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Article

Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses

by
Hao Liu
1,2,†,
Xianyang Li
1,†,
Yunfei Zi
3,
Guoqing Zhao
3,
Lihua Zhu
3,
Ling Hong
3,
Mingna Li
1,
Shiqing Wang
3,
Ruicai Long
1,
Junmei Kang
1,
Qingchuan Yang
1 and
Lin Chen
1,*
1
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2
College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
3
Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos 017000, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2023, 24(16), 12683; https://doi.org/10.3390/ijms241612683
Submission received: 22 July 2023 / Revised: 7 August 2023 / Accepted: 8 August 2023 / Published: 11 August 2023
(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses 3.0)
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Abstract

:
Heat shock transcription factors (HSFs) are important regulatory factors in plant stress responses to various biotic and abiotic stresses and play important roles in growth and development. The HSF gene family has been systematically identified and analyzed in many plants but it is not in the tetraploid alfalfa genome. We detected 104 HSF genes (MsHSFs) in the tetraploid alfalfa genome (“Xinjiangdaye” reference genome) and classified them into three subgroups: 68 in HSFA, 35 in HSFB and 1 in HSFC subgroups. Basic bioinformatics analysis, including genome location, protein sequence length, protein molecular weight and conserved motif identification, was conducted. Gene expression analysis revealed tissue-specific expression for 13 MsHSFs and tissue-wide expression for 28 MsHSFs. Based on transcriptomic data analysis, 21, 11 and 27 MsHSFs responded to drought stress, cold stress and salt stress, respectively, with seven responding to all three. According to RT–PCR, MsHSF27/33 expression gradually increased with cold, salt and drought stress condition duration; MsHSF6 expression increased over time under salt and drought stress conditions but decreased under cold stress. Our results provide key information for further functional analysis of MsHSFs and for genetic improvement of stress resistance in alfalfa.

1. Introduction

Plants are vulnerable to various abiotic stresses during their growth and development, such as high-temperature stress, salt stress, alkali stress and cold stress [1,2]. These abiotic stresses seriously threaten the normal growth and development of plants and even cause death [3]. During evolution, plants have developed various biological mechanisms to address these abiotic stresses [4]. Transcription factors play an important role in the plant response to abiotic stresses [5]. As a family of transcription factors widely present in plants, heat shock transcription factors (HSFs) regulate expression of downstream genes through specific cis-regulatory elements, enhancing the ability of plants to cope with different abiotic stresses [6].
Most HSF members contain five conserved domains: a DNA-binding domain (DBD) located at the N-terminus, an oligomerization domain (OD or HR-A/B), a nuclear localization signal (NLS), a nuclear export signal (NES) and an activation domain at the C-terminus (CTAD) [7]. Among the five domains, the DBD and OD are the most conserved [8]. The DBD domain specifically recognizes and binds to the conserved motifs of heat shock elements in target genes (5′-AGAAnnTTCT-3′), regulating the expression of downstream stress resistance genes [9]. The HR-A/B domain usually has a coiled-coil structure and is linked to the DBD domain through a flexible connector with variable length [10]. The HSF gene family is divided into three subgroups according to the length of the DBD domain from the OD domain and the number of amino acid residues between HR-A and HR-B: A, B and C [11]. The NLS domain is usually composed of basic amino acids, which guide the transport of HSF proteins from the cytoplasm to the nucleus [12]; conversely, the NES domain is usually rich in leucine, which promotes HSF protein export from the nucleus to the cytoplasm [13]. The CTAD domain is the least conserved among the five domains and typically contains the AHA motif, which is composed of large hydrophobic, aromatic and acidic amino acid residues [14]. In addition, the AHA motif is only found in members of the A subgroup and does not exist in the B and C subgroups [15].
The first HSF gene in plants was discovered in tomatoes in 1990 [16], and since then, an increasing number of HSF genes have been cloned with the continuous completion of reference genomes for different plants. Many studies have shown that HSF genes are involved in various processes of plant growth and development. In A. thaliana, AtHSFA9, which can be activated by ABI3, regulates the expression of downstream genes to modulate the process of embryonic development and seed maturation [17]. The 14 HSF members found in citrus fruits are all involved in the development and ripening process of fruit, among which CrHsfB2a and CrHsfB5 regulate the citrate content [18]. In addition, HSF family members have been confirmed to be widely involved in the response to various abiotic stresses, such as high-temperature stress, drought stress and salt stress. In Arabidopsis, overexpression of the HsfA2 gene can significantly improve the survival rate of transgenic lines under high temperatures, that is, enhancing their heat tolerance [19]. The AtHsfA1 gene can regulate the synthesis of downstream heat shock proteins under high temperatures, enabling plants to cope with high-temperature stress [20]. Overexpression of the SlHsfA3 gene in tomatoes also increases the ability of plants to withstand high-temperature stress [21]. Drought stress, salt stress and cold stress can also induce the gene expression of HSFs. In carrots, three HSF genes are upregulated under salt stress, and 33 HSF genes are downregulated under drought stress [22]. OsHsfB2b negatively regulates salt tolerance in rice [23], and overexpression of AtHsfA1b improves yield and the harvest index under drought stress [24]. These results indicate that members of the HSF gene family not only participate in the normal growth and development of plants but also play an important role in the processes by which plants respond to various abiotic stresses.
To date, 21, 25, 30, 41, 38 and 60 HSF members have been found in Arabidopsis [11], rice [25], maize [26], bamboo [27], soybean [28] and Brassica juncea [29], respectively. Alfalfa is one of the most important leguminous forage crops in the world, with rich nutritional value and is known as the “king of forage” [30]. At present, three reference genomes of alfalfa have been assembled. The reference genome “Zhongmu No.1” is a haploid genome with a genome size of 816 Mb [31]; reference genomes “Xinjiangdaye” and “Zhongmu No.4” are autotetraploid genomes with genome sizes of 3.15 Gb and 2.74 Gb [32,33], respectively. A previous study showed that there are 16 MsHSF members in the “Zhongmu No.1” reference genome, which is a haploid genome [34]. However, HSF gene family members remain unidentified in the tetraploid alfalfa reference genome, so it can be considered that more HSF genes can be identified in the tetraploid alfalfa reference genome. In this study, the MsHSF members were identified in the “Xinjiangdaye” autotetraploid genome. The genome position, gene structure, conserved motifs and cis-acting elements in the promoters of these MsHSF members were determined. The evolutionary relationship and gene replication events of these MsHSF members between alfalfa and Glycine max, M. truncatula and A. thaliana were comprehensively examined. Moreover, in order to determine their potential roles and the response level of each HSF gene to different stresses, expression patterns of these MsHSF members in six different tissues of alfalfa were analyzed in depth and their dynamic expression changes under drought stress, salt stress and cold stress were analyzed to preliminarily clarify the functions of different MsHSF genes in response to abiotic stresses in alfalfa. Our results provide valuable information for further clarifying the molecular regulatory mechanisms of MsHSF genes involved in various abiotic stresses in alfalfa in the future.

2. Results

2.1. MsHSF Gene Identification and Characterization in the Alfalfa Autotetraploid Genome

To identify MsHSF gene members in the alfalfa autotetraploid genome “Xinjangdaye”, Hidden Markov model (HMM) analysis and domain analysis were conducted in this study. A total of 104 MsHSF genes were found in the “Xinjiangdaye” reference genome. The gene ID, genomic position, length of CD sequence, length of proteins, molecular weight (MW), isoelectric point (pI) and subcellular location of these 104 MsHSF genes are shown in Table 1 and Table S1 and Figure 1.
Among the 104 MsHSF members, MsHSF23 has the shortest CD length of 369 bp; MsHSF16 has the longest CD length of 4506 bp. The protein MWs of these MsHSF members range from 14.55 kDa (MsHSF23) to 171.49 kDa (MsHSF16), and their pI values range from 4.51 (MsHSF31) to 8.8 (MsHSF93). Based on the results of subcellular location prediction, 101 MsHSF members are predicted to localize to the nucleus and MsHSF23 to the cytosol; two MsHSF members (MsHSF95 and MsHSF98) are predicted to localize to the chloroplast.
As shown in Figure 1, the 101 MsHSF members (MsHSF1–MsHSF101) are unevenly distributed on the 32 chromosomes of the “Xinjiangdaye” reference genome, but three MsHSF members (MsHSF102–MsHSF104) are not located on chromosomes. Six MsHSF genes are distributed on chr4.4 and chr6.3, the largest. Five MsHSF genes are distributed on chr4.1, chr4.3 and chr6.1. Four MsHSF genes are located on chr1.1, chr1.3, chr1.4, chr2.3, chr5.2, chr5.3, chr6.2 and chr6.4. Three MsHSF genes are distributed on chr1.2, chr2.2, chr4.2, chr5.1, chr5.4 and chr8.4. Only one MsHSF gene is located on chr3.1, chr7.2 and chr8.3. Finally, the 104 MsHSF genes were renamed based on their position in the reference genome.

2.2. Phylogenetic Analysis of HSF Genes in Alfalfa

To understand the classification and evolutionary relationships of MsHSF genes in alfalfa, 126 HSF protein sequences, including 104 from alfalfa and 22 from the model plant Arabidopsis thaliana [25], were used to construct a phylogenetic tree (Figure 2). Based on the clustering results, the 104 MsHSF members in alfalfa can be divided into three major subgroups: HSF-A, HSF-B and HSF-C. There are 68 MsHSF members belonging to the A subgroup. The A subgroup was further divided into four subclusters according to the phylogenetic relationship, defined as A1, A2, A3 and A4. Thirty-five MsHSF members belong to the B subgroup, with only one MsHSF member (MsHSF72) belonging to the C subgroup. Proteins in the same class usually have similar biological functions, providing valuable information for predicting the biological function of MsHSF members in the future.

2.3. Gene Structure and Conserved Motif Analysis of MsHSF Genes

As shown in Figure 3, all 104 MsHSF members in alfalfa contain at least one intron. MsHSF16, which belongs to subgroup A4, contains the largest number of introns, up to 14. Introns are involved in regulating variable splicing and expression of genes. In addition, we found the length of the introns of 104 MsHSF members to be diverse.
To identify conserved motifs among the MsHSFs, the MEME tool was used to conduct motif analysis. A total of 10 conserved motifs (Motif1–Motif10) were detected among the 104 MsHSF members. The 68 MsHSF members belonging to the A subgroup mainly contain Motif1, Motif2, Motif3, Motif4, Motif5, Motif6, Motif7, Motif9 and Motif10 and the 35 MsHSF members belonging to the B subgroup mainly Motif1, Motif2, Motif3, Motif6, Motif8, Motif9 and Motif10. MsHSF72, which belongs to the C subgroup, mainly contains Motif1, Motif2, Motif3, Motif4 and Motif9. Among the 10 conserved motifs, Motif1, Motif2 and Motif3 are present in the protein sequences of most MsHSF members. This result indicates that these three motifs (Motif1, Motif2 and Motif3) may comprise the conserved DBD domain and can be used as a criterion to determine whether a gene is a member of the HSF gene family. In addition, we found that some motifs only exist in specific subgroups and MsHSF members. For example, Motif8 was only found in the B subgroup of the MsHSF gene family, Motif5 only in the A subgroup and Motif7 only in the A4 subgroup. These results suggest that the MsHSF genes in the same subgroup have identical structures and conserved motifs and that the diversity of motifs led to the diversity of biological functions among MsHSF members.

2.4. Gene Duplication Events and Synteny Analysis among MsHSF Genes

To better understand potential gene duplication events among the MsHSF genes, tandem duplication and segmental duplication analyses were conducted in this study. As shown in Figure 4, 8 tandem duplication events involving 24 MsHSF members were found. For example, MsHSF21/MsHSF22, a tandem duplication event located at chr2.3, and MsHSF77/78/79/80/81, another tandem duplication event, involve five MsHSF genes located at chr6.3 (Table S2). In addition, a total of 172 segmental duplication events involving 86 different MsHSF members were detected (Table S3). For example, MsHSF1/MsHSF8/MsHSF12 are located on three different chromosomes, chr1.1, chr1.3 and chr1.4, respectively. These results indicate that duplication events have occurred widely among MsHSF genes, and that segmental duplication may be the evolutionary driving force of the MsHSF gene family in alfalfa.
Next, to clarify potential evolutionary events of the HSF gene family in various crops, collinearity maps of alfalfa with G. max, A. thaliana and M. truncatula were constructed. As illustrated in Figure 5, 55, 83 and 75 MsHSF genes show collinearity with A. thaliana, M. truncatula and G. max, respectively. Among these genes, there are 80 collinear gene pairs in A. thaliana, 118 in M. truncatula and 255 in G. max. The number of collinear genes between alfalfa and the two legumes (G. max and M. truncatula) is significantly greater than that between alfalfa and A. thaliana, suggesting that the MsHSF gene family is relatively conserved among legume plants.

2.5. Analysis of Cis-Elements in the Promoter Regions of MsHSF Genes

To further clarify the biological functions of MsHSF genes in alfalfa, cis-elements of promoter regions located approximately 2 kb upstream of the start codon (ATG) of the MsHSF genes were analyzed. As depicted in Figure 6, a total of 11 different cis-elements were found. In detail, 74.0% of the MsHSF members contain an abscisic acid responsiveness element (ABRE), 64.4% MeJA responsiveness elements (TGACG element and CGTCA element), 59.6% auxin responsiveness elements (AuxRR element, TGA-box element and TGA element), 48.1% GA responsiveness elements (GARE, P-box and TATC box), 37.5% the salicylic acid responsiveness element and 33.7% the zein metabolism regulation element. In addition, we found that some MsHSF genes contain specific cis-elements in their promoter regions. For example, there are 15 ABREs in the promoter region of MsHSF33; only one P-box element was found in the promoter region of MsHSF30, and only one TCA element was found in the promoter region of MsHSF43. These results indicate that expression of these MsHSF genes is likely induced by different hormones and stimuli.

2.6. Expression Patterns of MsHSF Genes in M. sativa Tissues

To clarify expression patterns of the MsHSF genes in different tissues in alfalfa, transcriptome data for six different alfalfa tissues (leaves, elongated stems, roots, preelongated stems, nodules and flowers) were obtained from a public database (Table S4). The results showed that 65 MsHSF genes were expressed in one or more of the six investigated tissues; the other 39 MsHSF genes showed no expression in these tissues, but they might be expressed in different tissues or under specific stress conditions. Overall, expression patterns of the 65 expressed MsHSF genes varied in different tissues. As shown in Figure 7, 13 MsHSF genes were expressed in only one specific tissue, indicating tissue specificity. For example, MsHSF29 and MsHSF30 were only expressed in flowers, MsHSF4 and MsHSF96 only in leaves and MsHSF42/70/90 only in roots. We also found that 8 MsHSF genes were expressed in two different tissues, 7 MsHSF genes in three different tissues, 4 MsHSF genes in four different tissues, 5 MsHSF genes in five different tissues and 28 MsHSF genes in six different tissues. Furthermore, the expression abundance of these MsHSF genes varied significantly among different tissues. For example, MsHSF100 was expressed in both roots and flowers, but its expression abundance in roots was significantly higher than that in flowers. MsHSF6/27/33 were expressed in six different tissues, but MsHSF6 was mainly expressed in leaves; MsHSF27/33 was mainly expressed in flowers. These results indicate that these MsHSF genes have different functions during normal growth and development.

2.7. Expression Analysis for MsHSF Genes under Different Abiotic Stresses

To clarify differential expression levels of the MsHSF genes under different abiotic stresses (drought, cold and salt), transcriptomic data of alfalfa seedlings under drought, cold and salt stress were obtained from a public database and analyzed (Table S5). As presented in Figure 8A–C, 21, 27 and 11 MsHSF genes responded to drought stress, salt stress and cold stress, respectively, with some responding to only one abiotic stress. For example, MsHSF31/38 only responded to drought stress, MsHSF18/43/50/62/101 only responded to salt stress and MsHSF31/38 only responded to cold stress in alfalfa. However, other MsHSF genes responded to two or three different abiotic stresses, 19 MsHSF members responded to both drought and salt stress simultaneously, 10 responded to both cold and salt stress simultaneously and 7 responded to both cold and drought stress simultaneously. Surprisingly, seven MsHSF genes (MsHSF6/12/27/33/58/82/86) were found to simultaneously respond to cold, drought and salt stress.
To verify the results based on transcriptomic data, an RT–PCR experiment was conducted for three selected genes (MsHSF27/33/6). The related primers are shown in Table S6. The expression abundance of MsHSF27/33 gradually increased over time under drought, cold and salt stress (Figure 9A–C). The expression abundance of MsHSF6 increased over time under salt and drought stress but decreased over time under cold stress. As these results are similar to the transcriptome expression results, these genes can be used as candidate genes for further study of their functions in response to abiotic stresses.

2.8. Identification and Analysis of Genes Coexpressed with MsHSF6/27/33 under Salt Stress

To investigate whether MsHSF6/27/33 is involved in salt stress in alfalfa, genes co-expressed with MsHSF6/27/33 were identified based on correlation analysis (Table S7). As shown in Figure 10, 56 genes correlated significantly with MsHSF6 under salt stress, 52 with MsHSF27 under salt stress and 42 with MsHSF33 under salt stress.
Among the 56 genes co-expressed with MsHSF6 under salt stress, 10 genes correlated negatively and 46 positively. Among the 46 genes correlating positively with MsHSF6 under salt stress, some are involved in the plant response to salt stress. For example, the correlation coefficient between the expression abundance of MsHSF6 and MS.gene067783, which encodes an NAC transcription factor, was 0.99. Expression of MS.gene36742, which encodes the auxin-responsive protein IAA26, also correlated significantly positively with MsHSF6 under salt stress.
Among the 52 genes co-expressed with MsHSF27 under salt stress, 8 genes correlated negatively and 44 positively. A previous study showed that HSF genes can regulate the expression of heat shock proteins [35]. Of the 8 genes correlating negatively with MsHSF27, MS.gene89106 encodes a heat shock protein. CBL-interacting serine/threonine-protein can respond to salt stress in many plants [36]. Among the 44 positively correlating genes, expression of MS.gene025407, which encodes a CBL-interacting serine/threonine-protein kinase, correlated significantly positively with MsHSF27 under salt stress.
Among the 42 genes co-expressed with MsHSF33 under salt stress, 9 correlated negatively and 33 positively. Of the nine negatively correlating genes with MsHSF33, MS.gene03590 encodes an NAC transcription factor and NAC transcription factors regulate the entire process of plant growth and development, including formation of the plant secondary wall and xylem, root growth, fruit ripening and leaf senescence [37]. Expression of MS.gene072903, which encodes the DEAD-box protein, correlated significantly with MsHSF33 under salt stress. A previous study showed that the DEAD-box protein can respond to drought and salt stress in plants through the ABA pathway [38].

3. Discussion

The HSF gene family is one of the important transcription factor families in plant growth and development and in response to abiotic stresses. Previous studies have shown that there are significant differences in the number of HSF gene family members in different plant species. Twenty-one AtHSF members have been found in Arabidopsis [11]. In soybean, a total of 38 HSF genes were identified in the reference genome [28]. In addition, 60 HSF members were found in Brassica juncea [29]. Overall, the number of HSF genes identified in the same species varies due to differences in reference genome versions and identification methods. For example, three different studies found 56, 61 and 82 TaHSF genes in wheat [39,40,41]. Interestingly, a previous study reported 16 MsHSF genes in alfalfa [34]. However, in our study, a total of 104 MsHSF members were found. We speculate that there are two main reasons for such a huge difference. The first is that different versions of the alfalfa reference genome were selected. The previous study used the “Zhongmu NO.1” reference genome, which is a haploid genome with a genome size of 816 Mb, while our study used the “Xinjiangdaye” reference genome, which is an autotetraploid genome with a genome size of 3.15 Gb. The second reason may be that different identification strategies and threshold settings in different studies lead to differences in the final number of HSF family members in alfalfa.
A gene family is a group of genes that usually originate from the same ancestor, and there may be multiple copies of this ancestor gene. Whole-genome duplication is one of the main driving forces for the expansion of gene family members in plants [42], and segmental duplication and tandem duplication are two main forms of expansion of gene family members in plants [43]. The genome of alfalfa experienced whole-genome duplication during evolution, and many TEs accumulated, which eventually led to the expansion of the alfalfa genome. Previous studies have shown that segmental duplication plays an important role in the expansion of the HSF gene family [7]. In a study of the HSF gene family in moso bamboo, 27 segmental duplications and 2 tandem duplication events were detected among the 41 PeHSF genes [27]. In wheat, 68.8% of TaHSF genes have been involved in segmental duplication events [40]. In our study, 172 segmental duplication events involved 86 MsHSF genes, with only 8 tandem duplication events involving 24 MsHSF members. These results are consistent with those of previous studies of the HSF gene family.
HSF genes have been proven by many studies to be widely involved in plant growth and development and various abiotic stress processes, including responses to salt stress, drought stress and high-temperature stress. Phylogenetic tree analysis can help predict the biological function of unknown genes through known gene functions. AtHSFA9 is activated by ABI3 to regulate the expression of downstream genes, participating in the process of plant seed maturation and embryo development in Arabidopsis [17]. In this study, we found 68 MsHSF genes, with AtHSFA9 belonging to the same subgroup. Among these MsHSF genes, MsHSF94 was significantly expressed in alfalfa flowers, which are the organs for seed development. Therefore, we inferred that MsHSF94 also participates in the seed maturation process of alfalfa. Overexpression of AtHsfA1 and AtHsfA2 from Arabidopsis and SlHsfA3 from tomato significantly improves heat tolerance [44,45,46]. In addition to heat stress, many HSF genes have been proven to be involved in salt and drought stresses. In Tamarix hispida, ThHSFA1 positively regulates salt tolerance by directly activating the expression of ThWRKY4 [47]. OsHsfB2b negatively regulates drought tolerance and salt tolerance in rice [23]. In a study of the HSF gene family in carrots, 3 HSF genes were upregulated under salt stress and 33 were downregulated under drought stress, which suggests that these HSF genes may be involved in the response to salt and drought stresses [22]. In the present study, we found that 21 and 27 MsHSF genes responded to drought stress and salt stress, respectively; moreover, 12 MsHSF genes (MsHSF29/89/46/66/14/59/3/10/76/55/92/91) responded to both drought and salt stress. Some studies have also found that HSF genes respond to cold stress in plants. For example, there are five VviHsf genes in wild Chinese grapevine, and six PvHsf genes in common bean were found to respond to cold stress [48,49]. We also found that 11 MsHSF genes (MsHSF1/6/12/22/27/33/51/58/82/86/104) responded to cold stress in alfalfa. Taken together, these results indicate that HSF genes play an important role in the response to various abiotic stresses in plants.
Alfalfa is an important forage crop worldwide and has a high content of protein and other nutrients. However, alfalfa often encounters a variety of abiotic stresses during growth and development, resulting in a decline in yield and quality. Therefore, cultivating new alfalfa varieties with strong stress resistance is of great significance for ensuring crop production. Recently, with the development of transgenic and gene editing technology, it is possible to cultivate alfalfa varieties with strong abiotic stress resistance. In this study, we identified 104 MsHSF members from the tetraploid genome of alfalfa and found that many MsHSF members can respond to drought, salt and cold stress. In future research, these MsHSF members can be precisely modified by using transgenic and gene editing technologies to cultivate new alfalfa germplasm. Hence, this study provides valuable information for further research on the biological function of MsHSF genes and the molecular mechanism of abiotic stress regulation in alfalfa and other plants.

4. Materials and Methods

4.1. Identification of MsHSF Genes in the Medicago Sativa Genome

The alfalfa genome was obtained from the Alfalfa Genome project (https://fgshare.com/projects/whole_genome_sequencing_and_assembly_of_Medicago_sativa/66380 (accessed on 20 May 2023)) [32]. Arabidopsis protein sequences were obtained from The Arabidopsis Information Resource (TAIR) (https://www.arabidopsis.org/ (accessed on 20 May 2023)), and the Medicago truncatula genome was obtained from the website (http://www.medicagogenome.org/ (accessed on 20 May 2023)). Hidden Markov model (HMM) analysis was carried out for the required sequence search, and the Pfam database (https://pfam.xfam.org/ (accessed on 21 May 2023)) was used to obtain the HMM configuration file for HSF domains (PF00447) [50]. A total of 104 MsHSF genes were identified in the alfalfa genome using BLAST, with a cutoff value of E-value > 1e−10. The identified MsHSFs were submitted to NCBI Conserved Domain Database (CDD, https://www.ncbi.nlm.nih.gov/cdd (accessed on 22 May 2023)) to check for the existence of conserved structural domains.

4.2. Chromosome Location and Gene Information

The chromosome information of MsHSFs was visualized using TBtools software (v1.108, Chen, C., GZ, China) [51]. MsHSFs were renamed according to the position of the gene on each chromosome. The characteristics of the identified MsHSF gene, including CD length, protein length, MW and pI, were studied using the Expasy website (https://web.expasy.org/compute_pi/ (accessed on 22 May 2023)).

4.3. Phylogenetic Analysis

The protein sequences used to construct phylogenetic trees were obtained from the UniProt database (https://www.UniProt.org (accessed on 23 May 2023)), and the phylogenetic trees were constructed by using MEGA software (v11.0, Tamura, K., Tokyo, Japan) [52] with the protein sequences of alfalfa and Arabidopsis HSF family genes. Clusterx2.0 software was used to compare multiple amino acid sequences of the identified MsHSF genes with default parameters. A phylogenetic tree was constructed using the neighbor-joining (NJ) method and 1000 bootstrap replicates were performed. The Poisson correction method was used to calculate evolutionary distance. The grouping of MsHSF refers to the method of Guo et al. [25].

4.4. Gene Structure, Motif Identification and Conserved Domains

The intron–exon distribution of MsHSF genes was obtained by using the GFF file for the alfalfa genome. Conserved amino acid sequences of HSF proteins were analyzed by the online MEME suite (https://meme-suite.org/meme/tools/meme (accessed on 24 May 2023)), and the maximum motif number was set to 10. The NCBI conserved domain database (https://www.ncbi.nlm.nih.gov/cdd/ (accessed on 24 May 2023)) was used to predict conserved domains in MsHSF.

4.5. Gene Duplication and Synteny Analysis

MCScanX software (http://chibba.pgml.uga.edu/mcscan2/ accessed on 23 May 2023) (Hu, Y., Herndon, VA, USA) [53] was used to determine replication events in MsHSF genes and identify collinear regions between them and HSF genes in M. truncatula, A. thaliana and G. max. TBtools software was employed to extract information related to gene function and chromosomal location [51].

4.6. Identification of Cis-Acting Elements

PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ (accessed on 22 May 2023)) was used to identify cis-acting elements. The upstream 2000 bp sequence was defined as the promoter region for predicting cis-acting elements.

4.7. Transcriptomic Data Analysis

Transcriptomic data for six alfalfa tissues (leaves, nodules, elongated stems, flowers, preelongated stems and roots) were retrieved from the NCBI database (SRP055547) [54]. Transcriptomic data for the MsHSF genes from the alfalfa plants subjected to drought, cold and salt stresses were also obtained from the NCBI database (SRR7160313-SRR7160357 and SRR7091780-SRR7091794) [55]. The obtained clean reads were mapped using TopHat2 [56] to the “Xinjiangdaye” reference genome. Gene expression levels were calculated based on the fragments per kilobase of exon per million mapped fragments (FPKM) value; differentially expressed genes were retrieved using DESeq with the following parameters: padj < 0.05 and |log2FC| ≥ 1 [57]. Data were visualized by TBtools software.

4.8. Details of Plant Material and Treatment

Seeds of the “Zhongmu No.1” cultivar of alfalfa were grown at the Institute of Animal Science, Chinese Academy of Agricultural Sciences. Briefly, seeds were first treated for 3 days at 4 °C before germination. Next, the seeds were cultured in a greenhouse under a light/dark (16/8 h) cycle with 70–80% relative humidity and a day/night temperature of 24 °C/20 °C for 2 weeks in hydroponic culture medium. Three stress conditions (salt, cold and drought) were then applied to the cultured plants. For drought conditions, treatment with mannitol (400 mM) was applied to simulate drought stress. After treatment, root tip samples were collected at the following 6 time points: CK at 0 h and M1, M2, M3, M4 and M5 at 1, 3, 6, 12 and 24 h, respectively. For cold treatment, leaves were placed at 4 °C, and the following 5 time points were selected for sampling: 0 h as CK and 2, 6, 24 and 48 h as C1, C2, C3 and C4, respectively. Simulated salt stress involved treatment with NaCl (250 mM), and root tip samples were collected at 7 time points (0 h as CK and 0.5, 1, 3, 6, 12 and 24 h as S1 to S6, respectively). Each stress treatment condition had three replicates, with 5 individual seedlings in each replicate. The samples were stored at −80 °C for subsequent RT–PCR analysis.

4.9. Expression Analysis of MsHSF Genes

Total RNA was extracted from all samples in this study using TRIzol reagent according to the manufacturer’s instructions. The corresponding cDNA was obtained using the EasyScript first-strand cDNA Synthesis kit. The primers used in the study were designed using Primer 5.0 software. The RT–PCR experiment was performed using SYBR Premix Ex Taq (Takala, Japan) and a 7500 real-time fluorescent quantitative PCR system (Applied Biosystems, Foster City, CA, USA). Three replicates were designed for each sample, and data were normalized using alfalfa actin gene expression. The relative gene expression level of MsHSF genes was calculated by the 2−ΔΔCT [58] method and the results were visualized in TBtools.

4.10. Genes Coexpressed with MsHSFs

Genes co-expressed with MsHSF were screened based on differentially expressed genes under salt stress in alfalfa, and the standard correlation coefficient was |R| > 0.98.

5. Conclusions

In this study, the HSF gene family in the “Xinjiangdaye” reference genome of alfalfa, which is an autotetraploid genome, was comprehensively identified and characterized. A total of 104 MsHSF genes were found; 101 MsHSF genes are unevenly distributed on 32 chromosomes of this genome, and the other 3 MsHSF genes were not found on chromosomes. Phylogenetic tree analysis indicates that the 104 MsHSF genes can be grouped into classes A, A1, A2, A3, A4, B and C, which is consistent with results for Arabidopsis. Compared with tandem duplication, segment duplication is the main driving force for the expansion of the MsHSF gene family in alfalfa. The expression patterns of the 104 MsHSF genes in six different tissues in alfalfa revealed that 13 MsHSF genes have tissue-specific expression but that 28 MsHSF genes are expressed in all six tissues studied. Based on transcriptome data analysis, 21, 27 and 11 MsHSF genes respond to drought, salt and cold stresses, respectively. In addition, 10 MsHSF genes respond to both cold stress and salt stress, 19 MsHSF genes respond to both drought stress and salt stress, 7 MsHSF genes respond to both cold stress and drought stress and 7 MsHSF genes respond to all three stresses. According to RT–PCR results, MsHSF27/33 expression gradually increased with time under cold, salt and drought stresses, and MsHSF6 expression increased with time under salt and drought stresses but decreased with time under cold stress. This study provides data to guide further research on how HSF gene family members respond to abiotic stress conditions and improve alfalfa quality.

Supplementary Materials

The supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms241612683/s1.

Author Contributions

Planning and designing of the study and manuscript writing, H.L., X.L. and L.C.; preparation of the figures and tables, Y.Z., G.Z., L.Z. and M.L.; data validation, L.H., S.W. and R.L.; data validation and reviewing and editing the manuscript, J.K. and Q.Y.; curating the software and data and manuscript review, L.C. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Central Public-Interest Scientific Institution Basal Research Fund (No. 2022-YWF-ZYSQ-04), the Ordos Science and Technology Plan (No. 2022EEDSKJZDZX011), the major demonstration project of “The Open Competition” for Seed Industry Science and Technology Innovation in Inner Mongolia (No. 2022JBGS0016) and the Agricultural Science and Technology Innovation Program (ASTIP No. CAAS-ZDRW202201).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Schematic diagram of the chromosomal distribution of HSF genes in Medicago sativa.
Figure 1. Schematic diagram of the chromosomal distribution of HSF genes in Medicago sativa.
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Figure 2. Phylogenetic tree of HSF genes in Medicago sativa and Arabidopsis thaliana.
Figure 2. Phylogenetic tree of HSF genes in Medicago sativa and Arabidopsis thaliana.
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Figure 3. Gene structures and motif compositions of MsHSF genes of Medicago sativa.
Figure 3. Gene structures and motif compositions of MsHSF genes of Medicago sativa.
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Figure 4. Schematic diagram of syntenic relationships of MsHSF genes in Medicago sativa. Gray ribbons represent syntenic blocks in the alfalfa genome, and segmental duplication events are marked in red.
Figure 4. Schematic diagram of syntenic relationships of MsHSF genes in Medicago sativa. Gray ribbons represent syntenic blocks in the alfalfa genome, and segmental duplication events are marked in red.
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Figure 5. Synteny analysis of the HSF genes between Medicago sativa and three representative plant species. Gray lines in the background indicate collinear blocks between M. sativa and the indicated plant species, whereas the red lines highlight syntenic HSF gene pairs.
Figure 5. Synteny analysis of the HSF genes between Medicago sativa and three representative plant species. Gray lines in the background indicate collinear blocks between M. sativa and the indicated plant species, whereas the red lines highlight syntenic HSF gene pairs.
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Figure 6. Distribution of cis-acting elements related to hormone responses in promoter regions of MsHSF genes.
Figure 6. Distribution of cis-acting elements related to hormone responses in promoter regions of MsHSF genes.
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Figure 7. Expression analysis of MsHSF genes in different tissues (flowers, leaves, elongated stems, preelongated stems, nodules and roots). (A–F). MsHSF gene expression in 1–6 tissues.
Figure 7. Expression analysis of MsHSF genes in different tissues (flowers, leaves, elongated stems, preelongated stems, nodules and roots). (A–F). MsHSF gene expression in 1–6 tissues.
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Figure 8. Expression of MsHSF genes under drought, salt and cold stress conditions. (A). Expression of MsHSF genes under drought stress. (B). Expression of MsHSF genes under salt stress. (C). Expression of MsHSF genes under cold stress. (D). Venn diagram of MsHSF genes expressed under the three abiotic stresses.
Figure 8. Expression of MsHSF genes under drought, salt and cold stress conditions. (A). Expression of MsHSF genes under drought stress. (B). Expression of MsHSF genes under salt stress. (C). Expression of MsHSF genes under cold stress. (D). Venn diagram of MsHSF genes expressed under the three abiotic stresses.
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Figure 9. RT–PCR expression of MsHSF27/33/6 under drought, salt and cold stress conditions. (A). Expression of MsHSF27. (B). Expression of MsHSF33. (C). Expression of MsHSF6.
Figure 9. RT–PCR expression of MsHSF27/33/6 under drought, salt and cold stress conditions. (A). Expression of MsHSF27. (B). Expression of MsHSF33. (C). Expression of MsHSF6.
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Figure 10. Genes co-expressed with MsHSF6, MsHSF27 and MsHSF33 under salt stress.
Figure 10. Genes co-expressed with MsHSF6, MsHSF27 and MsHSF33 under salt stress.
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Table 1. Details of the HSF family genes in Medicago sativa.
Table 1. Details of the HSF family genes in Medicago sativa.
Gene NameGene IDChr LocationCDS
Length
(bp)		Protein
Length
(aa)		MW
(kDa)		pISubcellular
Location
MsHSF1MS.gene47348chr1.1:46,491,236–46,493,679156052059.085.5Nucleus
MsHSF2MS.gene49374chr1.1:53,676,456–53,677,640102334140.175.44Nucleus
MsHSF3MS.gene006320chr1.1:72,806,609–72,807,60690930333.807.58Nucleus
MsHSF4MS.gene37701chr1.1:73,816,413–73,818,12597832638.085.72Nucleus
MsHSF5MS.gene50549chr1.2:54,664,413–54,665,621104734941.235.7Nucleus
MsHSF6MS.gene34469chr1.2:75,570,174–75,571,15791230433.937.56Nucleus
MsHSF7MS.gene34387chr1.2:76,550,116–76,551,77997832638.165.77Nucleus
MsHSF8MS.gene034932chr1.3:44,215,023–44,217,276137445851.614.87Nucleus
MsHSF9MS.gene036186chr1.3:51,302,463–51,303,647102334140.175.44Nucleus
MsHSF10MS.gene49062chr1.3:69,715,698–69,716,68791230433.856.55Nucleus
MsHSF11MS.gene006403chr1.3:70,669,752–70,671,41997832638.165.77Nucleus
MsHSF12MS.gene72412chr1.4:50,359,380–50,361,633137445851.594.87Nucleus
MsHSF13MS.gene39940chr1.4:58,394,993–58,396,193102334140.165.44Nucleus
MsHSF14MS.gene41406chr1.4:78,626,550–78,627,54089729933.408.15Nucleus
MsHSF15MS.gene070958chr1.4:79,551,444–79,553,15697832638.175.9Nucleus
MsHSF16MS.gene069887chr2.1:4,201,900–4,215,60445061502171.497.62Nucleus
MsHSF17MS.gene002630chr2.1:68,933,280–68,935,167126942348.374.98Nucleus
MsHSF18MS.gene36373chr2.2:2,555,932–2,562,788243081091.825.29Nucleus
MsHSF19MS.gene001530chr2.2:63,861,920–63,863,788126642248.144.97Nucleus
MsHSF20MS.gene01615chr2.2:66,867,654–66,869,539126942348.374.98Nucleus
MsHSF21MS.gene76552chr2.3:3,084,334–3,086,356145848654.635.16Nucleus
MsHSF22MS.gene76553chr2.3:3,087,812–3,090,547108936341.234.61Nucleus
MsHSF23MS.gene004307chr2.3:68,816,734–68,817,70836912314.556.28Cytosol
MsHSF24MS.gene03101chr2.3:68,965,280–68,967,152126642248.194.94Nucleus
MsHSF25MS.gene85167chr2.4:3,824,061–3,831,001249383194.395.5Nucleus
MsHSF26MS.gene004306chr2.4:68,163,087–68,164,955126642248.144.97Nucleus
MsHSF27MS.gene32806chr3.1:82,443,497–82,444,921114338142.844.93Nucleus
MsHSF28MS.gene38358chr3.2:84,790,567–84,791,844111637242.098.16Nucleus
MsHSF29MS.gene015008chr3.2:86,383,022–86,384,435114338142.834.93Nucleus
MsHSF30MS.gene38707chr3.3:84,309,749–84,311,026111637242.088.16Nucleus
MsHSF31MS.gene066508chr3.3:85,975,236–85,976,63585828631.934.51Nucleus
MsHSF32MS.gene012969chr3.4:89,680,036–89,681,313111637242.098.16Nucleus
MsHSF33MS.gene37417chr3.4:91,525,254–91,526,669114338142.864.82Nucleus
MsHSF34MS.gene015638chr4.1:1,466,842–1,468,746110136741.885.07Nucleus
MsHSF35MS.gene27848chr4.1:13,157,657–13,158,981120340145.935.33Nucleus
MsHSF36MS.gene09269chr4.1:14,521,522–14,524,663146148754.365.06Nucleus
MsHSF37MS.gene31937chr4.1:20,930,615–20,932,28263321124.505.82Nucleus
MsHSF38MS.gene006573chr4.1:26,940,377–26,942,558147949355.025.1Nucleus
MsHSF39MS.gene62673chr4.2:1,228,383–1,230,289111337142.195.07Nucleus
MsHSF40MS.gene08822chr4.2:13,315,350–13,318,491146148754.365.06Nucleus
MsHSF41MS.gene39449chr4.2:22,136,602–22,138,26663021024.416.25Nucleus
MsHSF42MS.gene95836chr4.3:1,296,902–1,298,804110136741.905.07Nucleus
MsHSF43MS.gene065968chr4.3:13,372,525–13,373,849120340145.935.33Nucleus
MsHSF44MS.gene023483chr4.3:15,605,046–15,608,184146148754.365.06Nucleus
MsHSF45MS.gene052478chr4.3:24,186,653–24,188,32163321124.566.02Nucleus
MsHSF46MS.gene031737chr4.3:30,991,732–30,994,076147949355.185.01Nucleus
MsHSF47MS.gene058589chr4.4:1,483,835–1,485,751110136741.835.02Nucleus
MsHSF48MS.gene023615chr4.4:13,251,720–13,253,044120340145.935.33Nucleus
MsHSF49MS.gene08977chr4.4:14,900,400–14,903,540146148754.355.1Nucleus
MsHSF50MS.gene33789chr4.4:23,836,186–23,837,85563321124.546.02Nucleus
MsHSF51MS.gene065779chr4.4:32,552,978–32,555,159147949355.025.1Nucleus
MsHSF52MS.gene065778chr4.4:32,564,463–32,566,644147949355.025.1Nucleus
MsHSF53MS.gene006572chr4.4:32,578,622–32,580,803147949355.025.1Nucleus
MsHSF54MS.gene015551chr5.1:4,238,143–4,239,348109536540.195.1Nucleus
MsHSF55MS.gene015144chr5.1:9,692,198–9,694,41486128732.198.37Nucleus
MsHSF56MS.gene016952chr5.1:70,548,465–70,549,71872924328.317.08Nucleus
MsHSF57MS.gene050384chr5.2:3,806,018–3,807,223109536540.195.1Nucleus
MsHSF58MS.gene041094chr5.2:9,587,990–9,590,20386128732.216.47Nucleus
MsHSF59MS.gene050386chr5.2:31,314,868–31,316,072109536540.195.1Nucleus
MsHSF60MS.gene47664chr5.2:75,725,943–75,727,20576225429.596.45Nucleus
MsHSF61MS.gene072808chr5.3:4,227,992–4,229,197109536540.195.1Nucleus
MsHSF62MS.gene047640chr5.3:9,771,172–9,773,10386128732.247.55Nucleus
MsHSF63MS.gene78932chr5.3:18,647,929–18,651,784150650255.354.73Nucleus
MsHSF64MS.gene70849chr5.3:71,945,341–71,946,60676225429.546.45Nucleus
MsHSF65MS.gene019282chr5.4:4,925,106–4,926,311109536540.195.1Nucleus
MsHSF66MS.gene010367chr5.4:10,594,467–10,602,650138346151.425.26Nucleus
MsHSF67MS.gene038168chr5.4:70,232,760–70,234,14172924328.267.08Nucleus
MsHSF68MS.gene054313chr6.1:24,564,039–24,566,28996332137.005.47Nucleus
MsHSF69MS.gene054312chr6.1:24,572,932–24,574,90896932337.005.19Nucleus
MsHSF70MS.gene054311chr6.1:24,590,934–24,592,84889729934.295.05Nucleus
MsHSF71MS.gene054310chr6.1:24,626,677–24,628,93390030034.315.14Nucleus
MsHSF72MS.gene052458chr6.1:75,626,062–75,628,744145248454.996.14Nucleus
MsHSF73MS.gene03506chr6.2:37,838,394–37,840,68196932337.045.12Nucleus
MsHSF74MS.gene03507chr6.2:37,852,586–37,854,50389729934.405.17Nucleus
MsHSF75MS.gene03509chr6.2:37,891,892–37,897,20390030034.265.37Nucleus
MsHSF76MS.gene98248chr6.2:55,114,403–55,115,562102334137.745.64Nucleus
MsHSF77MS.gene80513chr6.3:36,909,010–36,911,29796932337.025.18Nucleus
MsHSF78MS.gene80509chr6.3:36,932,369–36,934,43995731936.775.2Nucleus
MsHSF79MS.gene80508chr6.3:36,950,527–36,952,80796632237.105.3Nucleus
MsHSF80MS.gene80507chr6.3:36,994,105–36,996,07995731936.445.27Nucleus
MsHSF81MS.gene80504chr6.3:37,053,440–37,055,69690030034.315.22Nucleus
MsHSF82MS.gene84114chr6.3:52,909,236–52,910,395102334137.785.5Nucleus
MsHSF83MS.gene42038chr6.4:16,627,031–16,628,94089729934.345.31Nucleus
MsHSF84MS.gene42037chr6.4:16,648,745–16,650,96089729934.344.97Nucleus
MsHSF85MS.gene42036chr6.4:16,658,343–16,660,25789729934.325.32Nucleus
MsHSF86MS.gene000756chr6.4:34,113,335–34,114,494102334137.755.64Nucleus
MsHSF87MS.gene018149chr7.1:12,337,762–12,346,750150650257.706.02Nucleus
MsHSF88MS.gene42537chr7.1:16,183,243–16,184,97969923326.998.2Nucleus
MsHSF89MS.gene43382chr7.2:14,288,001–14,300,261173157766.185.84Nucleus
MsHSF90MS.gene054891chr7.3:15,394,234–15,396,45193931335.976.12Nucleus
MsHSF91MS.gene017872chr7.3:17,787,214–17,788,95669923326.998.2Nucleus
MsHSF92MS.gene020288chr7.4:13,679,001–13,681,20693931335.996.43Nucleus
MsHSF93MS.gene39054chr7.4:17,608,870–17,610,59668722926.698.8Nucleus
MsHSF94MS.gene012268chr8.1:6,048,162–6,050,222126342147.825.41Nucleus
MsHSF95MS.gene011821chr8.1:27,164,988–27,169,49383727930.936.48Chloroplast
MsHSF96MS.gene051856chr8.2:6,520,812–6,522,869126042047.655.4Nucleus
MsHSF97MS.gene56773chr8.2:25,831,390–25,835,79784028031.026.18Nucleus
MsHSF98MS.gene90514chr8.3:23,968,421–23,972,84083727930.936.48Chloroplast
MsHSF99MS.gene57572chr8.4:9,015,415–9,017,472125741947.515.47Nucleus
MsHSF100MS.gene57604chr8.4:9,044,302–9,046,00690630234.888.68Nucleus
MsHSF101MS.gene99195chr8.4:26,635,298–26,639,63877425828.495.92Nucleus
MsHSF102MS.gene06577633,245:8758–10,60495431835.336.09Nucleus
MsHSF103MS.gene06578033,246:5248–7429147949355.025.1Nucleus
MsHSF104MS.gene909898272:103,717–104,876102334137.735.5Nucleus
chr: chromosome; CDS: coding sequence; bp: base pair; aa: amino acid; MW: molecular weight; pI: isoelectric point.
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MDPI and ACS Style

Liu, H.; Li, X.; Zi, Y.; Zhao, G.; Zhu, L.; Hong, L.; Li, M.; Wang, S.; Long, R.; Kang, J.; et al. Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses. Int. J. Mol. Sci. 2023, 24, 12683. https://doi.org/10.3390/ijms241612683

AMA Style

Liu H, Li X, Zi Y, Zhao G, Zhu L, Hong L, Li M, Wang S, Long R, Kang J, et al. Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses. International Journal of Molecular Sciences. 2023; 24(16):12683. https://doi.org/10.3390/ijms241612683

Chicago/Turabian Style

Liu, Hao, Xianyang Li, Yunfei Zi, Guoqing Zhao, Lihua Zhu, Ling Hong, Mingna Li, Shiqing Wang, Ruicai Long, Junmei Kang, and et al. 2023. "Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses" International Journal of Molecular Sciences 24, no. 16: 12683. https://doi.org/10.3390/ijms241612683

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