The foxtail millet genome (version 2.2, Bennetzen et al., 2012) was downloaded from the plant genome database Phytozome.¹ The Hidden Markov Model (HMM) program hmmsearch was applied to identify CCT proteins with the parameter “--cut_tc” to control model-specific thresholding. The HMMER profile of the CCT domain (PF06203) was downloaded from the PFAM protein family dataset (Finn et al., 2010).² The basic properties of the CCT genes, namely, the length of amino acids, isoelectric point (PI), and molecular weights (MW), were estimated using the ExPASy program.³

To analyze the evolutionary relationship, the reference genome sequences of Setaria viridis (V2.1), Sorghum bicolor (V3.1.1), Oryza sativa (V7.0), and Zea mays (RefGen V4) were downloaded from Phytozome. Similarly, we identified the putative CCT genes in green foxtail, rice, maize, and sorghum by HMM profiles corresponding to the CCT domain. The primary protein of CCT family from these four species was aligned with clustalW and the phylogenetic tree was constructed by MEGA-X using the neighbor-joining (NJ) method with 1,000 bootstraps (Kumar et al., 2018). Finally, the evolutionary tree was visualized and illuminated by the software iTOL (Letunic and Bork, 2007).⁴ The conserved motifs of CCT proteins in foxtail millet were determined using the Pfam 33.1 database. Promoter sequences (2 kb upstream of the transcription start site) were extracted based on the genome sequence and annotation file, and promoter cis-acting elements were identified by Plantcare.⁵ The Gene Structure Display Service (GSDS 2.0; Hu et al., 2015) was used to draw the main protein domain and cis-regulatory elements distribution.

Chromosomal localization information for CCT genes in foxtail millet was identified from the reference genome database, and the genes were mapped to nine chromosomes using MapChart software according to the manual (Voorrips, 2002).⁶ To investigate the evolutional mechanism of the CCT family genes, five modes of duplication as whole-genome duplicates (WGD), tandem duplicates (TD), proximal duplicates (less than 10 gene distance on the same chromosome: PD), transposed duplicates (transposed gene duplications: TRD), or dispersed duplicates (DSD) occurred in CCT genes were obtained from PlantDGD database (Qiao et al., 2019).⁷ Gene duplication and synteny analysis were also performed using MCScanX software (Wang et al., 2012). The whole-genome duplication pattern was visualized using Circos software (Krzywinski et al., 2009).

The expression profile of some CCT genes in foxtail millet cultivar “Jingu 21” was extracted from the multi-omics database for S. italica (MDSi; Yang et al., 2020),⁸ which contained 23 samples from several tissues (including seeds, leaf, panicle, stem, and root) at vegetative and reproductive stages. The expression data (fragments per kilobase of transcript per million fragments mapped, FPKM values) were normalized into log2 (1 + FPKM), and the heat map was constructed using the R package “pheatmap” (version 1.0.12). To identify alternative splicing (AS) event, the genomic annotation file of the foxtail millet was used to extract all transcripts of CCT family genes. Then, AS events identification was performed by using ASTALAVISTA (Foissac and Sammeth, 2007).

To characterize the natural variation of CCT genes in foxtail millet, single-nucleotide polymorphisms (SNPs) in the coding region of CCT genes were identified based on the haplotype variation map from whole-genome resequencing of 312 accessions (Li et al., 2021). In addition, we extracted the SNPs from the genomic sequence, which referred to the sequence from the transcription initiation site to the transcription stop site. SNPs from the promoter region (within 2 kb upstream of the transcription start site) were also extracted. The average number of nucleotide differences per site between the two random sequences (π), the Watterson estimator (θ), and Tajima’s D were calculated using DnaSP v5.0 according to the manual (Librado and Rozas, 2009). The π ratio of genetic diversity in landraces to that in improved cultivars of foxtail millet was calculated for selection signals related to screening improvement.

We previously found that SiPRR37 had different haplotypes with or without the Tc1-Mariner transposon (Li et al., 2021). To validate the function of the CCT gene SiPRR37, we cloned the functional SiPRR37 haplotype and performed overexpression assays to generate the OE-SiPRR37 transgenic lines. Total RNA was extracted from the leaf tissue of foxtail millet landrace “Daqingmiaoyuci” using an RNAprep Prue plant kit (Tiangen Biotech Co., Ltd.). After isolation, first-strand cDNA synthesis was performed using the Transcriptor First Strand cDNA synthesis kit (Takara Biotech Co., Ltd) according to the manufacturer’s protocol. The 2.2-kb coding sequence of SiPRR37 was amplified using KOD FX (TOYOBO Life Science) and cloned into the binary vector pCUbi1390 driven by the ubiquitin promoter. The specific primers were designed using Primer-BLAST (National Center for Biotechnology Information, Maryland, United States) and are listed in Supplementary Table S7. The resultant plasmid was transformed into Agrobacterium tumefaciens strain EHA105. Agrobacterium-mediated ProUbi::SiPRR37 transformation was performed according to a previous study with some modifications (Yang et al., 2020). First, the palea and lemma of Ci846 mature seeds were removed and surface sterilized. The rinsed seeds were cultured on a medium for callus induction at 28°C in the dark for 8–10 weeks. Strain EHA105 harboring the ProUbi::SiPRR37 vector was cultured overnight and resuspended to a density of 600 nm (OD₆₀₀) = 0.5. High-quality calli were infected in resuspended cells for 5 min and transferred into a co-cultivation medium at 22°C in the dark. Then, calli were transferred to callus induction medium and selection medium with hygromycin B successively. Resistant calli were transferred to the shoot induction medium and cultured for root formation. Putative transgenic plants with healthy roots were moved to pots and detected by PCR. In addition, the expression level of positive transgenic plants was measured by qPCR.

The T₂ transgenic lines with a higher expression level of SiPRR37 were chosen to observe the phenotype change. Wild-type Ci846 and overexpressing transgenic lines were grown under field conditions in Beijing (40°13′N, 116°13′E). Heading date was scored by means ± SDs (n = 20) in the field conditions.

To examine the subcellular localization, Agrobacterium GV3101 containing pCAMBIA1305-GFP ligated to two haplotypes of SiPRR37 was transformed into Nicotiana benthamiana leaves. After 2 days of incubation, the infected leaves were harvested and used to observe GFP fluorescence using a confocal laser scanning microscope Nikon A1R. For the transcriptional activity assay, the functional and mutational SiPRR37 protein was amplified and cloned into the GAL4BD vector. The plasmids containing GAL4BD-SiPRR37/GAL4BD-Siprr37, pRTL, and 35sLUC were transformed into Arabidopsis protoplast cells as previously described with modifications (Yoo et al., 2007). The positive and negative controls were GAL4BD-VP16 and GAL4BD, respectively. Due to the transcriptional inhibitory activity of SiPRR37, the CDS of SiPRR37 and Siprr37 was cloned and introduced into GAL4BD-VP16. After incubation in the dark overnight, the protoplast cells were harvested and used to measure luciferase activity according to the manufacturer’s instructions for the Dual-Luciferase Reporter (DLRTM) Assay System (Promega).

RNA sequencing was performed on T₂ OE-SiPRR37 plants under long-day conditions. The leaf tissues with three biological replicates were harvested at the vegetative stage for T₂ plants. Six samples were prepared for 150 bp paired-end sequencing using an Illumina HiSeq X Ten platform. The raw data were trimmed and mapped to the foxtail millet reference genome using HISAT2 (hierarchical indexing for spliced alignment of transcripts; Kim et al., 2015). The FPKM of all genes was calculated using StringTie (v2.1.4, Pertea et al., 2015). Differentially expressed genes (DEGs) were detected using the R package edgeR (Robinson et al., 2010) following the criteria [|log₂(fold-change)| > 1 and false discovery rate < 0.01]. The DEGs were validated through qRT-PCR. MapMan bins of the foxtail millet genome were assigned (Thimm et al., 2004).⁹ Open-source MapMan software was used to identify the categories of differentially expressed genes. The RNA-seq raw data were submitted to the National Center for Biotechnology Information (NCBI) Bioproject under accession number PRJNA797949.

A total of 39 putative CCT genes were identified in the S. italic reference genome (Supplementary Table S1). The amino acid number of these CCT proteins varied greatly, ranging from 122 (Seita.8G159000) to 760 (Seita.9G445200), and the molecular weight ranged from 13.82 to 82.67 kDa. CCT family genes were distributed on each chromosome (Supplementary Figure S1). There were nine CCT genes on chromosome 9; chromosomes 1 and 4 harbored seven, and five CCT genes, respectively; chromosomes 2 and 3 each contained four CCT genes; chromosomes 6, 7, and 8 each contained three CCT genes; and chromosome 5 carried only one CCT gene.

To investigate the evolutionary relationship of CCT proteins in S. viridis, S. italic, O. sativa, S. bicolor, and Z. mays, a phylogenetic tree was constructed. A total of 208 CCT genes were identified from five Poaceae plants, with 39 CCT genes in foxtail millet, 39 CCT genes in green foxtail, 40 CCT genes in rice, 35 CCT genes in sorghum, and 55 CCT genes in maize. The number of genes in rice and maize was similar to previous studies (Figure 1; Zhang et al., 2015; Jin et al., 2018). Based on the domains they contained, all CCT genes were also divided into four subfamilies, with the largest CMF-like subfamily containing 108 members. The COL-like subfamily was composed of 54 members, the PRR-like subfamily had 27 members, and the TIFY-like subfamily involved 19 members. In each subfamily, CCT genes from the five species were closely clustered, suggesting that CCT gene families may have evolved before species differentiation.

Based on the topology of CCT genes in four Poaceae plants, there were 10 COL-like genes, 20 CMF-like genes, five PRR-like genes, and four TIFY-like genes in foxtail millet (Figure 2A). The analysis of these CCT protein structures showed a similar pattern with the CCT family divergence (Figure 2B). It also indicated that different subfamilies encoded proteins of various lengths and that the PRR subfamily was the longest. In addition, four genes only including the CCT domain were clustered in the COL subfamily or PRR subfamily, and one gene with zf-B box domain was clustered in the CMF-like subfamily. Partial CCT genes also exhibited a similar phenomenon in maize (Jin et al., 2018). It could be inferred that these genes lost the functional B-box type zinc finger domain during CCT gene family expansion.

The promoter sequences of CCT genes were analyzed in the PlantCARE database. The result showed that the promoters contained over 20 conserved elements, such as G-box, sp1, and TGA-element, with the highest number of G-box and ABRE elements (Figure 2C; Supplementary Table S2). These conserved elements were related to light responsiveness, plant hormones (abscisic acid, gibberellin, MeJA, and salicylic acid), and stress (low temperature and drought). Almost each CCT gene included a light responsiveness element, which inferred that the CCT domain genes were related to photoperiod.

To further study the functions of CCT genes, we detected the expression profile of partial CCT genes in different tissues and multiple growth stages. Overall, CCT genes in the same subfamily displayed similar expression patterns (Supplementary Figure S2). For example, most of the CMF subfamily genes were not expressed or had a lower expression level in all 23 tissues/stages, while the PRR subfamily genes showed a higher expression level. Moreover, we compared the expression patterns of segmentally duplicated genes. Some duplicated genes, including Seita.1G006700/Seita.4G001600, had similar expression patterns, while largely duplicated genes exhibited different patterns in most tissues. It was speculated that the newly duplicated genes played a powerful role in functional innovation.

In total, 11 AS events were identified in the CCT family genes, which were mainly distributed in six genes containing two CMF-like subfamily genes, two PRR-like subfamily genes, one COL-like gene, and TIFY-like subfamily gene (Table 1). Among of six AS genes, Seita.2G444300 and Seita.1G308800 consisted of two types of AS events, while AS events did not occur in their highly homologous genes.

Gene duplication is an important way for gene family expansion. To investigate the mode of duplication, we searched the PlantDGD database to extract all kinds of duplicates in foxtail millet CCT family genes. The results showed that a total of 48 duplication events occurred, including 11 WGD, 8 TRD, 28 DSD, and only one pair of tandem duplication genes, Seita.3G285700 and Seita.3G285800, closely clustering on chromosome 3 (Figure 3A; Supplementary Figure S1).

Eleven WGD events were identified, including four duplication events in the COL-like subfamily, five events in the CMF-like subfamily, one event in the PRR subfamily, and one in the TIFY subfamily (Figure 3B). Interestingly, four WGD events (Seita.1G006700/ Seita.4G001600, Seita.1G065300/Seita.4G192300, Seita.1G304900/Seita.4G122700, and Seita.1G308800/Seita.4G116600) arose between chromosomes 1 and 4 (Figure 3B; Supplementary Table S3). Among eight TRD events, we found that the transposon jumping near Seita.2G444300 was highly active, which was associated with the other two genes (Seita.1G236100 and Seita.2G286100). The intricate network of DSD events played a predominant role in CCT gene family expansion (Supplementary Table S3). The result indicated that DSD events mainly happened in the same subfamily. And most genes participated in two or three rounds of dispersed duplication events. Extensive duplication facilitates the rapid evolution of the CCT gene family.

In an attempt to characterize the nucleotide diversity of CCT genes, we analyzed the genomic region and the promoter region of CCT family genes within 203 foxtail millet landraces and 96 improved cultivars. The results showed that the average nucleotide diversity of each CCT subfamily was higher than that of the whole genome in foxtail millet (π = 1.621 × 10⁻³ in traditional landraces and π = 1.568 × 10⁻³ in improved cultivars; Li et al., 2021; Table 2). In the genomic region, the TIFY subfamily showed lower nucleotide diversity (π = 2.01 × 10⁻³) than that of the other three subfamilies. Overall, the nucleotide diversity in the promoter regions exhibited a similar level to the genomic regions, except for the TIFY subfamily (Table 2). In addition, Tajima’s D of three subfamilies except for the TIFY subfamily reached a significant positive level. Interestingly, we also found that the diversity of the COL and TIFY subfamilies was lower in improved cultivars than in landraces, while the opposite pattern appeared in the CMF family. Therefore, four subfamilies underwent selection to different extents during improvement.

Based on the haplotype map of 312 accessions in foxtail millet, we cataloged the SNP variation profile of 39 CCT genes. The results showed that a total of 19 CCT genes had a missense mutation, including four CMF-like genes, nine COL-like genes, three PRR-like genes, and three TIFY-like genes (Supplementary Table S4). Population genetic variation provides the rich potential to facilitate adaptation to novel environments. To determine whether the CCT gene family could be associated with improvement selection, we utilized π to screen the selective signals. We found only one TIFY-like gene (Seita.9G103000) located in the improvement-related selective interval (Supplementary Figure S3).

The protein family containing the CCT domain is mainly related to the flowering time pathway. To investigate the association between the CCT genes and heading date in foxtail millet, we collected heading date QTLs and GWAS signals according to previous studies and compared CCT gene localization with known heading date QTLs (Jia et al., 2013; Mauro-Herrera et al., 2013; Doust et al., 2017; Zhang et al., 2017; Li et al., 2021). Twenty-seven heading date-related QTLs and 40 GWAS signals were identified (Supplementary Tables S5, S6). Among 39 CCT family genes, 15 genes were located in the QTL regions or adjacent to the GWAS signals, including five COL-like genes, seven CMF-like genes, and three PRR-like genes (Supplementary Tables S5, S6). These genes may play an important role in regulating heading date.

In a previous study, we identified a significant association interval including SiPRR37 by GWAS (Li et al., 2021). SiPRR37 belongs to a member of the CCT transcription factor family. To validate the function of SiPRR37, we introduced the functional haplotype into the robust transformation receptor Ci846. The presence of the overexpression cassette in the transgenic lines was confirmed by PCR analysis and sequencing of the PCR fragment. Significantly enhanced expression of SiPRR37 in transgenic lines was also confirmed by real-time RT-PCR (Figure 4C). The positive transgenic lines showed an obvious difference in heading date compared with wild-type plants in the T1 generation under field conditions (Figure 4A). The SiPRR37-OE lines headed about 10 days later than the wild-type plant, indicating that SiPRR37 negatively regulated the heading date in foxtail millet (Figure 4B).

It was still unclear whether the SiPRR37-OE lines delayed the heading date under different conditions. To address this question, we planted the transgenic lines on June 22 and observed the phenotype in the greenhouse with a normal long-day photoperiod. We found that the transgenic line OX5 suppressed heading compared to the wild type (Supplementary Figure S4B). In addition, the SiPRR37-OE line OX5 influenced plant height simultaneously (Supplementary Figures S4A,C). Taken together, these results suggest that SiPRR37 is an important gene underlying heading date and plant architecture in foxtail millet.

SiPRR37 had two main haplotypes in foxtail millet of 312 accessions. In the mutant, transcription was truncated, and the CCT domain was lost due to Tc1-Marina transposon insertion (Li et al., 2021). Thus, we observed the sublocalization of two haplotypes. The two haplotypes (SiPRR37 and Siprr37) with GFP labels driven by the CaMV35S promoter were introduced into tobacco leaves. The SiPRR37-GFP signal appeared in the nucleus, while the Siprr37-GFP signal was detected in the nucleus and cytoplasm, similar to the localization of the blank control (Supplementary Figure S5A). These results validate that the CCT domain plays an important role in the nuclear localization of proteins (Robson et al., 2001). Thus, we evaluated the transcriptional activity of two haplotypes in Arabidopsis protoplasts. The results showed that SiPRR37 exhibited transcriptional inhibitory activity, which indicated that SiPRR37 functioned as a repressor in regulating heading date (Supplementary Figure S5B). In contrast, Siprr37 lost its transcriptional activity despite its nuclear localization.

To study the effect of SiPRR37 on the downstream genes, RNA-seq was performed on the leaves of the wild type and SiPRR37-OE transgenic line OX5 at the vegetative stage. Compared with the wild-type line, the SiPRR37-OE transgenic line has 1,295 DEGs, including 695 downregulated genes and 600 upregulated genes. DEGs were significantly enriched in MapMan categories, including signal, stress, protein, secondary metabolism, nucleotide metabolism, and cofactor metabolism, and the downregulated and upregulated gene compositions were different (Figure 5A). Among 695 downregulated genes, the most prominent subcategory was transcriptional regulation, which contained 36 transcription factors referring to the diverse aspects of development. In addition, an abundance of DEGs involved stress, which was also the target gene of PRR7 in Arabidopsis (Liu et al., 2013). This result indicated that SiPRR37 may participate in multiple regulation pathways besides heading date.

Combined with the known flowering time genes from Arabidopsis, 12 DEGs were identified by comparative analysis, which were involved in the circadian clock, photoperiodism, sugar, and general pathways (Figure 5B). SiPRR37 (Seita.2G444300) is a circadian clock-related gene whose overexpression influenced the expression of other circadian clock-related genes, such as Seita.6G055700 (SiLHY, the homolog of LATE ELONGATED HYPOCOTYL), Seita.1G236100 (SiTOC1, the homolog of TIMING OF CAB EXPRESSION 1), Seita.4G288100 (SiRVE2, the homolog of REVEILLE 2), and Seita.5G468100 (SiPCL1, the homolog of PHYTOCLOCK 1). The expression profile of the clock genes demonstrated that Arabidopsis PRR7 can inhibit the expression of LHY, while LHY can bind to and activate the expression of PRR7 and PRR9 (Salomé et al., 2010). Notably, multiple photoperiodic genes were downregulated, including Seita.3G325900 (the homolog of AS1, ASYMMETRIC LEAVES 1), Seita.5G052700 (the homolog of CDF2, CYCLING DOF FACTOR 2), Seita.2G035000 (LATE, LATE FLOWERING), and Seita.5G302800 (the homolog of SPA3, SPA1-RELATED 3). Seita.1G301300 (the homolog of COL9, CONSTANS-LIKE 9) was upregulated. One glycometabolism-related gene, Seita.9G247300 (the homolog of PGM1, PHOSPHOGLUCOMUTASE), was also significantly upregulated. We also found two other DEGs belonging to the CCT family, Seita.2G175000 (the homolog of OsCCT22; Zhang et al., 2021) and Seita.9G228800 (a member of the CMF subfamily), were also upregulated. The qRT-PCR results showed that the expression patterns of most genes were consistent with the RNA-seq results (Figure 5C).

The important feature of the CCT family is the 43–45 conserved amino acids in the carboxy terminus, which could possess the function of a nuclear localization signal (Strayer et al., 2000; Robson et al., 2001). The CCT domain proteins participate in the signal cascade of environmental factors, such as light, gravity, and temperature, which may be involved in the regulation of the photoperiod pathway, circadian clock, and abiotic responses (Putterill et al., 1995; Kaczorowski and Quail, 2003; Salomé and McClung, 2005). In maize, the CCT genes can be classified into four subfamilies corresponding to the encoded domains, namely, the COL subfamily, the CMF subfamily, the PRR subfamily, and the TIFY subfamily (Jin et al., 2018). The COL-like genes possessed CCT and B-box zinc finger domains. The CMF genes only had a CCT domain. The PRR genes had CCT and response regulator receiver domains, while the TIFY genes held CCT, TIFY, and GATA zinc finger domains.

To date, at least 18 CCT domain-containing genes in rice have been isolated that participate in regulating heading date (Zhang et al., 2021). Hd1 was the first CCT family gene to be identified, and its expression reached a peak during the night under long- and short-day conditions (Yano et al., 2000; Hayama et al., 2003). Apart from Hd1, the other three genes (Ghd7, Ghd7.1/OsPRR37, and DTH2) were also obtained by a map-based cloning strategy. DTH2 (days to heading on chromosome 2) encodes a COL-like protein, which enhances adaptation for the northward expansion of rice cultivation (Wu et al., 2013). Ghd7 belongs to the CMF-like subfamily, while Ghd7.1/OsPRR37 belongs to the PRR-like subfamily, and both genes could cause pleiotropic effects, including delaying heading date, increasing plant height, and grain number per panicle (Xue et al., 2009; Yan et al., 2013; Gao et al., 2014). Other CCT genes, for example, OsCCT01, OsCCT03, and OsCCT41 were obtained through reverse genetics and functioned as repressors or activators in the flowering regulation network (Zhang et al., 2015, 2021). In addition, multiple genes are involved in abiotic stress responses. For example, overexpression of Ghd7 increased drought sensitivity, and Ghd7 could strongly respond to abscisic acid, jasmonic acid, and high-temperature stress (Weng et al., 2014). In Arabidopsis, AtCOL4 also participates in stress to salt through the ABA-dependent signaling pathway (Min et al., 2015).

In this study, a total of 39 genes of the CCT family, including CMF-like, COL-like, PRR-like, and TIFY-like subfamilies, were identified in foxtail millet. Among the different species, genes of the corresponding subfamily were clustered. This further proved that the CCT domain genes evolved before species divergence (Cockram et al., 2012). For example, genes OsCOL4, OsCOL10, and OsCOL9 belong to the COL subfamily, and the overexpression of OsCOL4 or OsCOL10 in rice delays heading date regardless of day length, while the overexpression of OsCOL9 also enhances rice blast resistance by interacting with the receptor for activated C-kinase 1 (Lee et al., 2010; Liu et al., 2016; Tan et al., 2016). In addition, the expression pattern of partially homologous genes in different tissues also exhibited vast diversity (Supplementary Figure S2).

Comparative genome analysis showed that the genes among foxtail millet, sorghum, and maize were highly conserved and had a higher identity in the panicoids (Bennetzen et al., 2012; Zhang et al., 2012). Considering that the CCT family genes evolved before the divergence between the monocots and dicots (Cockram et al., 2012), we speculated that the CCT genes in cereal crops possessed a conserved function. Thus, it will provide a reference for functional genome research of CCT genes in foxtail millet.

In this study, we comprehensively analyzed the expansion mode of the CCT gene family in foxtail millet, which has not been performed in maize (Jin et al., 2018), rice (Zhang et al., 2015, 2021), wheat (Zheng et al., 2017), and soybean (Mengarelli and Zanor, 2021). A large number of duplicated genes occurred after the pan-grass polyploidization ~96 mya (Wang et al., 2015). Until now, 11 whole-genome duplicated CCT gene pairs are still identified in the foxtail millet genome (Figure 3A), including genes from CMF-like, COL-like, PRR-like, and TIFY-like subfamilies, which further inferred CCT gene family evolved before Poaceae species differentiation. Among these WGD events, four duplication events took place between Chr1 and Chr 4, two happened between Chr2 and Chr 9, one occurred between Chr1 and Chr 7, and one appeared between Chr3 and Chr 5, which was consistent with long synteny blocks in foxtail millet genome (Zhang et al., 2012).

We identified 48 duplication events that were classified into four categories: 11 WGD (22.9%), 28 DSD (58.3%), 8 TRD (2.1%), 1 TD (16.7%; Figure 3A). Our result suggested that DSD significantly contributed to CCT gene family expansion in foxtail millet. The duplication modes in different gene families or organisms may be discrepant. For example, the tandem duplication was the primary driving force for the expansion of the BpUGT gene family in Broussonetia papyrifera (Wang et al., 2021). While the dispersed duplication could directly affect the functional diversification by asymmetric regulatory divergence (Owens et al., 2013). Besides, alternative splicing is also an important regulatory mechanism for modulating gene expression and functional diversity (Lareau et al., 2004). However, AS events were only identified in six CCT genes (Table 1). One of the reasons may be that WGD-derived duplicated genes decrease the AS frequency (Shen et al., 2014). Therefore, the gene family could expand through duplication, while the duplicated genes maybe diverge over time to perform different functions.

SiPRR37, which is the homologous gene of PRR7 in Arabidopsis, encodes a circadian rhythm protein. Two allelic mutants of prr7 exhibited reduced sensitivity to both continuous red and far-red light, and the stability of the PRR7 protein was regulated by light and the circadian clock (Kaczorowski and Quail, 2003; Farré and Kay, 2007). There were five members in the PRR family in Arabidopsis, namely, TOC1 (PRR1), PRR3, PRR5, PRR7, and PRR9, and there was a close relationship between them. TOC1 (PRR1) was the first PRR-like gene to be cloned and was the central regulator (Strayer et al., 2000). PRR3 could modulate the stability of TOC1, yet both genes exhibited partially overlapped expression patterns (Para et al., 2007). PRR5 could interact with TOC1 in vitro and in vivo through the N-terminus, and TOC1–PRR5 oligomerization enhanced the accumulation of TOC1 in the nucleus (Wang et al., 2010). Overexpression of PRR5 could inhibit the expression of PRR7 and PRR9 while enhancing the expression of PRR3 and TOC1 (Sato et al., 2002). The gene PRR5/PRR7/PRR9 played an overlapping and distinctive role in the central oscillator and could repress the expression of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY; Nakamichi et al., 2005, 2010). In rice and Arabidopsis, five PRR members showed a similar expression order, and five members started accumulating sequentially after dawn with 2–3 h intervals in the order of PRR9, PRR7, PRR5, PRR3, and PRR1 (Matsushika et al., 2000; Murakami et al., 2003).

After the identification of PRR7 in Arabidopsis, homolog genes were gradually uncovered in many crops. Ppd-H1 was the major determinant of barley photoperiod response, which enhanced the adaptation of spring-sown varieties (Turner et al., 2005). OsPRR37 and SbPRR37 were involved in regulating heading date and yield, and the loss-of-function genotype contributed to cultivation at a wide latitude area (Murphy et al., 2011; Koo et al., 2013). Studies have shown that genes SbPRR37, OsPRR37, Ppd-H1, and PRR7 are all orthologous, possessing conserved functions in the photoperiodic pathway (Murphy et al., 2011; Gao et al., 2014). Here, we confirmed that overexpression of SiPRR37 delayed the heading date in natural long-day conditions, which suggests that SiPRR37 has a conservative function. The insertion of the transposon Tc1-Marina may be the result of adaptive selection.

The current research indicated that the PRR proteins also participate in abiotic stress regulation. Among the five PRR members in rice, OsPRR73 could inhibit OsHKT2;1 expression by binding the promoter and regulating the response to salt stress (Wei et al., 2021). In addition, PRR5 interacts with ABI5 and modulates expression to enhance ABA signal transduction during seed germination (Yang et al., 2021). In this study, we found that SiPRR37 may be involved in the stress-related pathway through transcriptome analysis. Therefore, we speculated that SiPRR37 also plays a role in the stress signal pathway, which requires further study.