 

  44. Chang SH, Tan CM, Wu CT, Lin TH, Jiang SY, Liu RC, et al. Alterations of plant architecture and phase transition by the phytoplasma virulence factor SAP11. J Exp Bot. 2018;69(22):5389–401. https://doi.org/10.1093/jxb/ery318.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Koyama T, Sato F, Ohme-Takagi M. A role of TCP1 in the longitudinal elongation of leaves in Arabidopsis. Biosci Biotechnol Biochem. 2010;74(10):2145–7. https://doi.org/10.1271/bbb.100442.

    Article  CAS  PubMed  Google Scholar 

  46. Aguilar-Martinez JA, Poza-Carrion C, Cubas P. Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds. Plant Cell. 2007;19(2):458–72. https://doi.org/10.1105/tpc.106.048934.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Diao YY, Zhan JJ, Zhao YY, Liu L, Liu PP, Wei X, et al. GhTIE1 regulates branching through modulating the transcriptional activity of TCPs in cotton and arabidopsis. Front Plant Sci. 2019;10:11. https://doi.org/10.3389/fpls.2019.01348.

    Article  Google Scholar 

  48. Singh RK, Maurya JP, Azeez A, Miskolczi P, Tylewicz S, Stojkovič K, et al. A genetic network mediating the control of bud break in hybrid aspen. Nat Commun. 2018;9:4173. https://doi.org/10.1038/s41467-018-06696-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. González-Grandío E, Pajoro A, Franco-Zorrilla JM, Tarancón C, Immink RC, Cubas P. Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds. Proc Natl Acad Sci U S A. 2017;114(2):E245–54. https://doi.org/10.1073/pnas.1613199114.

    Article  CAS  PubMed  Google Scholar 

  50. Shen JJ, Zhang YQ, Ge DF, Wang ZY, Song WY, Gu R, et al. CsBRC1 inhibits axillary bud outgrowth by directly repressing the auxin efflux carrier CsPIN3 in cucumber. Proc Natl Acad Sci U S A. 2019;116(34):17105–14. https://doi.org/10.1073/pnas.1907968116.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Liu WT, Chen PW, Chen LC, Yang CC, Chen SY, Huang GF, et al. Suppressive effect of microRNA319 expression on rice plant height. Theor Appl Genet. 2017;130(7):1507–18. https://doi.org/10.1007/s00122-017-2905-5.

    Article  CAS  PubMed  Google Scholar 

  52. Shi XP, Jiang FL, Wen JQ, Cui SY, Zhou YZ, Wu Z. MicroRNA319 family members play an important role in Solanum habrochaites and S lycopersicum responses to chilling and heat stresses. Biologia Plantarum. 2019;63:200–9.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to Prof. Dayong Li of Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences for providing the MIM319 expression vector.

Funding

This work was supported by the National Natural Science Foundation of China (32201454) to Yanrong Liu.

Author information

Authors and Affiliations

  1. College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China

    Mingxiao Zhang, Shangqian Qin, Jianping Yan, Lin Li, Mingzhi Xu, Yanrong Liu & Wanjun Zhang

Authors
  1. Mingxiao Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shangqian Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jianping Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mingzhi Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yanrong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wanjun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Yanrong Liu and Wanjun Zhang: Design the study and revised the manuscript. Mingxiao Zhang, Shangqian Qin, Yanrong Liu, Jianping Yan, Lin Li, and Mingzhi Xu: Performed the experiments and analyzed the data. Mingxiao Zhang and Yanrong Liu: Wrote the original manuscript. The author(s) read and approved the final manuscript.

Corresponding authors

Correspondence to Yanrong Liu or Wanjun Zhang.

Ethics declarations

Ethics approval and consent to participate

Experimental research and field studies on plants in this paper, including the collection of plant material, comply with relevant institutional, national, and international guidelines and legislation.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1: Fig. S1.

Chromosomal distribution of MsTCP genes. Fig. S2. Structure analysis of allele TCP genes. Fig. S3. Prediction of cis-elements of promoters among allele TCP genes. Fig. S4. The sequences of miR319 in alfalfa  and prediction of  miR319-targeted MsTCPs. a. The phylogenetic analysis of MsMIR319, MtMIR319, AtMIR319 and OsMIR319 and their mature miR319 sequences. b. Comparison of MIM319 sequence with miR319 in alfalfa. c. Prediction of target regions for miR319 in MsTCPs. Fig. S5. Comparison of MIM319 and WT plants under different level of salt stress. Table S1. Primers used for qRT-PCR. Table S2. Primers used in 5'RLM-RACE. Table S3. The expression profiling of MsTCP genes in different organs. Table S4. The expression level of MsTCPs in MIM319 plants. Table S5. Prediction of the binding region of TCP3 and TCP4 on the promoter of potassium-related iron-transport genes.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, M., Qin, S., Yan, J. et al. Genome-wide identification and analysis of TCP family genes in Medicago sativa reveal their critical roles in Na+/K+ homeostasis. BMC Plant Biol 23, 301 (2023). https://doi.org/10.1186/s12870-023-04318-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12870-023-04318-4

Keywords

BMC Plant Biology

ISSN: 1471-2229

Contact us