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Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors

Abstract

Background

The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agriculturally important crop that provides more than 20% of the calories and protein consumed in the modern human diet.

Results

We identified 125 IQDs in the wheat genome and divided them into four subgroups by phylogenetic analysis. The IQDs belonging to the same subgroup had similar exon–intron structure and conserved motif composition. Polyploidization contributed significantly to the expansion of IQD genes in wheat. Characterization of the expression profile of these genes revealed that a few T. aestivum (Ta)IQDs showed high tissue-specificity. The stress-induced expression pattern also revealed a potential role of TaIQDs in environmental adaptation, as TaIQD-2A-2, TaIQD-3A-9 and TaIQD-1A-7 were significantly induced by cold, drought and heat stresses, and could be candidates for future functional characterization. In addition, IQD genes in the A, B and D subgenomes displayed an asymmetric evolutionary pattern, as evidenced by their different gain or loss of member genes, expression levels and nucleotide diversity.

Conclusions

This study elucidated the potential biological functions and evolutionary relationships of the IQD gene family in wheat and revealed the divergent fates of IQD genes during polyploidization.

Peer Review reports

Background

As an intracellular second messenger, calcium (Ca2+) is involved in plant growth and development as well as the regulation of abiotic and biotic stress responses [1]. The Ca2+ ion levels, induced by dose-dependent intracellular signals transduced through Ca2+ sensors, differ in their spatiotemporal properties associated with the strength and duration of environmental challenges [2]. There are four major categories of Ca2+ sensor proteins in plants, namely calmodulins (CaMs), CaM-like proteins (CMLs), calcineurin B-like proteins (CBLs), and Ca2+-dependent protein kinases (CDPKs) [3,4,5]. Upon sensing Ca2+, CaMs, CMLs and CBLs undergo conformational changes in their structures and interact with their target proteins to induce Ca2+ signals, while CDPKs contain an inherent kinase domain that can directly transduce the signal to the target protein when sensing Ca2+ signal [6]. CaMs are among the most common Ca2+ sensor proteins. Although lacking the catalytic activity, CaMs can interact and activate a wide spectrum of target proteins, and thereby play a crucial role in mediating physiological functions through their downstream target proteins. These target proteins include chaperones, metabolic enzymes, transcription factors, and kinases referred to as calmodulin-binding proteins (CaMBPs) [7]. CaMBPs are characterized by their calmodulin-binding domain (CaMBD), which consists of three conserved motifs, specifically, one Ca2+-independent motif (IQ motif), and two Ca2+-dependent motifs (l-5–10 motif and l-8–14 motif) [8]. The IQD proteins are common representatives of CaMBPs, characterized by a central region of 67 conserved amino acid residues, commonly known as IQ67 domain (IQD) protein families [9, 10]. The IQ67 domain consists of 1–3 copies of the IQ motif (IQxxxRGxxxR or [ILV]QxxxRxxxx[R, K]), 1–4 copies of the 1–5-10 motif ([FILVW]xxx[FILV]xxxx[FILVW]) and 1–4 copies of the 1–8-14 motif ([FILVW]xxxxxx[FAILVW]xxxxx[FILVW]) [11]. These features allow the IQ67 domain to form a basic amphiphilic helix structure, further endowing these proteins with specific roles [11].

In recent years, the research on the IQD gene family has attracted considerable attention in various model and non-model plants, such as Arabidopsis, Oryza sativa [11], Solanum lycopersicum [12], Brachypodium distachyon [13], Glycine max [14], Populus trichocarpa [15], Zea mays [16], Cucumis sativus [17], and Brassica rapa ssp. pekinensis [18]. Numerous studies have shown that the IQD genes are widely involved in microtubule-related signaling pathways, and play essential roles in various plant growth and development processes [19]. The microtubule-associated protein AtIQD5 controls cortical microtubule dynamics that promotes proper microtubule organization, and subsequent cell growth, cell shape formation and pavement cell morphogenesis [20, 21]. More recently, Arabidopsis thaliana IQDs were found to function as cellular scaffolds that facilitate preprophase band formation and cortical division zone establishment during symmetric cell division [22]. In rice, OsIQD14 affects the grain shape by modulating microtubule cytoskeleton dynamics [23]. IQD12/SUN regulates tomato shape by redistribution of fruit mass, and also plays important roles in the growth of floral organ and leaf morphology [24, 25]. SUN24 positively regulates seed germination by repressing the expression of two key ABA signaling genes (SlABI3 and SlABI5) of the ABA signaling pathway in tomato [26]. PdIQD10 regulates the biosynthesis of the second cell wall and impacts biomass formation in Populus [27]. Several IQD proteins are also implicated in the response to biotic and abiotic stresses in plants. AtIQD1 can promote the accumulation of glucosinolates to reduce insect herbivory in Arabidopsis [10, 28]. In Gossypium hirsutum, knockdown of GhIQD31 and GhIQD32 negatively affected the responses of upland cotton to drought, salt, and cold stresses [29]. Overexpression of BrIQD5 conferred drought stress tolerance to Chinese cabbage, possibly by interacting with CaMs and other drought‑related proteins [18].

As one of the most successful crops since the dawn of agriculture, common wheat (Triticum aestivum L.) has expanded its original habitat from a limited area within the Fertile Crescent to a wide range of environments worldwide, making it the most widely grown and consumed crop [30]. Common wheat (2n = 6x = 42, AABBDD) is an allohexaploid species derived from two rounds of hybridization between three distinct diploid species, and is an informative system for analyzing the asymmetric evolutionary patterns between different subgenomes [31]. It originated from two natural interspecific hybridization events within the genera Triticum and Aegilops, which had similar but distinct genome structure and gene content that diverged between 2.5 and 6 million years ago [32]. First, Triticum urartu (2n = 2x = 14, AA) hybridized with an uncertain grass that was highly similar to Aegilops speltoides (2n = 2x = 14, SS) to generate the tetraploid species of wild emmer or Triticum turgidum (2n = 4x = 28, AABB) at about 0.5 to 3 million years ago. The subsequent polyploidization combined the genomes of Triticum turgidum and Aegilops tauschii ((2n = 2x = 14, DD) to form the allohexaploid genome of Triticum aestivum at around 8000 years ago [33].

The completion of the genome sequence of hexaploid wheat has provided an opportunity to investigate gene families at the genome-wide level [34]. In this study, 125 TaIQD genes were identified from the wheat genome. Their phylogenetic relationships, conserved motif composition, intron–exon structure and physicochemical characteristics of their proteins were comprehensively analyzed. In addition, we evaluated the expression pattern of TaIQDs during the stage of post anthesis and embryo development, and in response to various stresses, in which the proteins encoded by some TaIQD genes might potentially play a crucial role in stress resistance. The evolutionary relationships with its progenitors were systematically assessed. Comparative genomic analysis of TaIQD genes in wheat and its progenitors revealed asymmetric evolution and expansion during wheat polyploidization, as evidenced by their biased gene gain and loss, homoeologous gene expression and nucleotide diversity. This study can serve as a useful reference for unravelling the evolution of TaIQD genes and will further contribute to functional gene cloning in wheat.

Results

Identification of IQD genes in wheat

This study identified a total of 125 IQD genes in the wheat genome (Table S1). Since there is no standard nomenclature for IQD genes in wheat, the wheat IQD genes were designated as TaIQD-1A/1B/1D-1 to TaIQD-7A/7B/7D-3 for the A, B and D subgenomes according to their chromosomal location and homoeologous relationships, and TaIQD-U-1 to TaIQD-U-2 for unanchored genes. As shown in Table S2, the length of the TaIQD proteins ranged from 339 (TaIQD-1B-6) to 2,388 (TaIQD-3B-5) amino acids (aa) with an average of 785.46 aa, with corresponding molecular weight from 37.1 to 271.15 kDa, and isoelectric point from 4.93 (TaIQD-2D-8) to 11.47 (TaIQD-4D-4). Noteworthy, all the IQD proteins has negative GRAVY values, indicating that these proteins have hydropathicity. The results of the subcellular localization revealed that 117 of the 125 (93.6%) TaIQDs were only found in the nucleus, the remaining TaIQDs were found in chloroplast, mitochondrion, endoplasmic reticulum, cell membrane and cell wall.

Sequence alignment, phylogenetic analysis and structure of TaIQDs

The analysis of the domain conservation in the TaIQDs identified a total of 263 IQ motifs in wheat, with an average of 2.1 IQ motifs per protein, which was higher than that in rice (1.71), maize (1.65) and Arabidopsis (1.57). The length of the consecutive amino acid sequence of the IQ motifs ranged from 17 to 20 aa. As shown in Fig. 1, amino acid residues Ile-6, Gln-7, Arg-11, Gly-12, and Arg-16 were determined to be conserved amino acids with the conservative ratio of more than 60%. Notably, the conserved sequence ratio of Gln-7 was 100%, suggesting that this amino acid may be essential for the biological function of IQD proteins. Moreover, a similar pattern was observed in Arabidopsis, rice and maize (Table S3) [11, 16]. Besides IQ motifs, the search for calmodulin-binding sites revealed that TaIQDs have one to five CaM-binding sites with the consecutive amino acid length ≥ 7. Among them, TaIQD-2B-3 and TaIQD-2D-3 contain five CaM-binding sites, ranking as the most abundant CaM-binding domain containing TaIQDs. The predicted calmodulin interaction sites in 58 TaIQDs overlapped with the IQ motif (Table S4).

Fig. 1
figure 1

Conserved residue analysis of IQ domains. The height of each residue indicates the conservation rate. A Sequence logo generated by WebLogo, B Amino acid composition

In order to assess the evolutionary relationships of wheat TaIQD genes, an unrooted phylogenetic tree was constructed based on the alignment of the full-length sequence of IQD proteins from wheat (125 proteins) and maize (26 proteins). The TaIQDs were classified into four subgroups designated as I, II, III and IV on the basis of the classification principle used in maize (Fig. 2). The ratio of memberships within each subgroup in wheat was similar to that in maize, Arabidopsis and rice [11, 16]. Specifically, subgroup I had the most IQD proteins (68), followed by subgroup III (26) and subgroup IV (25), while subgroup II had the fewest with only six members (TaIQD-3A/3B/3D-4 and TaIQD-1A/1B/1D-7) (Table S5).

Fig. 2
figure 2

Phylogenetic tree analysis of IQD proteins from wheat and maize. The four IQD subgroups were marked with different colors. Red for subgroup I, orange for subgroup II, blue for subgroup III, green for subgroup IV

The exon–intron structure could also have certain reference value to understand the relative relationships of TaIQD genes. As shown in Fig. 3, the number of exons of IQD genes ranged from 2 (TaIQD-5A-2) to 53 (TaIQD-3B-5). The average exon length was 184.6 bp, whereas the intron length varied from 63 to 19,468 bp with an average length of 356.18 bp, indicating that the noncoding regions were subjected to lower selection pressure, thereby exhibited higher sequence diversity. It is noteworthy that TaIQDs grouped within the same subgroup shared a similar exon–intron structure and number of exons.

Fig. 3
figure 3

Phylogenetic relationships, exon–intron organization, and motif composition of TaIQDs. Exons and introns are indicted by grep rectangles and black lines. Conserved motifs are represented by colored boxed. A Subgroup I, B Subgroup II, C Subgroup III, D Subgroup IV

Further analysis of the motif composition of TaIQD proteins predicted a total of 10 conserved motifs (Figure S1). The most abundant motif 1 and motif 7 were exclusively present in 75 and 46 TaIQDs, respectively. Both motifs represented the core sequence region of the IQ motifs. Motif 1 represented the conventional IQ motif (IQxxxRGxxxR), whereas motif 7 was relaxed version of the IQ motif ([IL]QxxxRxxxxR). Motifs 2, 3, 4, 6 and 8 were uniquely present in Group I and Group IV. Subgroup II only contained motif 1, possibly due to its conserved exon–intron structure. In addition, a conserved motif arrangement was observed within each subgroup, but different subgroups contained their specific organization, and we thus inferred that TaIQDs have conserved and diverse functions.

Syntenic relationships of TaIQD genes in wheat and its relatives

The TaIQD genes were found to be unevenly distributed along the wheat chromosomes. Out of the 125 IQD genes identified in the wheat genome, a total of 123 TaIQDs, comprising 41 for A, 42 for B and 40 for D subgenomes, were mapped to the chromosomes (Figure S2). Most of the TaIQDs (81.6%) had three copies associated with subgenomes A, B and D. Group 3 chromosomes contained more IQD genes than other chromosomes, with 11 IQD genes in the A, B and D subgenomes, respectively. In addition, group 6 chromosomes had the lowest number of IQD genes, with only two members for each subgenome. Most of the TaIQDs were located at the distal regions of the chromosome. Genetic and cytological studies have demonstrated that recombination events predominately occur at distal regions of the chromosome, but suppressed at pericentromeric regions [35, 36].

It should be noted that TaIQD-U-2 and TaIQD-U-1 were not located on definite chromosomes. Given that TaIQD-U-1 showed homology with TaIQD-7A-2 and TaIQD-7B-2, and TaIQD-U-2 was homologous with TaIQD-5A-2, we thus speculated that TaIQD-U-1 and TaIQD-U-2 were located at the middle of chromosome 7D and the top of chromosome 5D, respectively.

As the representative allopolyploid species, the genomic duplication of A, B and D subgenomes play an indispensable role in the expansion of the total gene dose within the genome. For this reason, we further performed the analysis of the syntenic relationships among different subgenomes. Ultimately, a total of 87 gene pairs consisting of 101 IQD genes were found to be syntenic genes. There were 25 homoeologous gene groups with the three complete copies associated with A, B and D (Figure S3). The TaIQD-5A/5B-7, TaIQD-1B/1D-7and TaIQD-1A/1D-3 syntenic groups were only observed for that between A and B, B and D, and A and D, respectively. However, no tandem duplication was detected in our study, suggesting that genomic polyploidization led to the expansion of the IQD family in wheat. The Ka/Ks ratios for the 87 TaIQD syntenic gene pairs were estimated and the values varied from 0.0234 to 0.5865, with an average value of 0.1677, suggesting that the IQD gene family experienced strong purifying selection pressure (Table S6).

To further elucidate the evolutionary mechanism of IQD genes in wheat and its progenitors, a unified identification standard as described for wheat was used to identify the IQD genes in other species. A total of 232 IQD genes were identified, comprising 36 from Triticum urartu, 76 from Triticum dicoccoides, 78 from Triticum turgidum and 42 from Aegilops tauschii (Fig. 4, Table S7). For the A subgenome, 36 IQD genes from Triticum turgidum showed syntenic relationships with those of wheat, followed by Triticum dicoccoides (32), and Triticum urartu (28). It was found that 20 TaIQDs of the A subgenome were also present in the three related species. We thus speculate that since these genes may have important biological functions, they have a definite conservation rate during evolution. In addition, seven IQD genes (TaIQD-1A-1, TaIQD-1A-2, TaIQD-2A-8, TaIQD-3A-5, TaIQD-3A-9, TaIQD-3A-10, TaIQD-5A-1) were identified as homologs between Triticum aestivum and Triticum dicoccoides as well as between Triticum aestivum and Triticum turgidum. However, no homologous genes were found between Triticum aestivum and Triticum urartu, suggesting that these homologous pairs might be formed after wheat tetraploidization. For the B subgenome, 36 IQDs were identified as syntenic gene pairs between Triticum aestivum and Triticum dicoccoides, and 37 between Triticum aestivum and Triticum turgidum. The TaIQD-3B-2 formed no homologous gene pairs or showed homologous relationships with other genes in other species. For the D subgenome, 40 TaIQDs showed homologous relationships with 39 IQD genes in Aegilops tauschii. Noteworthy, one IQD in Triticum aestivum and three IQDs in Aegilops tauschii showed no collinearity with the other species, suggesting that these genes might experience gene acquisition, gene loss or chromosome translocation after wheat polyploidization.

Fig. 4
figure 4

Syntenic analysis of IQD genes among common wheat and its progenitors. The genomes of Triticum urartu, Triticum dicoccoides, Triticum trugidum and Aegilops tauschii surround the central Triticum aestivum. Syntenic gene pairs are linked by lines

Furthermore, the calculation of the Ka/Ks ratios revealed the orthologous relationships of IQD genes between wheat and its relatives (Table S8). The Ka/Ks ratios of 2, 10, 14 and 15 homologous gene pairs values were found to be higher than 1 in Triticum urartu, Aegilops tauschii, Triticum dicoccoides, Triticum turgidum, suggesting that these genes might undergo positive selection during the evolutionary process. In contrast, the rest of the homologous gene pairs had negative Ka/Ks ratios, suggesting that most of the IQD genes were subjected to purifying selection pressure.

Expression profiling of TaIQD genes in various stages

The investigation of the potential biological functions of TaIQDs through the analysis of the expression profiles of TaIQDs using publicly available RNA-seq data identified a greatly divergent expression pattern in different developmental stages or tissues. TaIQD-4D-4 and TaIQD-2D-8 were preferentially expressed in root (Fig. 5A). High expression levels of TaIQD-5A-2, TaIQD-7A-3, TaIQD-2B-7, and TaIQD-1D-2 were found in stem and five-days young spike. Moreover, the expression patterns of TaIQDs at ten time points after anthesis were also identified (Fig. 5B). The expressed genes were divided into three major groups. The TaIQDs in the first group, such as TaIQD-2A-2, TaIQD-1D-3, TaIQD-2A-1, TaIQD-2A-4, TaIQD-2B-1, TaIQD-2D-1, TaIQD-3A-3, showed relatively high expression level at most time points, suggesting that these genes may play critical roles during the whole anthesis period in wheat. In addition, we also found several TaIQDs with high tissue-specificity. For example, TaIQD-2D-2 exhibited preferential expression at 17 DAA, while TaIQD-2B-2 was unevenly expressed at 26 DAA time point.

Fig. 5
figure 5

Expression pattern of TaIQDs during different developmental stage. Red indicates high expression and blue indicates low expression. The left represents gene clusters. A different developmental stages. FL: flag leaf at heading stage, YS5: young spike at early booting stage, YS15: spike at heading stage. R, S, and L represent root, stem, and leaf of five-leaf stage seedling, GR5, GR10, GR15, and GR20 represent grain at 5, 10, 15, and 20 days post-anthesis, respectively. B 3 to 26 days after anthesis, C ten different stages during embryo development. TC: two cells, PE: pre-embryo, TS: transition, LE: leaf early, LM: leaf middle, LL: leaf late, MT: mature, EEd: early endosperm, Led: late endosperm, SC: Pericarp

Further analysis of the expression profiles at ten different time points during embryonal development (Fig. 5C) showed that 64 TaIQD genes were expressed in at least one time point. The highly tissue-specific IQDs were also identified. For instance, TaIQD-3A/3B/3D-2 showed expression bias in two cell types, pre-embryo, and transition stages, implying that the three homoeologous genes may participate in early embryogenesis. In contrast, TaIQD-2A/2B/2D-1 showed relatively high expression in the late endosperm stage. TaIQD-3A/3B-4, TaIQD-4A/4B-1 and TaIQD-3D-4 were mainly expressed in seed coat.

Expression profiling of TaIQD genes in response to various stresses

We also investigated the biological function of TaIQD genes in the response to various abiotic stresses, specifically cold, salt, drought/heat, and metal starvation. The results showed that 45 genes expressed in response to cold stress (Fig. 6A). The TaIQD-3D-10, TaIQD-3B-5, TaIQD-5A-7, and TaIQD-5B-9 genes were markedly upregulated. Remarkably, TaIQD-5A-7 showed about 6.62-fold higher expression level compared to the control. TaIQD-5B-9 was not expressed under untreated condition, but was markedly expressed in response to cold stress. Additionally, TaIQD-3D-3, TaIQD-5B-6, TaIQD-2B-4 and TaIQD-2A-5 were weakly expressed when subjected to cold treatment. Under salt stress (Fig. 6B), seven genes showed upregulated expression patterns. TaIQD-5D-5 and TaIQD-1A-7 showed 6.47 and 3.42-fold upregulation after exposure to salt. Moreover, the expression of TaIQD-2D-5 and TaIQD-5B-9 were induced in response to salt stress. When the plants were subjected to the combined stresses of drought and heat (Fig. 6C) with the following six treatment and time point conditions (DS_1h, DS_6h, HS_1h, HS_6h, HD_1h and HD_6h), a total of 2, 2, 3, 7, 2 and 5 TaIQD genes were upregulated and 2, 7, 13, 8, 10, and 7 TaIQD genes were downregulated, respectively. TaIQD-5A-6 showed 2.13 and 2.02-fold upregulation under the HS_6h and HD_6h treatments, and TaIQD-2A-5 showed more than twofold upregulation under the DS_1h, DS_6h, HS_6h and HD_6h treatments. The expression profiles of TaIQDs under phosphorus and iron deprivation were also determined (Fig. 6D). Remarkably, the expression levels of TaIQD-4A-2, TaIQD-1B-4, TaIQD-5B-11, TaIQD-3D-3, TaIQD-7D-1, and TaIQD-U-1 showed more than fivefold upregulation than those of their respective control. The rest of the TaIQDs showed weak or moderate expression levels, suggesting that only a few genes are involved in the response to various stresses in wheat.

Fig. 6
figure 6

Expression analysis of TaIQDs in response to various abiotic stress. Red indicates high expression and blue indicates low expression. The left represents gene clusters. A Cold, B Salt, C Heat with drought, D Phosphorus and iron starvation. DS: drought stress, HS: heat stress, HD: heat with drought stress, PS: Phosphorus starvation, IS: Iron starvation

In order to gain a deep understanding into the expression of TaIQD family genes in response to multiple stresses, 9 TaIQD genes from four different subgroups were randomly selected to study their expression profiles under salt, drought, cold and heat stresses by qRT-PCR analysis (Figure S4). Under salt stress, the selected TaIQDs were upregulated at different time points. For example, TaIQD-2A-2 and TaIQD-3A-9 were upregulated at all time points and reached their maximum expression level at 6 h and 1 h, respectively. The expression of TaIQD-1A-7 peaked at 12 h with a 6.96-fold upregulation. At different time points of the cold stress treatment, two TaIQDs (TaIQD-2A-2 and TaIQD-5B-9) were upregulated, whereas TaIQD-3B-5 was downregulated at all time points. Meanwhile, some TaIQD genes showed variable expression profiles at different time points. For instance, TaIQD-5A-6 and TaIQD-3D-9 were downregulated at 6 h, but upregulated at the remaining time points. In addition, the expression levels of the selected TaIQDs were analyzed after drought stress treatment. The expression levels of TaIQD-3B-5, TaIQD-3D-10 and TaIQD-3D-9 were suppressed compared with those of the control. The expression of levels of TaIQD-1A-7 and TaIQD-3A-9 were significantly upregulated, and peaked at different times. Specifically, the expression of TaIQD-1A-7 peaked at 1 h and was upregulated 4.84-fold, whereas the expression of TaIQD-3A-9 was initially slightly upregulated and peaked at 12 h. The results of the qRT-PCR analysis revealed that heat treatment had a marked effect on the expression patterns of TaIQDs. With the exception of TaIQD-3B-5 and TaIQD-5B-9, whose expression was inhibited compared with the control, the expression levels of a total of six TaIQDs (TaIQD-1A-7, 2A-2, 3A-9, 3B-11, 3D-9 and 5A-6) peaked at 24 h, suggesting that these TaIQDs might primarily function in the terminal stage in the response to heat injury. Notably, the expression of TaIQD-2A-2, TaIQD-3A-9 and TaIQD-1A-7 was significantly altered in response to salt, cold, heat and drought stresses, indicating that they might be excellent targets for the molecular breeding of wheat.

Cis-regulatory elements and co-expression network analysis of TaIQDs

As the region containing the transcription factor binding site that initiates transcription, the promoter plays an essential role in controlling the expression of genes that are involved in plant organogenesis, hormone signal transduction and stress responses. In total, six hormone-related cis-regulatory elements associated with gibberellin (GA), auxin, methyl jasmonate (MeJA), ethylene, salicylic acid (SA) and abscisic acid (ABA) were detected (Table S9 and Figure S5). Except for TaIQD-2B/2D-3, the majority of the TaIQDs had more than 13 hormone- or stress-responsive related cis-elements. In particular, gibberellin- (GARE-motif, P-box, TATC-box), MeJA- (CGTCA-motif, TGACG-motif), ABA- (ABRE), auxin- (TGA-element, AuxRR-core), ethylene- (ERE) and salicylic acid- (SARE, TCA-element) were found in 59, 104, 105, 58, 19, and 32 TaIQDs, respectively. Abundant hormone-responsive cis-regulatory elements were enriched in the promoter regions of TaIQD-1B-4, TaIQD-5A-4, TaIQD-2B-4, and TaIQD-3B-6. In addition, numerous abiotic stress cis-elements were also found, such as low-temperature responsive element LTR (53 genes), drought responsive element MBS (50 genes), salinity, as well as dehydration responsive elements DRE (three genes), DRE core (64 genes) and DRE1 (17 genes). Additionally, three kinds of biotic stress related cis-regulatory elements were also detected, including defense responsive TC-rich repeat elements (27 genes), wounding responsive element WUN-motif (23 genes) and wounding responsive element 3 (WRE3) (82 genes). These results implied that TaIQD genes might play critical roles in biotic and abiotic stresses, and might be involved in hormone stimulus responses.

MicroRNAs (miRNAs) can direct the cleavage of target mRNA or translation inhibition to regulate plant development and response to environmental fluctuations [37]. In this study, the putative miRNAs targeting the mRNAs of TaIQDs were predicted by psRNATarget. A total of 20 miRNA-TaIQD putative targeting relationships comprising 13 miRNAs and 13 TaIQDs were predicted with more than 90% sequence alignment (Table S10). Specifically, tae-miR9653a precisely binds to TaIQD-1A-7 with 100% alignment. All the miRNAs silenced the post-transcriptional expression of TaIQDs through transcript cleavage. Moreover, except for miR1120c-TaIQD-2D-5, the rest of the miRNA-TaIQD interactions were found to act upstream of the IQ domains. Overall, these results suggest that miRNAs may have crucial roles in the post-transcriptional regulation of the expression of TaIQD, and further research on the miRNA-mediated interaction relationships will provide valuable information to understand the functional roles of TaIQDs in plant growth and development as well as stress responses.

To investigate the regulatory functions of TaIQDs associated with other wheat genes, the available 110 RNA-seq samples were used to construct a co-expression network (Fig. 7A). The network consisted of a total of 913 links consisting of 12 TaIQDs and 68 other genes. Among them, the highly connected TaIQD-1D-3 and TaIQD-2A-2, located at the core node position, were co-expressed with 53 (66.25%) and 13 (16.25%) related genes, respectively, suggesting that these two TaIQDs might play a central role in the regulatory network. Two TaIQD genes (TaIQD-2B-5 and TaIQD-6D-2) had co-expression relationships with PYR6, CIPK23, PME31, PAL1, and ATR2. The genes co-expressed with TaIQDs were significantly enriched in functional categories that included terpenoid backbone biosynthesis, biosynthesis of secondary metabolites, metabolic pathways, carbon metabolism and other KEGG pathways (Fig. 7B). GO enrichment analysis of the TaIQD co-expressed genes revealed that they were most enriched in the terms related to multiple developmental process (Fig. 7C), such as cellular response to nitrogen starvation (GO:0,006,995), regulation of photosynthesis (GO:0,010,109), response to cold (GO:0,009,409), response to abscisic acid (GO:0,009,737), and cellular response to salt stress (GO:0,071,472).

Fig. 7
figure 7

The co-expression network between TaIQDs and other wheat genes based on WGCNA analysis. A WGCNA analysis, B KEGG enrichment of TaIQD co-expressed genes, C GO enrichment of TaIQD co-expressed genes

Nucleotide variation and population structure analysis of TaIQD genes

The genetic landscapes with the genera Triticum and Aegilops have been comprehensively analyzed at the whole-genome level [30], but studies of the nucleotide variation patterns of TaIQDs are rather limited. By taking advantage of the cutting-edge analysis tools of whole-genome sequencing datasets, the nucleotide variation analysis uncovered 5,145 TaIQD-related SNPs, including 1,430, 1,297 and 2,418 for the A, B and D subgenomes, respectively. The majority of the SNPs were located within the upstream (38.46%) or downstream (32.69%) regions, followed by the intronic regions (17.47%), while only 10.65% SNPs were in exonic regions (Table S11). Within the coding regions, we observed 4.30% synonymous and 2.93% non-synonymous SNPs with a synonymous versus non-synonymous ratio of 1.46.

The evolutionary relationships and population structure of the different subspecies were further studied at the sub-genomic level. For the A subgenome, principal component analysis (PCA) showed that the first principal component accounted for 61.4% of the total variance and mainly distinguished the Triticum urartu from the other species, whereas Triticum aestivum (landrace) was mainly distinguished by the second principal component (15.93% of total variance), and Triticum turgidum was distinguished by the third (Fig. 8B and C, Table S12). A more obvious subgroup that included from top to bottom Triticum urartu, Triticum dicoccoides, Triticum dicoccum, Triticum turgidum and Triticum aestivum, was identified through the phylogenetic tree (Fig. 8A). Admixture analysis provided similar evidence (Fig. 8D). When K = 2, the species Triticum urartu was firstly recognized. With the increase of K to 3, the landraces and cultivars of common wheat were separated from the others. With the continuous increase of the K value, a certain proportion of gene flow between common wheat and its progenitors was observed, indicating the continuous gene flow between its diploid and tetraploid ancestors and hexaploid wheat during and after the process of polyploidization. The nucleotide diversity increased gradually from the diploid wheat (Triticum urartu) to tetraploid wheat (Triticum dicoccoides, Triticum dicoccum and Triticum turgidum) and then to hexaploid wheat (Triticum aestivum). The genetic diversity of Triticum dicoccum and Triticum turgidum populations was basically the same, but a significant genetic loss (40.2% reduction) occurred in the Triticum dicoccoides population during domestication. The fixation index (Fst) is an important index used to evaluate gene flow intensity and population differentiation [38]. If the Fst value is larger than 0.25, populations are considered to be extremely divergent [39]. In this study, the Fst values between Triticum urartu and other populations were larger than those within the other populations, which was consistent with the results of the phylogenetic relationships with the deviated cluster groups of the Triticum urartu population.

Fig. 8
figure 8

Phylogenetic relationships, PCA and population structure analysis for the group A genomes based on TaIQD-related SNPs. The SNPs from the A subgenome/genome of Triticum urartu, Triticum dicoccoides, Triticum dicoccum, Triticum turgidum and Triticum aestivum were used. A Neighbor-joining phylogenetic tree, B PCA analysis of PC1 vs PC2, C PCA analysis of PC1 vs PC3, D Population structure was estimated by ADMIXTURE with the K range from 2 to 8

For the B subgenome, all accessions were assigned to five subgroups according to their biological sources. The first, second and third components mainly captured the difference of Triticum dicoccoides, Triticum dicoccum and Triticum turgidum, respectively. Within the phylogenetic tree, the Triticum dicoccum population was definitely separated from the others, but there was no obvious boundary between the landrace and modern cultivar accessions for both the tetraploid wheat and hexaploid wheat. The same population affinities were recovered in the stacked bar based on the Admixture analysis. When K = 2, a genetic admixture was observed for Triticum dicoccoides and Triticum turgidum. However, it was not until K increased to 4 that Triticum turgidum formed a relatively independent subgroup. When K increased above 5, the landrace and hexaploid wheat gradually diverged, but there was still obvious genetic admixture between the two populations. We further evaluated the genetic diversity of the B subgenome for different populations. The nucleotide diversity of TaIQDs decreased continuously from Triticum dicoccoides (0.2472) to Triticum dicoccum (0.1685), and ultimately to Triticum turgidum wheat (0.1282) (Fig. 9, Figure S6).

Fig. 9
figure 9

Distribution of nucleotide diversity (π × 102) and Fst values across the group A, B and D genomes, respectively. The Fst values larger than 0.25 are marked with red. A A subgenome, B B subgenome, C D subgenome

We also profiled the nucleotide variation atlas of TaIQDs for the D subgenome. As described in subparagraph A of Figure S7, a significant genetic divergence was observed between the D subgenome of hexaploid wheat and its ancestral species Aegilops tauschii. Identical results were obtained when the high Fst values were calculated for wheat varieties versus Aegilops tauschii (0.602) and wheat landraces versus Aegilops tauschii (0.579), which suggested that these populations were highly differentiated between each other. Moreover, the average nucleotide diversity of Aegilops tauschii ranked the highest among the studied populations of different subgenomes. However, the nucleotide diversity of the D subgenome decreased ~ 85% from the ancestral species to hexaploid wheat. In summary, the evolutionary patterns of TaIQD genes provide novel insights into the process of wheat polyploidization, which might be useful in wheat genetic research and germplasm resource utilization in the future.

Discussion

The first characterization of IQD gene family in wheat

The members of the plant-specific IQD gene family, encoding a class of calmodulin-binding proteins involved in calcium signaling pathways, play essential roles in plants coordinating a wide range of developmental processes and responses to environmental stimuli [11]. Wheat is one of the most important cultivated grain crops worldwide, contributing approximately a fifth of the food consumption for the majority of the human populations [40]. In total, 125 non-redundant IQD genes were identified in the wheat genome. The number of IQD genes in wheat is more than three times higher than that in Arabidopsis thaliana (33) [11], Brachypodium distachyon (23) [13], Brassica rapa ssp. pekinensis (35) [18], maize (26) [16], Oryza stative (29) [11], Populus trichocarpa (40) [15], potato (23) [41], and tomato (34) [12]. Compared with its progenitors, the number of IQD in Triticum aestivum is approximately three times higher than in Triticum urartu (36) and Ae. tauschii (42), whereas the ratio of TaIQDs between Triticum aestivum and Triticum dicoccoides or between Triticum aestivum and Triticum turgidum was approximately 1.5. This finding is consistent with those of previous studies on various gene families, including the TaPRX (374 in Triticum aestivum, 159 in Triticum urartu and 169 in Aegilops. tauschii) [42], WOX (43 in Triticum aestivum, 23 in Triticum dicoccoides, 28 in Triticum. turgidum, 16 in Triticum urartu and 13 in Aegilops tauschii) [43] and Hsp70 (113 in Triticum aestivum, 79 in Triticum dicoccoides and 30 in Aegilops tauschii) [44] gene families. This phenomenon can be explained by the two rounds of polyploidization that directly led to the expansion of the IQD genes in wheat.

A comparative genomic analysis of IQD gene family members from wheat and maize was performed to investigate the phylogenetic relationships. The phylogenetic analysis revealed that TaIQD proteins fell into four subgroups within the tree. Subgroup I was the largest subgroup, followed by subgroup III, which was in agreement with the results in maize, Arabidopsis and rice [11, 16]. The TaIQD proteins in the same subclade tend to cluster with each other more than proteins from the same species in different subclades. Meanwhile, genes within the same subgroup had a similar gene structure and conserved motif composition. Motif 1 and motif 7, which were the most common motifs, represented the conventional IQ67 motif (IQxxxRGxxxR) and a more relax version ([IL]QxxxRxxxxR). In addition, the subgroup specific motifs were also identified, which may be related to the functional diversification of TaIQDs.

The potential function of TaIQDs might be in plant growth, development and response to various stresses

The biological functions of IQD proteins have been extensively studied in many plants, especially model plants [19]. The elucidation of the expression patterns of TaIQDs during plant growth and development will provide new insights into the potential functions of their proteins. It was recently demonstrated that OsIQD14 acts as a key regulator in cortical microtubule rearrangements thereby affecting the grain shape [23]. TaIQD-U-1 (or TaIQD-7D-2), which is homologous to OsIQD14, showed high tissue-specificity with a τ ≈ 1 and biased expression in the stem of five-leaf-stage seedlings. These results suggested that TaIQD-U-1 might perform different functions in wheat. Moreover, there was a relatively high expression level of TaIQD-1D-1 during the whole stage of anthesis. Its orthologous gene AtIQD1 encodes a protein found in microtubules that interacts with the KLCR1 (kinesin light chain related 1) protein to expedite cellular transportation [10]. Our results suggest that TaIQD-1D-1 might be involved in mediating the transition from vegetative to reproductive development in barley. In Arabidopsis, AtIQD5 was reported to be involved in the process of cell shape morphogenesis, whereas its orthologous gene in wheat, TaIQD-5B-1 was preferentially expressed in embryonal leaf middle and mature stages [21], implying that TaIQD-5B-1 might be involved in these processes. Homologous analysis reveals the potential function of TaIQDs, but to ascertain the function of TaIQDs further extensive experimental work is needed.

As sensible organisms that are not able to move, terrestrial plants are often exposed to a wide array of adverse challenges, such as drought, high salinity, extreme temperatures, and pathogen infection [45]. To adapt to such environmental stimuli in an appropriate manner, plants have evolved complex signal transduction pathways that enable them to perceive stress signal and coordinate their growth and development [46]. In this study, we identified several cold, salt, drought/heat, and metal starvation induced IQD genes. Most TaIQDs tend to be induced by drought/heat rather than cold stress. For instance, TaIQD-2B-2, TaIQD-2D-3, and TaIQD-5A-10 were significantly upregulated by more than 20-fold after exposure to drought/heat. In Chinese cabbage, over-expression of BrIQD5 conferred plants drought tolerance, while BrIQD5-silenced plants exhibited drought sensitivity [18]. TaIQD-3A-9, one of the BLAST hits of BrIQD5 in wheat, displayed significant up-regulated expression patterns at 1, 6, 12, and 24 h under drought stress. Abundant MBS cis-acting elements associated with drought inducibility within the promoter regions were also identified. These results suggested that TaIQD-3A-9, which showed homology to BrIQD5, might be involved in the response to drought stress. Although the identified candidate IQD genes could serve as targets for subsequent genetic isolation and functional investigation in wheat, further studies are needed to determine the biological functions of these TaIQDs.

As a systems biology approach for determining the potential interactions among genes, WGCNA is an effective method to identify clusters of highly correlated genes, summarizing clusters, relating modules to sample traits, and for calculating module membership [47]. The genes adjacent to TaIQDs were found to be related to signaling pathways, cellular process, metabolic process, reproductive process, developmental process, and response to stimulus. To further identify the potential interactions of TaIQDs, we also constructed the protein–protein interaction (PPI) network of the corresponding Arabidopsis orthologs. It is noteworthy that CIPK23 was found to be highly involved in WGCNA and PPI networks (Figure S8). In Arabidopsis, CIPK23 functions in calcium (Ca2+)-related signaling pathways and is therefore involved in multiple physiological and developmental processes, such as iron acquisition [48], stomatal opening [49] and nutrient transporter [50]. Remarkably, two Ca2+ sensor proteins, namely CBL1 and CBL9, were identified as the upstream regulators of CIPK23. The CBL1/CBL9-CIPK23 complexes are required for activation of the K+ uptake channel AKT1 and for enhanced K+ uptake under low K+ conditions [51]. These results suggested that TaIQDs might be involved in these signaling pathways, and additionally play essential roles in wheat growth, development, and various stress responses, but in-depth functional studies are needed.

The asymmetric evolution patterns of IQD genes in hexaploid wheat

Plant polyploidization, together with the asymmetry in the process of co-evolution between different subgenomes, has contributed to sufficient genetic variation for environmental adaption [52]. A large number of studies have found that polyploid species have undergone asymmetric evolution in all aspects of their genomes. The draft genome of Brassica oleracea revealed the multi-layered asymmetrical evolution patterns between the Brassica subgenomes, such gene loss between subgenomes, amplification of tandem duplication and transposable elements, preferential enrichment for specific pathways and divergence in gene expression [52]. Asymmetric selection of defense-response genes also has led to ecotype change in Brassica napus [53]. More recent studies have provided evidence indicating that common wheat and cotton might have experienced asymmetric selection between different subgenomes [54, 55].

In order to find the asymmetric evolution patterns of TaIQDs, the member composition of the IQD gene families between common wheat and its progenitors was compared. For the A subgenome, a total of 4 (two for 2A and two for 7A) IQD genes were lost and 10 (three in 1A, two in 3A, two in 4A and three in 5A) were identified when compared with Triticum urartu. By contrast, only one in 1A and two in 3A IQDs were identified and one in 2A was lost after hexaploidization compared to Triticum turgidum. For the B subgenome, three IQD genes belonging to 2B, 3B and 4B were gained in hexaploid wheat. For the D subgenome, one more IQD gene on 1D was found in contrast to Aegilops tauschii. Noteworthy, the shorter the time taken by the ancestors to form the hexaploid wheat, the higher the consistency of the gene composition for IQD genes. In additions, previous studies have demonstrated that the gene number tend to be reversed towards diploid levels through gene loss following plant polyploidization [56]. In contrast, a slight increase was observed for IQD genes in wheat. We hypothesized that the exogenous introgression after the formation of hexaploid wheat may lead to the expansion of the TaIQD gene family, or any other complex mechanisms that remain unclear.

The presence of the homoeologous triads (composed of A, B and D genome copies) led us to examine the divergence from gene structure to biological function between subgenomes. The results indicated that around ~ 52.94% of the homoeologous genes from the A, B and D subgenomes have different predicted exon numbers. However, there was only 1 out of 34 homoeologous gene pairs (TaIQD-1A/1B/1D-10) that showed the divergent motif composition. Analysis of a total of 110 RNA-seq data revealed that most of the homoeologous genes showed a similar expression pattern. At the whole genome level, approximately 30% of the wheat homoeologous genes showed a biased expression pattern with lower or higher expression levels for a single homoeolog compared with the other two [31]. Regarding the IQD genes in wheat, a small portion of TaIQDs were differentially expressed in different stages/tissues or in response to exposure to stress. For example, TaIQD-2A-5 and TaIQD-2D-5 were upregulated in salt stress, TaIQD-2B-5 was downregulated in heat stress. Under cold treatment, TaIQD-2A-5 was downregulated, and TaIQD-2B-5was upregulated, and TaIQD-2D-5 was not expressed. These findings suggest the potential sub-functionalization or neo-functionalization of these genes.

As the most common type of genomic variation, SNPs have become an increasingly powerful molecular genetic marker for producing high-resolution genetic maps, linkage disequilibrium analysis, and marker-assisted breeding [57]. By taking advantage of the high-confidence TaIQD-related SNPs, the nucleotide diversity was calculated for each subgenomes with B > A > D in hexaploid wheat, which is basically consistent with previous studies [30, 58]. The asymmetric patterns of IQD genes in wheat will broaden our understanding on wheat genome evolution and will support research into the various important crops in the Triticum genus.

Conclusions

This study comprehensively analyzed for the first time the wheat IQD genes. A total of 125 TaIQDs were thoroughly identified in the wheat genome. We also categorized the genes into four subgroups according to the phylogenetic relationships between wheat and maize, which was supported by the exon–intron structure and conserved motif composition analysis. The expression and co-expression analysis showed that the TaIQDs were widely involved in plant development, and in the response to environmental stresses. The expression of TaIQD-2B-5, TaIQD-6B-2 and TaIQD-6D-2 was significantly induced by exposure to various types of abiotic stresses, which might make these genes excellent targets for the molecular breeding of wheat. In addition, some of the IQD genes in the A, B and D subgenomes had different gene gain and loss rates, expression patterns and nucleotide diversity. Taken together, the findings of this study provide new insights into the biological function and molecular evolution of the IQD gene family in wheat during polyploidization.

Materials and methods

Identification of the IQD gene family in wheat

The sequence-related data of wheat were downloaded from the Ensembl Plants database (http://plants.ensembl.org/index.html). The previously reported IQD protein sequences from Arabidopsis thaliana, rice (Oryza sativa) and maize (Zea mays) were considered as reference sequences to blast against the proteins in the wheat whole genome using BLASTP with an e-value ≤ 1e-5 and identity ≥ 50%. In addition, the hidden Markov model (HMM) profiles of the IQ domain (Pfam ID: PF00612) were retrieved from the Pfam database (http://pfam.xfam.org/) and used as query to search the wheat proteins using HMMER v3.0 (https://www.ebi.ac.uk/Tools/hmmer/) with an e-value ≤ 0.01. The redundant sequences from BLAST and HMMER were manually removed and further verified using the online Pfam (http://pfam.xfam.org/search/sequence) databases. Only candidate proteins that had the IQ domain were retained. To confirm the presence of all candidate genes, a BLASTN search was conducted against the wheat expressed sequence tag (ESTs) downloaded from the National Center for Biotechnology Information (NCBI, Bethesda, MD, USA) database (https://www.ncbi.nlm.nih.gov/) using the following criteria: e-value ≤ 1e-5 and identity ≥ 80%. The physicochemical characteristics of TaIQD proteins, including molecular weight (MW), theoretical isoelectric point (pI) and grand average of hydropathy (GRAVY), were calculated by the online ExPASy server (https://web.expasy.org/protparam/). The subcellular localization of TaIQDs was predicted by the predictor tool in the Plant-mPLoc server (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/). The calmodulin target database (http://calcium.uhnres.utoronto.ca/ctdb/ctdb/sequence.html) was used to identify the putative CaM-binding sites of TaIQDs. Arabidopsis and rice orthologs were obtained using the program InParanoid v4.1.

Phylogenetic analysis, gene structure and conserved motif analysis of TaIQD genes

The full-length IQD proteins from wheat as well as those from maize were used to generate multiple sequence alignment by ClustalX v1.83 with default parameters. The WebLogo tool (http://weblogo.berkeley.edu/logo.cgi) was used to display the sequence logo of the IQ motif. Then, the phylogenetic tree was constructed by the neighbor-joining (NJ) method using MEGAX v10.0 [59] with 1,000 replications, 95% partial deletion and a Poisson model. Ten motifs were scanned using MEME v.5.0.5 with a width ranging from 8 to 50 amino acids [60] (http://meme-suite.org/tools/meme). The Gene Structure Display Server [61] (http://gsds.cbi.pku.edu.cn/) was used to visualize the exon–intron composition of TaIQD genes.

Gene duplication, homoeologous relationships and ka/ks estimation

The chromosomal location of TaIQDs was obtained from the wheat genome annotation file (http://plants.ensembl.org/index.html) and diagrams were drawn using MG2C v2.1 (http://mg2c.iask.in/mg2c_v2.0/). In order to establish the syntenic relationships of IQD genes among the A, B and D subgenomes in wheat, we performed an all vs. all BLASTP search for all the TaIQD proteins. TaIQDs clustered within the same branches of the phylogenetic tree and displaying more than 95% similarity between each other were considered as homoeologous groups. According to their chromosome location, MCScanX was used to determine the syntenic relationships of the TaIQD gene family among the A, B and D subgenomes [62].

To evaluate the evolutionary relationships of IQD genes between wheat and its relatives (Triticum urartu, Triticum dicoccoides, Triticum turgidum and Aegilops tauschii), the proteins of these four species were retrieved from the Ensembl Plants database. Then, we used the same methods and criteria as described for wheat to identify the IQD genes in Triticum urartu, Triticum dicoccoides, Triticum turgidum and Aegilops tauschii. The synteny analysis of IQD genes between the homologs of wheat and its relatives was performed using MCScanX. The syntenic maps were visualized using Circos v0.67. The Ka (non-synonymous substitution)/Ks (synonymous substitution) ratio value was calculated using the PAML v4.9e package to estimate the divergence of the homologous genes [63].

Analysis of the expression profiles of TaIQD genes using transcriptome data

A total of 110 spatiotemporal and stress treatment RNA-seq samples of wheat, including root, stem, leaf, young spike (PRJNA525250), embryonal stage (PRJNA532455), 3 to 26 days after anthesis (DAA) leaves (PRJNA497810), and abiotic stresses (cold, heat, drought, salt, and P and iron starvation) (PRJNA253535, PRJNA257938, PRJNA487922 and PRJNA529036), were downloaded from the NCBI Sequence Read Archive (SRA) database. Detailed sample information is listed in Table S13. The fragments per kilobase per million (FPKM) value was calculated using HISAT2 v2.1.0 and the StringTie v1.3.5 pipeline. The log2 (FPKM + 1) value of TaIQDs was used to generate the expression heatmaps using the pheatmap package in R. We used τ (Tau) as a measure of the tissue specificity [64]. The τ values ranged from 0 to 1, with a large value representing high tissue specificity and a low value representing low tissue specificity. We considered τ > 0.6 as high tissue-specificity.

Cis-acting elements and regulatory network analysis

The 1.5 kb upstream DNA sequences from the gene transcription initiation site of TaIQDs were extracted and submitted to the PlantCARE online database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) to search for the putative cis-acting elements within the promoter region. The cDNA sequences of TaIQD genes were uploaded to the psRNATarget (http://plantgrn.noble.org/psRNATarget/) to find the candidate miRNA target sites. The co-expression network between TaIQDs and other related genes were constructed using the weighted gene co-expression network analysis (WGCNA) package in R according to their expression levels generated by the RNA-seq data. The co-expression relationships with weighted values larger than 0.25 were retained for subsequent analysis. The PPI network was also constructed based on the orthologous of TaIQDs in Arabidopsis using the STRING online tools (https://string-db.org/). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the co-expressed genes were performed using the KOBAS software (http://bioinfo.org/kobas), the potential relevancy between TaIQDs and other wheat genes was visualized using Cytoscape v3.8.0.

Plant material, stress treatment, RNA extraction and qRT-PCR analysis

Seeds of Triticum aestivum landrace ‘Chinese Spring’ were geminated on petri dishes under dark condition, and cultured in the growth chamber with a 16 h light/8 h dark cycle at 23 ± 1 °C. The three-leaf stage seedlings were subjected to abiotic treatments. For salt, drought, cold and heat stresses, the plants were subjected to treatment with 150 mM NaCl, 20% PEG-6000, at 4℃ and 42℃, respectively. The leaves were sampled at 0, 1, 6, 12 and 24 h with three independent biological replications, and the untreated plants were used as controls. The sampled leaves were rapidly pre-cooled in liquid nitrogen and then stored at -80℃ for subsequent analysis.

The plant RNA Kit Reagent (Omega Bio-Tek Inc., Norcross, GA, USA) was used to isolate total RNA. The cDNA was synthesized using the Evo M-MLV RT Mix Kit (Accurate Biology, Changsha, China). The quantitative real-time polymerase chain reaction (qRT-PCR) analysis was performed using a SYBR® Green Premix Pro Taq HS qPCR Kit (Accurate Biology) on an Applied Biosystems™ 7500 Real-Time PCR System (Thermo Fisher Scientific Inc., Waltham, MA, USA). The Primer Premier v5.0 software was used to design the primer sequences for TaIQD genes. The Elongation Factor 1-Alpha gene was used as the internal control. The primer information is listed in Table S14. The PCR cycling conditions were as follows: 95℃ for 30 s for 1 cycle, followed by 40 cycles of 95℃ for 5 s, 60℃ for 30 s. The 2−ΔΔCT method was used to evaluate the mRNA relative expression levels of TaIQDs [65]. The significance analysis was performed using the t-test package in R. The 0.05 and 0.01 significance level are indicated by one asterisk (*) and two asterisks (**), respectively.

Nucleotide variation and population structure analysis

The early released whole-genome sequencing population from the genera Triticum and Aegilops were used to identify the nucleotide variation of TaIQD genes. The genomic variation data was downloaded from the Genome Variation Map database under accession number GVM000082 [30]. The following criteria were used for filtration: minor allele frequency (MAF) > 0.05, and maximum missing rate < 0.1. To avoid the difference due to sampling, the same number of samples for different population was selected as much as possible. Therefore, we use a total of 27 Triticum rartu, 28 Triticum dicoccoides, 26 Triticum dicoccum, 10 Triticum turgidum, 26 Triticum aestivum (landrace), 20 Triticum aestivum (cultivar) and 30 Aegilops tauschii (Table S15). The PCA was performed using the smartpca subroutine in EIGENSOFT v6.1.4 [66]. An unrooted phylogenetic tree was generated by the neighbor-joining method with the parameters (1,000 bootstrap replications, 95% partial deletion and Poisson model), using the MEGAX v10.0 software. The population structure was analyzed by Admixture v1.3 [67] with the following parameters: the number of subgroups K ranged from 2 to 10, 10,000 times iteration and each K value was repeated five times. The VCFtools v0.1.17 genome toolbox was used to calculate the nucleotide diversity (π) and fixation index (Fst). The above-mentioned analysis was performed for the A, B and D subgenomes, respectively.

Availability of data and materials

All data supporting the conclusions of this article are provided within the article and its additional files. The sequences of Arabidopsis thalianaOryza sativa, Triticum urartu, Triticum dicoccoides, Triticum turgidum, Aegilops tauschii and Triticum aestivum are available in the Ensemble Plants database (http://plants.ensembl.org/index.html). The gene expression data was downloaded from the NCBI database (http://www.ncbi.nlm.nih.gov/geo/) under accession number PRJNA525250, PRJNA497810, PRJNA532455, PRJNA257938, PRJNA529036, PRJNA253535 and PRJNA487922. The genomic variation data was downloaded from the SnpHub (http://wheat.cau.edu.cn/WheatUnion/b_4/).

Abbreviations

aa:

Amino acids

ABA:

Abscisic acid

CaM:

Calmodulin

CML:

CaM-like

CBL:

Calcineurin B-like

CDPK:

Ca2+-dependent protein kinase

CaMBP:

Calmodulin-binding protein

CaMBD:

Calmodulin-binding domain

DAA:

Days after anthesis

EST:

Expressed sequence tag

FPKM:

Fragments per kilobase per million

F st :

Fixation index

GA:

Gibberellin

GO:

Gene Ontology

GRAVY:

Grand average of hydropathy

HMM:

Hidden Markov Model

IQD:

IQ67-domain

Ka:

Non-synonymous substitution

Ks:

Kynonymous substitution

MAF:

Minor allele frequency

MeJA:

Methyl jasmonate

MW:

Molecular weight

NJ:

Neighbor-joining

PCA:

Principal components analysis

pI:

Theoretical isoelectric point

PPI:

Protein-protein interaction

qRT-PCR:

Quantitative real time polymerase chain reaction

SA:

Salicylic acid

SNP:

Single nucleotide polymorphism

SRA:

Sequence Read Archive

WRE3:

Wounding responsive element 3

π:

Nucleotide diversity

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Acknowledgements

We thank the High-Performance Computing center of Northwest A&F University for providing computational resources in this work.

Funding

This research was mainly funded by the National Natural Science Foundation of China (Grant No. 32060458), Jiangxi Natural Science Foundation (Grant No. 20202BAB215002), and partially supported by the Science and Technology Research Project of Jiangxi Provincial Department of Education (Grant No. GJJ180241). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Authors and Affiliations

Authors

Contributions

Y.L. and L.C. designed the study. Q.K. and H.S. performed the data analysis. R.L., Y.Z. and M.W. collected the plant materials and performed the qRT-PCR experiments. Q.K. and R. L. validated the data. Q.K., Z.L., M.T., M.W. and L.C. wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Licao Cui.

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Ethics approval and consent to participate

The common wheat (Triticum aestivum L.) cultivar Chinese Spring was grown and collected by College of Bioscience and Engineering, Jiangxi Agricultural University (Nanchang, China), and all samples from this cultivar was adopted for all experiment. These plant materials don’t include any wild species at risk of extinction. No specific permits are required for sample collection in this study. We comply with relevant institutional, national, and international guidelines and legislation for plant study.

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Not applicable.

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The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Supplementary Information

Additional file 1: Figure S1.

The predicted ten motifs of TaIQD proteins based on MEME online software.

Additional file 2: Figure S2.

The chromosomal location of TaIQDs in the wheat genome.

Additional file 3: Figure S3.

Syntenic relationships of IQD genes among A, B and D subgenomes in common wheat.

Additional file 4: Figure S4.

qRT-PCR analysis of TaIQDs in response to salt, drought, heat and cold treatments. Error bars indicate standard errors from three independent replications. One asterisk (*) indicates 0.05 significance level. Two asterisks (**) indicates 0.01 significance level.

Additional file 5: Figure S5.

Analysis of the representative cis-regulatory elements in the promoter regions of TaIQDs.

Additional file 6: Figure S6.

Phylogenetic relationships, PCA and population structure analysis for the group B genomes based on TaIQD-related SNPs. The SNPs from the B subgenome of Triticum dicoccoides, Triticum dicoccum, Triticum turgidum and Triticum aestivum were used. A: Neighbor-joining phylogenetic tree, B: PCA analysis of PC1 vs PC2, C: PCA analysis of PC1 vs PC3, D: Population structure was estimated by ADMIXTURE with the K range from 2 to 8.

Additional file 7: Figure S7.

Phylogenetic relationships, PCA and population structure analysis for the group D genomes based on TaIQD-related SNPs. The SNPs from the D subgenome/genome of Triticum dicoccoides, Triticum dicoccum, Triticum turgidum and Triticum aestivum were used. A: Neighbor-joining phylogenetic tree, B: PCA analysis of PC1 vs PC2, C: PCA analysis of PC1 vs PC3, D: Population structure was estimated by ADMIXTURE with the K range from 2 to 8.

Additional file 8: Figure S8.

The protein-protein interaction (PPI) network of TaIQDs according to the orthologs in Arabidopsis.

Additional file 9: Supplementary tables. Table S1.

Validation of the IQ domain using the SMART, HMMER, and NCBI-CDD online databases. Table S2. Characteristics of IQD gene family in common wheat. Table S3. Conserved amino acids composition of IQ domain in different species. Table S4. Predicted calmodulin-binding sites in wheat IQD proteins. Table S5. Distribution of subgroup members of IQDs in different species. Table S6. The Ka/Ks ratios for syntenic TaIQD genes. Table S7. Characteristics of IQD gene family in wheat progenitors. Table S8. The Ka/Ks ratios for syntenic IQD genes in common wheat and its progenitors. Table S9. Characteristics of cis-acting regulatory elements in the promoter regions of TaIQD genes. Table S10. List of putative miRNAs that targeted to TaIQD genes. Table S11. Genomic distribution of nucleotide variations of TaIQD genes. Table S12. TW test of TaIQD-related genes for A, B and D subgenomes. Table S13. Accession numbers and samples information of RNA-seq data used in this study. Table S14. The primers information used in the qRT-PCR analysis. Table S15. Passport information of the resequencing accessions used in this study.

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Ke, Q., Sun, H., Tang, M. et al. Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors. BMC Genomics 23, 264 (2022). https://doi.org/10.1186/s12864-022-08520-w

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Keywords

  • Wheat
  • IQD gene family
  • Expression profiles
  • Polyploidization
  • Asymmetric evolution