Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer

Abstract

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait.

1. Introduction

The transition from the vegetative to the reproductive phase is a major developmental switch in flowering plants. Flowering time control plays a key role in domestication and crop productivity, and is regulated by multiple endogenous signals and environmental conditions [1,2,3]. Chickpea (Cicer arietinum L.) is a major grain legume and good source of plant-based protein [4,5]. However, the genetic mechanisms of flowering time regulation in Cicer remain far from understood.

Much of our current understanding of the genes involved in flowering time control is based on studies of the model species Arabidopsis thaliana. To date, more than 300 flowering time genes have been identified in Arabidopsis, including a number of key regulators. These genes are integrated into several major pathways [6] (Figure 1). The main signal responsible for floral promotion is encoded by the FLOWERING LOCUS T (FT) gene, the expression of which is induced in the leaves by numerous endogenous and exogenous signals [7]. These signals are encoded by genes from the ’photoperiod/circadian clock’, ’vernalization/ambient temperature’, ’autonomous’, ’hormone’, and ’sugar’ pathways [6,8,9] (Figure 1). Following the induction of FT gene expression, the FT protein moves from the leaves to the shoot apex where it activates meristem identity genes, including the major regulators APETALA1 (AP1) and LEAFY (LFY) [10,11,12]. These genes promote flowering by specification of the floral fate of shoot apical meristems, and act upstream of the floral organ identity genes. Unlike the FT protein, the TERMINAL FLOWER1 (TFL1) gene product functions as an ’anti-florigen’, and represses meristem identity genes [12,13,14].

Vernalization responsiveness in Arabidopsis depends on the regulation of the FLOWERING LOCUS C (FLC) gene, which encodes the MADS box transcription factor [15,16,17,18]. Before cold treatment, high levels of FLC transcription are provided by the FRIGIDA (FRI) complex [19]. The FLC protein represses the FT gene by binding to its first intron [20]. Vernalization induces FLC silencing through the action of many factors, including components of the ’autonomous’ and ’vernalization’ pathways, the PHD-PCR1 complex, and the COOLAIR complex [18,21,22] (Figure 1). This leads to de-repression of the FT gene and its activation by the ’photoperiod’ pathway, resulting in floral transition.

The most important gene in photoperiodic control of flowering in Arabidopsis is CONSTANS (CO), which integrates signals from regulators such as GIGANTEA (GI), LATE ELONGATED HYPOCOTYL (LHY), CRYPTOCHROME (CRY), CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX (CIB), PHYTOCHROME (PHY), CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), CYCLING DOF FACTORS (CDFs), and others [8,23,24,25].

Extensive research has revealed that the flowering pathways described in A. thaliana are largely conserved in legumes [26,27,28,29,30]. However, there are three main differences. First, genome evolution has led to many changes in the number of gene copies [31,32,33,34]. Legumes have multiple FT genes, which are organized in three subclades, (FTa, FTb, and FTc), as well as multiple TFL1 genes [26,27,34,35,36]. This results in high complexity of the genetic networks involved in the activation of FT expression in the leaves and transmission of multiple FT and TFL1 signals to meristem identity genes [37,38] (Figure 1). Moreover, different FT and TFL1 genes may possess distinct patterns of regulation with respect to environmental cues and tissue specificity [26,27]. Second, vernalization-sensitive legume species generally lack FLC orthologs, and the molecular mechanisms of vernalization response in these species are largely unknown [34,39,40] (Figure 1). However, as in Arabidopsis, FT genes appear to be major targets of vernalization in legumes [27,36,40]. Third, the CO gene presumably does not play a central role in photoperiodic regulation in legumes, as suggested by studies of CO homologues (COL genes) in Medicago truncatula and pea (Pisum sativum) [41,42,43].

In Cicer, multiple loci responsible for flowering time control have been discovered, including the Early flowering (Efl1, Efl2, Efl3) loci, a genomic region in the central portion of chromosome three and a “hot spot” on linkage group (LG) four [41,44,45,46,47,48,49,50]. Nevertheless, the expression and function of the genes underlying these loci remains under investigation. Recent studies have shown that Efl1, an ortholog of Arabidopsis EARLY FLOWERING 3 (ELF3) [35], and a cluster of three FT genes (FTa1-FTa2-FTc) within the quantitative trait locus (QTL) DTF3A on chromosome three both play an important role in the early flowering of domesticated chickpea [50]. Overall, there are five FT genes in Cicer; however, they are differently distributed within subclades compared to pea and Medicago [50]. In total, there are three FTa genes (FTa1, FTa2, and FTa3), the FTb gene, and the FTc gene. In addition, there are five TFL1 genes: TFL1a, TFL1b, TFL1c1, TFL1c2, and TFL1c3 [50].

Regarding tissue specificity, a global transcriptome analysis study has characterized the gene expression in vegetative and reproductive tissues of domesticated Cicer [51]. However, similar analyses have not been performed for wild Cicer species. Recent research has characterized the transcriptome landscape of inflorescence development in chickpea and identified candidate regulators such as ELF3a. Results from this work suggest the importance of LFY and AP1 regulation during inflorescence and floral development of C. arietinum [52].

In addition to C. arietinum, which is an annual cultivated chickpea, the genus Cicer includes both perennial and annual wild species. C. reticulatum and C. echinospermum are the annual wild species most closely related to the domesticated chickpea. C. reticulatum is the immediate progenitor of C. arietinum, while C. echinospermum meets the criteria for the secondary gene pool of C. arietinum [5,53]. Vernalization responsiveness is inherent to annual wild Cicer species, including C. reticulatum and C. echinospermum, but it is considered to be lost from the cultivated chickpea [54,55,56]. During domestication, C. arietinum has been transformed from a winter crop to a summer crop [50,57]; however, the sensitivity of cultivated chickpea to vernalization remains debatable. Although the vernalization response appears to be lost in many early flowering accessions, recent publications suggest that it may be preserved in the later-flowering varieties [56,58]. In this regard, the analysis of changes in gene expression in response to vernalization treatment in cultivated chickpea is of particular interest. A major QTL for the vernalization response in Cicer has been discovered on linkage group three (LG3) of the chickpea genetic map, in approximately the same genomic region as the FTa1-FTa2-FTc cluster [50]; however, the individual genes responsible for vernalization sensitivity have not yet been characterized [59].

In this study, we consider a high-throughput transcriptomic dataset obtained for the cultivated chickpea and two wild species, C. reticulatum and C. echinospermum, from leaves and floral buds after vernalization and without vernalization treatment. The elite early flowering cultivar ICCV 96029 [48,60] carries a number of mutations, which include an 11 bp deletion in the first exon of the ELF3 gene [35]. ICCV 96029 was considered separately from the other C. arietinum accessions and referred to as ‘mutant’. Although ICCV 96029 has been reported to be photoperiod insensitive, it preserves the function of circadian clock genes [35]. We analyzed differential expression of 278 Cicer orthologues of A. thaliana flowering time genes [6] between tissue types, conditions, and species/accessions. The most attention was paid to the analysis of FT genes, their regulators, and their targets. We sought to address the following questions. (1) How does the expression of flowering time genes depend on tissue type? (2) Does the domesticated chickpea respond to vernalization? (3) What is the difference in gene expression between ICCV 96029 and other cultivated chickpea accessions? (4) How does the expression of flowering-related genes differ between wild and domesticated Cicer?

We believe that our results can improve knowledge of the genes involved in the regulation of flowering time in Cicer and in other legumes.

2. Results

2.1. Differential Gene Expression between Tissue Types

First, we analyzed the differences in gene expression between three tissue types: leaves before flowering initiation (leaves BF), leaves after flowering initiation (leaves AF), and the early buds. The number of differentially expressed genes (DEGs) between the leaves (at any stage) and the buds was twice that between leaves BF and leaves AF. We detected 66 DEGs between leaves BF and leaves AF, 128 DEGs between leaves AF and buds, and 147 DEGs between leaves BF and buds (Figure 2a).

A number of DEGs varied across species/accessions and conditions (columns, labeled with different colors in Figure 2a). In the comparison between two types of leaf tissues (leaves BF and leaves AF), the highest number of DEGs was detected for C. echinospermum after vernalization (43 DEGs) and C. arietinum (31 DEG), while very few DEGs were found in mutant ICCV 96029, with five DEGs without vernalization and no DEGs after vernalization (Figure 2a). This variation was much lower in the comparison between leaves AF and flower buds, where we found the maximum number of DEGs in the mutant without vernalization (93 DEGs) and the minimum number in C. arietinum (69 and without vernalization and 67 DEGs after vernalization) (Figure 2a). The comparison between leaves BF and floral buds showed minimal variation, with a large number of DEGs in all species/accessions and conditions (Figure 2a).

Interestingly, the direction of regulation did not change with respect to species/ accession and condition when an individual DEG was up- or downregulated in the comparison between two tissue types (Figure 2b, Supplementary Tables S3–S5). Of all DEGs, only three genes did not follow this rule; LHY and CDF2, which in Arabidopsis encode transcription factors from the ’photoperiod/circadian clock’ pathway, changed the direction of regulation in two comparisons, leaves BF vs. leaves AF and leaves BF vs. buds (Figure 2b,c). The same was observed in the comparison between leaves AF and buds for the SHORT VEGETATIVE PHASE (SVP) gene (Figure 2b,c). This suggests that the tissue-specific expression of these genes is highly dependent on species/accession and condition.

The expression of the FTa1 gene was upregulated in leaves AF of mutant ICCV 96029 after vernalization and in leaves BF of C. arietinum after vernalization when compared with buds (Figure 2c, Supplementary Table S3). An ortholog of the Arabidopsis AP1 gene showed the most dramatic difference in gene expression between leaves and buds. The log2 fold change values (FC) in the comparisons of buds with leaves AF and leaves BF were 7.0–7.5 and 8.1–9.9, respectively (Figure 2c, Supplementary Table S3). The expression of another meristem identity gene LFY, acting in synergy with AP1, was upregulated in the buds, though with lower FC values (Figure 2c).

2.2. Vernalization Response in Cultivated Chickpea

We sought to check the vernalization responsiveness of the early flowering mutant ICCV 96029 in comparison with other C. arietinum accessions.

As expected, in cultivated chickpea the number of DEGs between the two conditions (with and without vernalization) was very small, ranging from one to five genes depending on the tissue studied. All the DEGs are presented in Figure 3.

The ortholog of the Arabidopsis FTa3 gene (Ca_19141) was upregulated by vernalization in all tissue types of both C. arietinum and ICCV 96029 (Figure 3). FTa3 upregulation was higher in the mutant ICCV 96029 compared to other C. arietinum accessions; FC values ranged from 3.0 to 6.6 in C. arietinum and from 5.5 to 7.8 in the mutant. Maximum levels of FTa3 activation were detected in leaves BF for both types of chickpea accessions.

In addition to FTa3, all DEGs in both mutant and other C. arietinum accessions were found in two tissue types, namely, leaves BF and leaves AF (Figure 3). In the mutant, all DEGs were upregulated by vernalization, including LHY and CDF2 as well as another FT family member, FTa1 (Figure 3).

In C. arietinum, five genes were differentially expressed in response to vernalization treatment; three were from the ’hormone’ pathway (encoding gibberellin oxydases GA2OX2 and GA20OX1 and the gibberellin receptor GID1B), one was the DNA methylation factor VARIANT IN METHYLATION 1 (VIM1), and the last was the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5 (SPL5) gene, which encodes an ortholog of transcription factor involved in the regulation of FT, LFY, and AP1 in Arabidopsis. The expression of SPL5 and two genes from the ’hormone’ pathway was downregulated in response to vernalization, while GA20OX1 and VIM1 were upregulated (Figure 3).

2.3. Flowering Time Genes That Differentiate ICCV 96029 from Other Cultivated Accessions

The early flowering ICCV 96029 mutant was reported to be photoperiod-insensitive due to a mutation in the chickpea homologue of the major Arabidopsis circadian clock gene ELF3. This mutation provides early induction and increased expression of FT genes while maintaining the rhythms and expression levels of the circadian clock genes [35]. Thus, it was interesting to compare gene expression between ICCV 96029 and other C. arietinum accessions in various tissue types, with particular attention to the expression and regulation of the photoperiod/circadian clock and FT genes.

The number of DEGs between ICCV 96029 and other C. arietinum cultivars was relatively small (Figure 4a). The maximum number of DEGs was detected in leaves AF, suggesting that this tissue is critical with respect to the differences between the two types of chickpea accessions (Figure 5). The expression of all genes from the ‘photoperiod/circadian clock’ pathway in this tissue type was upregulated in the mutant. We found differentially expressed orthologs of the Arabidopsis photoperiodic genes CALCIUM DEPENDENT PROTEIN KINASE 6 (CPK6) (FC = 1), CDF2 (FC = 1.9), MYB-RELATED PROTEIN 2 (MYR2) (FC=1.4), and FE (FC = 1.1), as well as the circadian clock genes LHY (FC = 2.5) and ELF4 (FC = 3.23) (Figure 5). In terms of condition specificity, nineteen DEGs were revealed in the leaves AF after vernalization treatment (shown in blue) and in ten DEGs without vernalization (shown in green) (Figure 5). Genes differentially expressed in specific conditions included FTa1 (upregulated in ICCV 96029 after vernalization treatment, FC = 2.9) and TFL1c2 (upregulated in C. arietinum without vernalization, FC = 2.1). Five genes, mostly belonging to the ‘autonomous’ pathway, were expressed differentially in both conditions (shown in red) (Figure 5).

A significantly smaller number of DEGs was found in tissues other than leaves AF (Figure 5). No DEGs were revealed in the leaves BF collected from vernalized plants (Figure 4a), and only four DEGs were detected in the same tissue type without vernalization. The expression of all these genes except for AGAMOUS-LIKE 6 (AGL6) was downregulated in the mutant ICCV 96029. In the flowering buds, the expression of all DEGs was downregulated in the mutant as well. In the buds of vernalized plants, only one gene, VERNALIZATION INDEPENDENCE 5 (VIP5) from the ‘Vernalization/temperature’ pathway, FC = 1.1, was differentially expressed, while in the buds of non-vernalized plants nine DEGs, including two photoperiod/circadian clock genes (PHYTOCHROME INTERACTING FACTOR 4 (PIF4) (FC = 1.2) and CPK6 (FC = 1.3)), were found.

Our data showed that the differential expression between ICCV 96029 and other C. arietinum accessions was vernalization-sensitive (Figure 4a). For example, of 38 DEGs detected in all tissue types (Figure 5), only five were differentially expressed in both conditions. The remaining 33 genes were differentially expressed in specific conditions, specifically, 18 genes in plants without vernalization and 15 genes in vernalized plants (Figure 5). Remarkably, out of 18 DEGs found in plants without vernalization, only three genes were upregulated in the mutant. On the contrary, after vernalization, we found that nine genes were upregulated in the mutant, while six genes were upregulated in other C. arietinum accessions (Figure 5). Thus, the number of genes upregulated in ICCV 96029 increased significantly after vernalization treatment.

2.4. Differences in Flowering Time Gene Expression between C. reticulatum and C. echinospermum

The number of DEGs between these two wild species was twice that between two types of cultivars under the same conditions (after vernalization treatment) (Figure 4a). This reflects the evolutionary distance between C. reticulatum and C. echinospermum. Interestingly, most genes were upregulated in C. reticulatum compared to C. echinospermum (Figure 4a and Figure 5).

The number of DEGs from the ‘photoperiod/circadian clock’ pathway was highest in the leaves AF (Figure 5).

We did not reveal any difference in expression of the FT gene orthologs between C. reticulatum and C. echinospermum. Interestingly, the orthologs of the Arabidopsis FT-INTERACTING PROTEIN 1 (FTIP1) gene, which encodes an endoplasmic reticulum protein involved in the transport of the FT gene product [61], were differently expressed between the two wild species: FTIP1a (Ca_00020) and FTIP1$\kappa$ (Ca_19710) were upregulated in C. echinospermum, while FTIP1h (Ca_14215) was upregulated in C. reticulatum (Supplementary Table S1, Figure 5). This points to the complex mechanisms of FT protein transport, which can have distinct features in each species.

Two orthologs of the Arabidopsis TFL1 gene were upregulated in C. reticulatum (Figure 5). It is noteworthy that TFL1c2 expression was upregulated in all tissue types (FC = 2.5–3.3), while TFL1c3 showed upregulation only in the buds (FC = 5.7). This suggests stronger negative control of flowering promotion in C. reticulatum compared to C. echinospermum.

A number of genes were differentially expressed in two or three tissue types, which suggests their major role in flowering time variation between wild species. The Arabidopsis TOPLESS (TPL) gene ortholog (TPLf, Ca_14764) was upregulated in C. reticulatum in all tissue types, while the ortholog of the CRY2 gene (CRY2b, Ca_23164) was upregulated in C. reticulatum in leaves AF and buds (Figure 5). On the contrary, the ortholog of the SVP gene had a tissue-specific mode of regulation; it was upregulated in the leaves AF and downregulated in the flower buds of C. reticulatum. The expression of the SUCROSE SYNTHASE 4 (SUS4) gene ortholog from the ‘Sugar’ pathway (SUS4c, Ca_03475) was upregulated in C. echinospermum in all tissue types (FC = 4.2 in leaves BF, FC = 4.6 in the leaves AF, and FC = 3.2 in the buds) (Figure 5, Supplementary Tables S1 and S6–S8).

2.5. Comparison of Gene Expression between Wild and Cultivated Cicer

The largest number of differently expressed genes from the ‘photoperiod/circadian clock’ pathway between wild and cultivated Cicer was detected in the leaves BF (Figure 5 and Figure A1). This could be explained by the early induction of light-signaling genes in cultivated chickpea compared to wild Cicer. These genes were mostly upregulated in cultivated chickpea. The number of ‘photoperiod/circadian clock’ DEGs decreased in the leaves AF, and was the lowest in flowering buds. On the contrary, in the buds we found that an increased number of DEGs from the ‘sugar’ pathway were found (Figure 5 and Figure A1). This trend was evident when comparing both types of cultivated Cicer with wild species.

The expression of FT genes was upregulated in the ICCV 96029 when contrasted with wild species. The difference in FTa3 gene expression in leaves BF was only significant when the mutant was compared with C. echinospermum, while the difference in FTa1 gene expression in leaves AF was significant when comparing the mutant with both wild species. The orthologs of the Arabidopsis FTIP1 gene were differently expressed in all comparisons between wild and cultivated Cicer and in all tissue types. As was the case in the comparison between wild species, the direction of regulation varied between different copies of the FTIP gene (Figure 5 and Figure A1).

The expression of the TFL1c ortholog was upregulated in cultivated chickpea, pointing to the higher level of repression of its targets, namely, LFY and AP1 (Figure 5 and Figure A1). Indeed, LFY was downregulated in both mutant and C. arietinum in comparison with C. reticulatum in the leaves AF (shown in black in Figure A1). Because the FT genes perform flowering induction via activation of meristem identity genes, different directions of regulation of FT and LFY could underlie variations in the activator/repressor balance required for floral promotion in wild and cultivated Cicer.

The DEGs found in most tissue types were largely consistent with those detected in the comparison between the two wild species. The orthologs of the TPL and CRY2 genes (TPLf) and CRY2b) were upregulated in cultivated chickpea compared with C. echinospermum in all tissue types. The SVP gene was upregulated in the buds in cultivated chickpea accessions and leaves AF of the ICCV 96029 mutant and downregulated in leaves AF of C. arietinum, while multiple copies of the SUS4 gene showed either up- or downregulation in cultivated chickpea in comparison with wild Cicer (Figure 5 and Figure A1, Supplementary Tables S6–S8).

2.6. Verification of Transcriptomic Data by Quantitative Real-Time PCR Assay

To validate the differential expression results obtained by RNAseq assay, we analyzed expression of four genes (FTa1, LFY, LHY, and TFL1c2) by qPCR in two random samples from our dataset (Figure A3). Both samples were leaves AF of C. arietinum: #32 after vernalization, and #38 without vernalization. The results of qPCR for three technical replicates are shown in Figure A3b.

We estimated differences in gene expression between the two samples by two methods, then compared FC values obtained by RNAseq and qPCR. The qPCR results showed the same direction of gene expression regulation as RNAseq (Figure A3a), confirming the reliability of RNAseq analysis.

3. Discussion

3.1. The Defining Role of Tissue Type in Differential Expression of Individual Genes

In the between-tissue comparison, the direction of regulation of an individual gene was gene-specific and did not change with species/accession or condition (Figure 2b). This highlighted the leading role of tissue type in defining the difference in expression of individual genes.

However, three exceptions were found: the direction of expression regulation of LHY, CDF2, and SVP genes varied between species/accessions and conditions (Figure 2b,c), which may be explained by the function of these genes. In Arabidopsis, LHY encodes a transcription factor that plays a major role in circadian clock regulation, while CDF2 regulates blue light signaling and miRNA biogenesis [62] and is putatively regulated by LHY [63]. The SVP gene is a major regulator controlling the effect of environmental cues in floral induction [64]. It is likely that in Cicer these genes are involved in environmental signal processing as well, necessitating the need to tune gene expression in response to external and internal cues.

Our results clearly indicate a larger difference in gene expression between leaves and floral buds than between that of two types of leaves. This observation is consistent with a previous study suggesting the existence of different transcriptional programs in chickpea vegetative and flower tissues [51].

With regard to major flowering regulators, we detected that FTa1 expression was upregulated in leaf tissues compared to buds in cultivated chickpea after vernalization (Figure 2 and Supplementary Tables S4 and S5). This is consistent with earlier published results [50]; however, it indicates a possible dependence of tissue-specific FTa1 expression on vernalization treatment.

On the contrary, the expression of meristem identity genes AP1 and LFY was upregulated in the buds (Figure 2c). In Arabidopsis, LFY is expressed in the inflorescence and floral meristems and activates the expression of AP1 and floral organ identity genes [10,65,66,67]. The expression of both genes is generally conserved in legumes [68,69], although with a few functional differences. For example, the pea homologue of LFY is involved in the regulation of complex leaf development along with its role in the initiation of floral meristems [67,68,70]. Upregulation of LFY in the flower buds of all Cicer species/accessions does not suggest any function of this gene in the leaf tissue.

3.2. The FTa3 Gene Is Upregulated by Vernalization in Cultivated Chickpea

During the process of domestication, chickpea was transformed from an autumn-sown crop to a spring-sown crop, providing maturation during summer and avoiding Ascochyta blight disease in winter. Due to these breeding attempts, the vernalization responsiveness is considered to have been lost from the domesticated chickpea, in contrast to its wild relatives [54,55,56]. Interestingly, the analysis of different cultivated accessions revealed that the late-maturating varieties continue to respond to vernalization, unlike the early-maturating varieties [56].

In our analysis, we found that the number of DEGs was very small in both the early-flowering ICCV 96029 mutant and the later-maturating C. arietinum accessions (Figure 3). Nevertheless, DEGs in the mutant and C. arietinum generally belonged to different regulatory pathways, with an exception for the ’Development’ pathway (Figure 6).

Remarkably, all DEGs in the early-maturating mutant were upregulated by vernalization. They included LHY and CDF2 from the ’Photoperiod/circadian clock’ pathway and two FT genes, FTa1 and FTa3. CDF2 activation by vernalization treatment is non-trivial, as in Arabidopsis it represses FT transcription [71].

On the contrary, vernalization treatment in C. arietinum affected the expression of three genes from the ’hormone’ pathway, VIM1 from the ’autonomous’ pathway, and two genes from the ’development’ pathway, FTa3 and SPL5 (Figure 6). In Arabidopsis, the SPL5 gene is regulated by FT and activates expression of AP1 [72,73]. It has been recently reported that SPL5 is involved in the timing of cold-induced floral transition in rapeseed (Brassica napus) [74]. Downregulation of SPL5 by vernalization in C. arietinum presumably underlies the timing of the vernalization response in Cicer. In Arabidopsis, VIM proteins regulate epigenetic silencing via histone modification and DNA methylation [75]. In C. arietinum, upregulation of the VIM1 ortholog may contribute to silencing of the unknown FT repressor, thereby promoting activation of the FT genes by vernalization.

Interestingly, in both mutant and C. arietinum, the FTa3 gene was up-regulated by vernalization in all tissue types (Figure 3 and Figure 6). Moreover, the FTa3 FC values were higher in the early flowering mutant compared with the other chickpea accessions, which is not consistent with the previously reported vernalization insensitivity of the early flowering cultivars [56].

The data on narrow-leafed lupin L. angustifolius and Medicago trancatula suggest that the FT family genes may be the main targets of vernalization in legumes [27,36]. However, unlike the vernalization-sensitive genes from the FTa1 subclade, the representatives of the FTa3 subclade, namely, MtFTa3, LanFTa1, and LanFTa2, were not involved in vernalization response [36]. Further studies of wild and cultivated accessions are required in order to decipher the role of the FTa3 gene in vernalization-induced flowering in Cicer.

3.3. Differential Gene Expression between ICCV 96029 and Other Cultivated Accessions Depends on Vernalization Treatment

According to the previous results, the early flowering ICCV 96029 mutant is photoperiod-insensitive, although with an apparently preserved function of the circadian clock genes [35]. Thus, a difference could be expected in the expression of light-signaling genes in the mutant compared to the later flowering C. arietinum accessions.

The maximum number of DEGs was detected in the leaves AF, suggesting that this tissue type is critical with respect to the difference in gene expression between the mutant and C. arietinum. In the leaves AF, all genes from the ’photoperiod/circadian clock’ pathway were upregulated in ICCV 96029 (Figure 5), as was with the ortholog of the FTa1 gene, which plays a major role in the promotion of early flowering in M. trancatula and P. sativum [26,27,76,77]. The same upregulation was detected for the ortholog of the AGL6 gene, encoding an important positive regulator of flowering [78]. On the contrary, the expression of the ’anti-florigen’ TFL1c2 was downregulated in the mutant, which is consistent with the early maturation of this cultivar and confirms previous results [35,79].

Remarkably, most genes showed differential expression between ICCV 96029 and other C. arietinum accessions in a specific condition. For example, in the mutant, FTa1 and AGL6 were upregulated in the vernalized leaves, while TFL1c2 was downregulated in the leaves AF without vernalization (Figure 5). Only five DEGs, mostly belonging to the ‘autonomous’ pathway, were expressed differentially in both conditions (Figure 5).

The number of genes differentially expressed between ICCV 96029 and other C. arietinum cultivars depended on vernalization treatment. We found a threefold increase in the number of genes activated in the early flowering mutant after vernalization compared to the nonvernalized data (Figure 4a). This suggests a role for vernalization in gene expression differences between early and later flowering C. arietinum accessions.

3.4. Shared DEGs in the Comparison between Two Wild Species and between Cultivated and Wild Cicer

We found many shared DEGs in our comparisons of two wild species and wild species with cultivated Cicer accessions (Figure 4b and Figure 5). For example, a copy of the TPL ortholog (TPLf) was upregulated in cultivated chickpea, in contrast with wild species, as well as in C. reticulatum as compared to C. echinospermum (Figure 5 and Figure A1). In Arabidopsis, the TPL co-repressor is involved in modulation of gene expression in diverse developmental processes, including photoperiodic flowering [80,81]. The same pattern of regulation was inherent to orthologs of the TFL1 gene in all comparisons, and to another major repressor, SVP, in the buds (Figure 5). In the leaves AF, SVP was upregulated in C. echinospermum as compared with both C. reticulatum and C. arietinum.

Interestingly, our results showed that almost all genes had the same direction of expression regulation in comparisons of C. echinospermum with C. reticulatum and C. echinospermum with cultivated Cicer (Figure 7 and Figure A2). This suggests similarity in the mechanisms of flowering time regulation in C. reticulatum and cultivated chickpea, which is hardly surprising, as this species is regarded as the wild progenitor of domesticated varieties.

Considering that the C. arietinum varieties flower earlier than wild species even after vernalization treatment [56], the elevated levels of the flowering time repressors (TPL, TFL1, and SVP) in cultivated chickpea are unusual, and require a detailed analysis of the activator/repressor balance during flowering transition in different Cicer species.

3.5. Differences in Expression of FT and FTIP1 Genes between Wild and Cultivated Cicer and between C. reticulatum and C. echinospermum

A recent study has revealed the major contribution of the FT cluster, located on the Cicer chromosome 3 and includes the FTa1, FTa2, and FTc genes, to the difference in flowering time between cultivated chickpea and C. reticulatum [50]. We found upregulated expression of FTa1 and FTa3 orthologs in the ICCV 96029 mutant compared to wild species, suggesting that these genes contribute to the early flowering of this cultivar. On the contrary, no differences in FT expression were found between the two wild species (Figure 5 and Figure A1). This suggests a minor variation in flowering time between C. reticulatum and C. echinospermum after vernalization treatment, and confirms the previous observation [56].

In our dataset, we revealed fourteen orthologs of the Arabidopsis FTIP1 gene, which encodes the endoplasmic reticulum membrane protein required for FT protein transport. In Arabidopsis, FTIP1 shares mRNA expression and subcellular localization with the FT gene [61]. It is likely that the large number of copies of the FTIP1 gene is related to the extended number of FT genes in Cicer as compared to Arabidopsis.

Remarkably, different copies of the FTIP1 gene had variable directions of regulation both when comparing cultivated chickpea with wild species and C. reticulatum with C. echinospermum (Figure 5 and Figure A1). The transport of FT proteins through the phloem to the shoot apex, where they transfer information on environmental signals to meristem identity genes, plays a key role in flowering induction in Arabidopsis and legumes [26,61]. In Arabidopsis, loss-of-function mutations in FTIP1 result in delayed flowering under long days [61]. The variability in the direction of FTIP1 regulation suggests complex mechanisms of FT transport, which differ between Cicer species.

4. Materials and Methods

4.1. Plant Materials and Sample Collection

Four C. arietinum accessions (ICCV 96029, ICC 16201, CDC Frontier, and Consul), two C. reticulatum accessions (Bari3 and Cudi 1022), and two C. echinospermum accessions (610380 and 610381) were grown under long days (16 h light: 8-h dark photoperiod) in a climatic chamber at +26 °C. All seeds were vernalized at +4 °C in the dark for 30 days. For C. arietinum, non-vernalized seeds were additionally sown. For each of the growing conditions (with or without vernalization), 6–8 seeds of each accession were planted at a time. The experiment was repeated twice to ensure a sufficient amount of samples for each accession.

We collected plant material from the following tissue types: (1) leaves before flowering initiation (leaves BF); (2) leaves after flowering initiation (leaves AF); and (3) flower buds at the initial stages of their formation (FB1 and FB2) [51,82]. The samples were collected during the daytime between 1 p.m. and 3 p.m. Leaves BF were harvested 15 days after sowing [82,83] by collecting a second uppermost leaf from each plant.

For each accession, tissue type, and condition, biological material was harvested from three plants, resulting in three independent biological replicates. The samples were placed into RNA later-stabilizing reagent (Thermo Fisher) at +4 °C and then stored at −20 °C.

In total, 144 samples with a sufficient amount of plant material were used for further RNA extraction.

4.2. RNA Extraction and Library Preparation

RNA was extracted using RNeasy Mini Kit (Qiagen). For each extraction, we took about 50 mg of plant material. RNA concentration was measured using a Qubit RNA BR Assay kit (Invitrogen, Carlsbad, CA, USA) and Qubit 2.0 fluorometer (Invitrogen). RNA quality was assessed by capillary electrophoresis on a Bio-analyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) using a chip and an RNA 6000 Pico reagent kit (Agilent Technologies). The degree of RNA degradation was determined according to the RNA integrity index (RIN) [84].

For library preparation, we used RNA samples with RIN higher than 6.5. Preparation of cDNA libraries was performed using commercial NEBNext Ultra II RNA kits (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s protocol. To increase the proportion of target transcripts, we applied an additional step of poly (A) + mRNA enrichment using oligo dT probes. This resulted in the efficient removal of rRNA. The cDNA samples were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN, USA). The concentration of the resulting libraries was measured with an DNA BR Assay kit (Invitrogen) and a Qubit fluorometer. The quality of the libraries was assessed by capillary electrophoresis using a High Sensitivity DNA reagent kit (Agilent Technologies). When a peak corresponding to the adapter dimers was detected in the library, additional purification was performed using magnetic beads.

4.3. Illumina Sequencing and Gene Expression Quantification

The libraries were sequenced using HiSeq4000 (Illumina) with a read length of 75 nucleotides in paired-end mode.

The sequencing reads were trimmed and filtered to remove low quality bases with AfterQC software [85] version 0.9.6. The average fraction of filtered out bases was 9.36%. Expression quantification was reformed using the kallisto program, version 0.46.1 [86], and the coding sequences of the C. arietinum genome, version 1.0 [87]. The average expression (tpm) was 3584.23.

4.4. Search for Orthologs of the Arabidopsis Flowering Time Genes

Flowering signaling pathways have been well studied in Arabidopsis thaliana, and are summarized in the interactive database of flowering time gene networks FLOR-ID (http://www.phytosystems.ulg.ac.be/florid/, accessed on 22 January 2023). These networks include 306 genes, most of which are members of multigenic families [6].

Most orthologs of the Arabidopsis flowering genes are not annotated in the reference chickpea genome. Thus, the expression of these genes cannot be analyzed using standard annotation, and orthologs must be identified. The nucleotide sequences of the A. thaliana flowering time genes from the FLOR-ID database were downloaded from Ensembl plants, genome version TAIR10. Their orthologs in the C. arietinum genome (version 1.0) were found using the tblastx program and their coding sequences were compared between A. thaliana and Cicer. The filtering threshold for candidate selection by bit score was set to 100. Accession numbers of several key regulators not identified via homologue search were taken from the literature [50].

As a result, 278 sequences of Cicer genes highly homologous to A. thaliana flowering time genes were included in the analysis. The short names of Arabidopsis genes (“Alias” in Supplementary Table S1) were taken from the section “Detailed Gene Information” of the FLOR-ID database.

4.5. Analysis of Differential Gene Expression

Differential expression analysis was performed using the DESeq2 package, version 1.28.1 [88]. Significant DEGs had an adjusted p-value (padj) < 0.01 and log2 fold change values greater than 1 or less than −1. To evaluate sampling between biological replicates, we applied the variance stabilizing transformation (VST) function from the DESeq2 package and then performed principal component analysis (PCA) on the transformed data. An example PCA plot is shown in Supplementary Figure S1.

Gene expression did not differ significantly between the three C. arietinum accessions (ICC 16201, CDC Frontier, and Consul) or between individual accessions of C. reticulatum (Bari3 and Cudi 1022) or C. echinospermum (610380 and 610381); thus, we integrated RNAseq data for these accessions within each species. ICCV 96029, one of the world’s earliest chickpea cultivars, has been developed by the International Crop Research Institute for the semi-arid tropics (ICRISAT, India) [48,60]. It has recently been found to carry an 11-bp deletion in the first exon of the ELF3 gene [35]. Here, we considered ICCV 96029 separately from the other C. arietinum varieties and referred to it as ‘mutant’. This resulted in four species/accessions being analyzed in this paper: C. arietinum, the ICCV 96029 mutant, C. reticulatum, and C. echinospermum (Figure 8).

DEGs were identified in the following pairwise comparisons: (1) between tissue types (species/accessions and conditions remained fixed): leaves BF—leaves AF; leaves AF—buds; buds—leaves BF; (2) between conditions (species/accessions and tissue types remained fixed): without vernalization—after vernalization; and (3) between species/accessions (conditions and tissue types remained fixed): C. arietinum—ICCV 96029 mutant; C. arietinum—C. reticulatum; C. arietinum—C. echinospermum, ICCV 96029 mutant—C. reticulatum; ICCV 96029 mutant—C. echinospermum; C. reticulatum—C. echinospermum.

We attributed chickpea orthologs to the following pathways according to the information from the FLOR-ID and TAIR databases [6,89]: photoperiodism, light perception, and signaling; vernalization and temperature; hormones, Gibberellin signaling, and metabolism; sugar pathway; general processes and autonomous pathway; development; and main targets of floral homeotic genes. We used the following short names of these pathways: (1) photoperiod and circadian clock; (2) vernalization and temperature; (3) hormone; (4) sugar; (5) autonomous; (6) development; and (7) main targets.

A. thaliana flowering time gene products are frequently involved in a variety of biological processes. For the sake of convenience, in our analysis each gene was attributed to one major pathway (Supplementary Table S1), with their additional roles discussed in the text.

4.6. Real-Time PCR Assay

The RNA concentrations in the samples were determined using a Qubit 4 fluorometer (Thermo Fisher, Waltham, MA, USA) and an RNA HS Assay Kit (Thermo Fisher). RNA integrity was assessed by electrophoresis using 1% agarose gel with GelRed^® Nucleic Acid Gel Stain (Biotium). The first complementary DNA (cDNA) strands were obtained by reverse transcription using an MMLV RT Kit (Evrogen, Moscow, Russia) according to the manufacturer’s protocol. cDNA concentration prior to quantitative PCR was measured using a P360 Nanophotometer (Implen, München, Germany). Negative controls (no enzyme) were used to monitor genomic DNA contamination.

Oligonucleotide primers for qPCR were constructed using the BeaconDesigner software tool and synthesized by Evrogen Company (Supplementary Table S2). Quantitative PCR was performed using a CFX96 Touch Real-Time PCR Detection System with three replicates for each point. The expression levels of target genes were normalized to the expression of ACT1 or EF1α (Figure A3b).