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Article

Genome-Wide Identification of the CRY Gene Family in Solanum tuberosum and Response to Abiotic Stresses

by
Yan Gao
1,
Xueying Yang
1,
Xin Lv
1,
Yuxuan Li
1,
Kuihua Li
1,* and
Yuliang Gao
2,*
1
Agricultural College, Yanbian University, Yanji 133002, China
2
Yanbian Academy of Agricultural Sciences, Longjing 133400, China
*
Authors to whom correspondence should be addressed.
Genes 2025, 16(10), 1234; https://doi.org/10.3390/genes16101234
Submission received: 13 September 2025 / Revised: 9 October 2025 / Accepted: 16 October 2025 / Published: 18 October 2025
(This article belongs to the Section Plant Genetics and Genomics)
Browse Figures
Versions Notes

Abstract

Background: Cryptochromes (CRYs) are not only blue-light receptors in plants but also participate in abiotic stress responses, making them essential for plant growth and development. Methods: In this study, the CRY gene family in potato (StCRY) was identified and analyzed using bioinformatics approaches, and the expression patterns of StCRY genes under different abiotic stresses were validated through transcriptome datasets and RT-qPCR analysis. Results: A total of 7 StCRY genes were identified, unevenly distributed across 4 chromosomes. The StCRY genes exhibit conserved structures, with predicted subcellular localization primarily in the nucleus, cytoplasm, and plastids. Promoter region analysis revealed the significant presence of cis-acting elements related to light, plant growth and development, hormones, and stress responses. Phylogenetic analysis classified the CRY gene family into three subgroups and identified one pair of collinear genes. StCRY genes show a closer evolutionary relationship with tomato, followed by Arabidopsis thaliana, and are least related to rice. Transcriptome and RT-qPCR analyses under cold, drought, and salt stresses revealed differential expression among StCRY genes: StCRY3 and StCRY7 respond positively to cold stress, StCRY1 and StCRY5 are upregulated under drought and salt stresses, and StCRY7 expression is positively correlated with salt stress. Conclusions: Collectively, this study provides a preliminary characterization of the CRY gene family in potato and establishes a theoretical foundation for further investigations into the molecular mechanisms of blue-light receptors in abiotic stress responses.

1. Introduction

Light is the primary source of energy for plants, influencing photosynthetic reactions and playing a decisive role in plant growth and development [1]. Variations in photoperiod, light intensity, and light quality affect plant growth in different ways, among which light quality is particularly critical [2]. Light quality refers to the wavelength composition of light, that is, its color or spectral distribution. Plants exhibit distinct responses to different wavelengths, such as blue light, red light, and far-red light [3,4]. Light quality transmits signals by activating specific photoreceptors in plants and subsequently modulates intracellular signaling pathways, thereby influencing enzyme activity and hormonal changes, which ultimately affect plant growth and development, secondary metabolism, and yield quality [5,6]. In practical production, supplementary red and blue light is commonly applied to optimize plant growth and improve the quality of horticultural products [7,8].
To better adapt to the light conditions of their environment, plants have evolved a variety of photoreceptors during evolution, including phytochromes, the UV-B receptor UVR8, and cryptochromes, among others [9,10,11]. Blue-light photoreceptors mainly consist of cryptochromes (CRYs) and phototropins [12]. CRYs regulate multiple key stages of plant growth and development, such as seedling de-etiolation, photosynthesis, hypocotyl elongation, and responses to abiotic stresses [13,14,15]. Cryptochromes are primarily composed of CRYs and CRY-DASH [16,17]. It is generally believed that CRY1 acts as the major factor in blue-light-dependent photomorphogenesis, while CRY2 is mainly involved in photoperiodic regulation of flowering time, with functional redundancy between the two in the regulation of flowering [13]. The CRY-DASH protein contains only an N-terminal domain, and its precise role in plants remains unclear. Some studies suggest that it can directly bind DNA and RNA and mediate light-dependent repair of UV-damaged DNA [15,16,17].
During plant growth and development, AtCRY1 directly interacts with AUX/IAA to inhibit the binding of TIR1 and AUX/IAA, thereby preventing the degradation of AUX/IAA. This suppression leads to inhibited hypocotyl elongation and enhanced anthocyanin accumulation. Moreover, cry1 mutants exhibit delayed flowering under various light conditions [18]. AtCRY2 primarily suppresses the transcription of root cell division genes in darkness, while blue light alleviates this inhibitory effect [19]. In tomato, cry1a mutants display relatively taller plants and increased fruit set, whereas overexpression produces the opposite phenotype [20]. In rice, OsCRY1s inhibit coleoptile and leaf growth under blue light and mediate the de-etiolation response, while OsCRY2 is involved in promoting flowering time [21].
CRYs play important roles in plant responses to temperature, drought, and salt stresses [22,23]. CRY1 regulates plant thermotolerance through the Constitutive Photomorphogenic 1 (COP1)–Elongated Hypocotyl 5 (HY5) module. Under normal- and high-temperature dark conditions, COP1 mediates the degradation of HY5 protein, thereby releasing the repression of heat shock transcription factors (HSFs) by HY5; as a result, HSFs are highly expressed in response to heat stress in darkness. Under high-temperature blue light conditions, elevated temperature inhibits the activity of CRY1-associated protein kinases (PPKs), leading to a reduction in blue-light-dependent phosphorylation of CRY1, weakened CRY1–COP1 interactions, increased COP1 activity, and decreased HY5 abundance, ultimately resulting in enhanced expression of HSFs [24]. The CRY2-COP1-HY5 module in Arabidopsis positively regulates plant freezing tolerance by activating a subset of cold-responsive genes through BBX7/8 transcription factors, in a manner independent of CBF/DREB2 pathways [25]. In addition, the blue-light receptor CRY integrates abscisic acid (ABA) and jasmonic acid (JA) signaling into the plant salt stress response by interacting with GBF1 and other regulatory factors [26].
Potato (Solanum tuberosum), a member of the Solanaceae family, is an annual herbaceous plant widely cultivated worldwide and ranks as the fourth most important food crop [27]. Its tubers are rich in starch, proteins, and various vitamins and minerals [28]. In recent years, with increasing research on its nutritional value, the applications of potato in food processing, animal feed, and biofuel production have attracted growing attention [29]. Studies indicate that potato not only contributes to improving human health but also plays a vital role in agricultural economies [30,31]. The present study identifies and analyzes the CRY gene family in potato using bioinformatics approaches and further characterizes them through transcriptome datasets under multiple abiotic stresses and RT-qPCR analyses. These findings provide a theoretical foundation for future research on potato yield improvement.

2. Materials and Methods

2.1. Plant Materials and Abiotic Stress Treatments

The potato cultivar daxiyang was selected as the experimental material. Potato tubers were planted in soil (nutrient soil:vermiculite = 3:1) and incubated for 30 days under controlled conditions of 24 °C, a light intensity of 2000 Lx, and a 16 h light/8 h dark photoperiod. Subsequently, plants with five leaves and a single shoot apical meristem were selected for further experiments. The plants were subjected to cold treatment (4 °C), salt stress (80 mM NaCl) [32], and drought stress (20% PEG600) [33], and samples were collected at 0 h, 1 h, 3 h, 6 h, 12 h, and 24 h [34,35,36]. All treatments were performed with three biological replicates. The samples were immediately frozen in liquid nitrogen and stored at −80 °C for subsequent analyses.

2.2. Identification of StCRY Gene Family Members

The potato genome (Solanum tuberosum v6.1), protein sequence files, and genome annotation files were downloaded from the Phytozome website (https://phytozome-next.jgi.doe.gov/, accessed on 10 July 2025). The CRY hidden Markov model (HMM, PF00875; DNA_photolyase) was obtained from the Pfam database (https://www.ebi.ac.uk/interpro/, accessed on 10 July 2025), and HMMER v3.3 software was used to search the potato protein sequence files. Additionally, A. thaliana CRY protein sequences were downloaded from Phytozome and used as queries for BLASTp searches against the potato protein sequences to identify candidate genes. The candidate genes obtained were further verified for domain composition using SMART (http://smart.embl.de/, accessed on 10 July 2025), NCBI Conserved Domain Database (https://www.ncbi.nlm.nih.gov/cdd/, accessed on 10 July 2025), and Pfam, resulting in the final identification of confirmed potato CRY genes.

2.3. Chromosomal Localization and Physicochemical Properties Analysis of StCRY Genes

Based on the potato genome annotation file, the lengths of the 12 chromosomes and the chromosomal positions of the StCRY genes were obtained. TBtools (v2.333) was used to generate a chromosomal localization map of StCRY genes, displaying the positions and relative distances of all members of the StCRY gene family on the chromosomes [37]. The protein sequences of StCRY genes were submitted to the ProtParam website (https://web.expasy.org/protparam/, accessed on 10 July 2025) for physicochemical property analysis. Subcellular localization of StCRY proteins was predicted using the Cell-PLoc-2.0 website (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/, accessed on 10 July 2025).

2.4. Analysis of Conserved Domains, Promoter Regions, and Gene Structures of StCRY Proteins

Conserved motif analysis of StCRY proteins was performed using the MEME software (https://web.mit.edu/meme_v4.11.4/share/doc/meme-format.html, accessed on 10 July 2025) with the minimum motif width set to 6 and the maximum width set to 100. MEME analysis data were extracted using a Perl script. Gene structure annotation information for CRY genes was obtained from the potato genome annotation file, and TBtools was used to visualize motifs, and gene structures.
For promoter analysis, 2 kb upstream sequences of all StCRY genes were extracted from the potato genome and annotation files. These sequences were submitted to the PlantCARE database for cis-acting element analysis, and the results were visualized using ggplot2 in R (v4.02).

2.5. Phylogenetic and Synteny Analysis of the StCRY Gene Family

Genome files and CRY family protein sequences of Oryza sativa, A. thaliana, and Solanum lycopersicum were downloaded from the Phytozome database and the Sol Genomics Network website(https://solgenomics.net/, accessed on 15 July 2025). A phylogenetic tree was constructed using MEGA software (version: X) [38], with sequence alignment performed by Clustal W and the Maximum Likelihood method applied for tree construction. The resulting phylogenetic tree was visualized and beautified using Evolview v2 (https://evolgenius.info/evolview-v2/, accessed on 15 July 2025).
For duplication analysis, the potato whole-genome sequences were self-compared using TBtools to identify duplication events among StCRY family members. Based on protein sequences and genome annotation files of rice, Arabidopsis, tomato, and potato, MCScanX was used to analyze the genomes and determine the collinearity relationships of StCRY genes between potato and rice, Arabidopsis, and tomato.

2.6. Protein–Protein Interaction and miRNA Prediction of StCRY

To construct the miRNA-gene interaction network, we conducted an analysis of miRNA targeting StCRY genes on the psRNATarget website (https://www.zhaolab.org/psRNATarget/, accessed on 15 July 2025). Protein–protein interaction (PPI) predictions among potato CRY proteins were performed using STRING (https://string-db.org/, accessed on 15 July 2025), and the results were visualized in R. To construct the miRNA-gene interaction network, miRNAs targeting StCRY genes were analyzed using the psRNATarget website (https://www.zhaolab.org/psRNATarget/, accessed on 17 July 2025).

2.7. Expression Analysis of StCRY Gene Family Members Based on Abiotic Stress Transcriptome Data

Transcriptome data of potato under cold, drought, and salt stress were downloaded from the NCBI GEO database. Salmon was used to map the transcriptome data and extract expression levels of all members of the CRY gene family [39]. Heatmaps were generated in R to visualize the results, and the expression changes in CRY family members under cold stress were analyzed.

2.8. Gene Ontology Enrichment Analysis

Gene Ontology (GO) enrichment analysis of the StCRY gene family was performed as follows. First, functional annotation of all StCRY family members was conducted using eggNOG-mapper (http://eggnog-mapper.embl.de/, accessed on 17 July 2025). Based on the annotation results, GO enrichment analysis was carried out to identify significantly overrepresented biological processes, molecular functions, and cellular components within the gene family. Finally, the enrichment results were visualized using R, enabling a clear representation of GO term distributions and their significance.

2.9. Quantitative Real-Time PCR (RT-qPCR) Analysis

Total RNA was extracted from potato leaves using Plant RNA Rapid Extract Kit (Coolaber, Beijing, China) and reverse transcribed into cDNA using NotionScript qPCR First-strand cDNA Synthesis Mix (Coolaber, Beijing, China). Fluorescent quantitative analyzed using 2× SYBR Green qPCR Mix (Coolaber, Beijing, China) for RT-qPCR. Primer sequences are provided in Table S3. The RT-qPCR reaction system and conditions were adjusted based on the methodology described by. Relative gene expression levels were calculated using the 2−∆∆Ct method [40]. The β-actin gene was used as a standardized internal reference and 3 biological replicates were set up for each sample [41].

2.10. Statistical Analysis

Experimental results are presented as the mean ± standard error, based on at least three independent biological replicates. Statistical analyses were performed using two-way analysis of variance (ANOVA) in SPSS version 25.0 (SPSS Inc., Chicago, IL, USA) to determine p-values, with p < 0.05 considered statistically significant. Data visualization was carried out using GraphPad Prism 9.

3. Results

3.1. Identification and Physicochemical Property Analysis of StCRY Gene Family Members

First, we identified 6 StCRY genes by aligning potato protein sequences with Arabidopsis CRY protein sequences. We then performed a genome-wide search of potato using the known CRY HMM profile (PF00875), which led to the identification of 7 StCRY genes in total. By integrating the results from both approaches and conducting transcriptome-based redundancy removal, domain analysis, and sequence alignment, we ultimately confirmed seven StCRY genes. These seven genes are distributed across four chromosomes (Figure 1): chr4 (StCRY1), chr8 (StCRY2 and StCRY3), chr9 (StCRY4 and StCRY5), and chr12 (StCRY6 and StCRY7). Based on their chromosomal positions, we named the genes StCRY1~7. The encoded proteins range from 385 to 679 amino acids in length, with predicted isoelectric points between 5.23 and 9.23. All proteins have GRAVY values below zero, indicating that they are hydrophilic. Subcellular localization prediction suggests that StCRY proteins are mainly localized in the nucleus, cytoplasm, and plastids, implying that CRY genes may perform diverse functions (Table S1).

3.2. Phylogenetic Analysis of the CRY Gene Family

To further investigate the evolutionary relationships of StCRY genes, we retrieved CRY protein sequences from rice, Arabidopsis, and tomato to construct a phylogenetic tree (Figure 2). Our results classified the CRY genes into three major groups: StCRY1, StCRY5, and StCRY6 were assigned to the first group; StCRY7 formed the second group; and StCRY2, StCRY3, and StCRY4 clustered into the third group. Phylogenetic analysis further revealed that StCRY7 and SlCRY3 belong to the same subgroup. These findings indicate that CRY genes in potato are more closely related to those in tomato, while rice CRY genes are more distantly related, suggesting that CRY genes may perform similar functions in potato and tomato.

3.3. Analysis of Conserved Motifs and Gene Structures of StCRY

We analyzed and visualized the conserved motifs of StCRY proteins using MEME and TBtools (Figure 3). Based on motif analysis, we classified the StCRY genes into three groups: the first group includes StCRY2, StCRY4, and StCRY7; the second group comprises StCRY1, StCRY5, and StCRY6; and the third group contains StCRY3. All genes in the first group contain motifs 8, 14, 13, and 15. The second group primarily includes motifs 4, 5, 11, 3, 1, 5, 2, and 7. The third group mainly consists of motifs 8 and 13. Proteins encoded by genes within the same group exhibit highly similar types and numbers of conserved motifs, indicating a strong conservation of motif composition within each subgroup.
We visualized the gene structures of StCRY based on the annotation files (Figure 3). We found that the number of exons and introns in StCRY genes ranges from 4 to 13. Both StCRY2 and StCRY7 contain 13 exons and introns. StCRY4 and StCRY6 each contain 4 exons, while StCRY1 and StCRY5 each contain 5 exons. Notably, the 3′UTR of StCRY3 contains three discontinuous segments. Although the coding sequence lengths are similar, the variation in exon and intron numbers during evolution leads to significant differences in the full gene lengths. This structural diversity may contribute to functional variability and provides valuable reference for further studies on the evolutionary relationships of the StCRY gene family in potato.

3.4. Cis-Element Analysis of StCRY Promoters

We analyzed the promoter regions of StCRY genes and classified their cis-acting elements into four categories (Figure 4): light-responsive elements, elements related to plant growth and development, hormone-responsive elements, and stress-responsive elements. Among the light-responsive elements, we found that all genes except StCRY1 contain G-BOX elements, with StCRY2 containing five copies. StCRY3 and StCRY7 lack T-motif elements, whereas StCRY1 contains six copies. Although StCRY genes function as blue-light receptors, not all genes possess the corresponding cis-elements. All genes from StCRY3 to StCRY7 contain ERE elements, suggesting that these genes may participate in regulating plant senescence. Various hormone-responsive elements are present in StCRY genes, including ABA-responsive ABRE elements (StCRY2–StCRY7), methyl jasmonate-responsive CGTCA-motif and TGACG-motif elements (StCRY1, StCRY2, StCRY3, StCRY4, and StCRY6), and the auxin-responsive TGA-element (StCRY4). Additionally, all StCRY genes contain MYC, MYB, and ARE elements, indicating potential roles in stress responses.

3.5. Tandem Gene Duplication and Segmental Gene Duplication of StCRY

The Ka/Ks ratio, which compares nonsynonymous substitutions (Ka) to synonymous substitutions (Ks), is a key indicator of selective pressure on protein-coding genes and holds significant importance in evolutionary analysis [42]. In this study, we analyzed the Ka/Ks values of the coding regions of StCRY genes and found that all StCRY members exhibited Ka/Ks ratios below 1, indicating strong purifying selection during their evolutionary history and suggesting potential functional conservation among these genes (Table S2). Given that StCRY genes are unevenly distributed across four chromosomes (Figure 5), we conducted segmental duplication analysis and identified a segmental duplication between StCRY1 and StCRY6. Such duplications may promote genetic diversity within the genome by altering gene copy number and structural variation, thereby influencing growth and development, trait expression, genetic variation, and other vital biological processes.
To further investigate the genetic relationships among CRY family members, we performed interspecies collinearity analysis using the genomes of Arabidopsis, rice, and tomato (Figure 6). We found two collinear gene pairs between Arabidopsis and potato, one pair between rice and potato, and five pairs between tomato and potato. These results suggest a closer evolutionary relationship among species within the same family, with genes likely sharing similar functions. Therefore, we infer that these duplication events may have occurred during the evolutionary history of the CRY gene family.

3.6. GO Enrichment Analysis of StCRY Genes

We performed Gene Ontology (GO) functional annotation to classify StCRY genes (Figure 7) into three categories: biological process, cellular component, and molecular function. Since the proportion of cellular component annotations was the lowest, the majority of annotations were concentrated in biological process and molecular function. We ranked the results by p-value and selected the top 20 categories for visualization. Our analysis revealed that the annotations were primarily enriched in biological process and molecular function, with molecular function representing the largest proportion. Specifically, StCRY genes are mainly involved in FAD binding (GO:0071949, GO:0050660) and photoreceptor activity (GO:0009881). In terms of biological processes, StCRY genes are predominantly associated with blue-light response, light signaling pathways, phototropism, photoperiod regulation, energy metabolism, and cell development.

3.7. Prediction of miRNA-StCRY Gene Interaction Network

To investigate the potential regulatory roles of miRNAs on StCRY genes, we predicted miRNA targets using the psRNATarget website. Our results indicated that multiple StCRY genes correspond to multiple miRNAs (Figure 8). For example, members of the miR166 family (such as stu-miR166a-3p, stu-miR166b, stu-miR166c-3p, and stu-miR166d-3p) were predicted to target StCRY7, StCRY5, and StCRY6, demonstrating a one-to-many relationship in which multiple miRNAs share the same target genes. Additionally, stu-miR396-3p was predicted to simultaneously target StCRY6 and StCRY2, illustrating a single miRNA regulating multiple genes. The relationships between miRNAs and StCRY genes are complex and highly specific, suggesting that these miRNAs may participate in regulating multiple physiological processes in plants.

3.8. Prediction of Protein–Protein Interactions of StCRY

Proteins are the primary executors of gene function, and analysis of their interaction networks is an important approach to elucidate biological mechanisms. To further investigate the biological functions of StCRY proteins, we constructed a protein–protein interaction network based on the STRING database (Figure 9). Our analysis revealed a significant interaction between StCRY1 and StCRY5, suggesting a potential functional synergy between these two proteins. Notably, StCRY3 was identified as a key hub protein, potentially interacting with multiple family members, including StCRY1, StCRY2, StCRY4, StCRY5, and StCRY7. This indicates that StCRY3 may play a central regulatory role in mediating light signaling pathways.

3.9. Expression Analysis of StCRY Genes Under Abiotic Stress

As the fourth largest food crop worldwide, potato growth and development are significantly inhibited by abiotic stresses such as temperature extremes, drought, and salinity, which directly affect tuber yield and quality and pose potential threats to food security. We analyzed the expression of StCRY genes using publicly available transcriptomes under cold stress (PRJNA753086), drought stress (PRJNA998742), and salt stress (PRJNA882516) from NCBI (Figure 10). Under cold stress (Figure 10A), the expression levels of StCRY2, StCRY3, and StCRY7 were upregulated, whereas StCRY4 and StCRY6 were significantly downregulated. During drought stress (Figure 10B), StCRY1, StCRY2, and StCRY7 showed decreased expression. In the salt stress transcriptome (Figure 10C), the expression of StCRY2, StCRY3, StCRY6, and StCRY7 decreased at 6 h and 12 h but increased at 24 h, with StCRY3 showing a pronounced increase at 24 h. StCRY1, StCRY4, and StCRY5 exhibited an initial increase followed by a decrease. These genes may serve as potential candidates for studying abiotic stress responses in potato.
In this study, we subjected potato plants to cold, drought, and salt stresses and analyzed the expression levels of StCRY genes at different time points (0 h, 1 h, 3 h, 6 h, 12 h, and 24 h) using RT-qPCR (Figure 11). Under cold stress, StCRY3 and StCRY7 showed a marked upregulation compared to 0 h, with StCRY3 exhibiting approximately a 10-fold increase at 12 h and 24 h. Under drought stress, StCRY1 displayed an upregulation at 6 h, with expression levels roughly three times higher than at 0 h. Under salt stress, StCRY1 and StCRY5 were upregulated at 1 h and 3 h but decreased significantly at 12 h and 24 h. Notably, StCRY7 showed an approximately 8-fold increase in expression at 24 h compared to 0 h.

4. Discussion

Potato, as a globally important food crop, is rich in essential nutrients required by the human body, and its yield plays a critical role in ensuring food security and promoting economic development [30]. Light conditions are one of the key factors affecting potato yield, with different light qualities and photoperiods significantly influencing plant growth and productivity [43,44]. Studies have shown that blue light can enhance plant height, fresh weight, and dry weight of potato plants, as well as promote tuber enlargement [45]. In practical cultivation, an appropriate red-to-blue light ratio can optimize potato growth and yield, while reducing the red-to-blue light ratio promotes tuber expansion, thereby increasing overall yield [44]. Therefore, the rational management of light conditions is of significant importance for improving both the yield and quality of potatoes.
Based on GO annotation classifications, CRY proteins serve as key blue-light photoreceptors in plants and play critical roles in regulating plant growth and development. In this study, seven StCRY genes were identified through bioinformatics analyses, which were unevenly distributed across four chromosomes. Motif analysis grouped these genes into three major classes, with members within the same class exhibiting similar motifs and gene structures, suggesting potential functional similarity. It is noteworthy that the phylogenetic and motif analyses produced slightly different groupings of StCRY genes. For example, StCRY7 clusters with StCRY2 and StCRY4 in the motif analysis but forms an independent group in the phylogenetic tree. This suggests that despite evolutionary divergence, these genes may retain conserved functional motifs, indicating potential functional similarity. The number of CRY genes varies among different species, with strong collinearity observed between potato and tomato, followed by Arabidopsis and then rice. The Ka/Ks ratios of StCRY genes were all less than 1, indicating that these genes may have undergone purifying selection and segmental duplication throughout evolution. These tandem and segmental duplications likely facilitated the expansion of new members and functions within the CRY gene family in the potato genome, thereby enhancing the environmental adaptability of potato.
CRY receptors exist as monomers in the dark and undergo conformational changes and oligomerization upon blue-light absorption, thereby altering their interactions with other proteins and influencing plant growth and development. CRY receptors can be activated not only by blue light but also function in the dark [46,47]. The G-BOX is an important light-responsive cis-element; in this study, only StCRY1 lacked this element, indirectly suggesting that StCRY1 may play a significant role under dark conditions.
Due to their sessile growth habit, plants must constantly perceive changes in their surrounding environment. Recent studies have shown that plants adjust their responses to abiotic stress signals based on environmental light cues [48,49]. In this study, transcriptome analyses under cold, drought, and salt stress were conducted to examine StCRY gene expression. CRY genes exhibited differential responses under these stresses, indicating their involvement in environmental adaptation. These results indicate that potato responds to environmental stresses in part through the blue-light receptor StCRY. It is worth noting that some discrepancies were observed between the transcriptome heatmap (Figure 10) and the RT-qPCR results (Figure 11), such as StCRY1 and StCRY6 under cold stress. This may be due to the higher sensitivity and broader dynamic range of RNA-seq compared with RT-qPCR, and the differences in sampling time points may also contribute to the observed expression variations. Nevertheless, the overall expression trends are consistent, supporting the reliability of our findings. These results suggest that StCRY proteins may similarly integrate light cues with hormonal signaling (ABA/JA) and the COP1–HY5 module to orchestrate adaptive responses to environmental stresses in potato, consistent with mechanisms reported in Arabidopsis [24,25].
MiR166 is a highly conserved microRNA widely present in plants, capable of regulating the expression of HD-ZIP III family transcription factors to modulate plant growth, development, and stress responses [50,51]. In alfalfa (Medicago sativa), miR166 expression is downregulated after 6 h of drought stress but upregulated at 24 h [52]. During salt stress, reduced miR166 expression leads to increased PHB expression, thereby affecting root development [53]. MiR166 also plays a significant role in soybean responses to cold, drought, and salt stress [54]. Through miRNA target prediction, StCRY7, StCRY5, and StCRY6 were identified as potential interaction partners of miR166, suggesting their involvement in stress response regulation.
Protein–protein interaction predictions identified StCRY3 as a central hub gene, potentially interacting with multiple other StCRY proteins. Analysis of its promoter region revealed that StCRY3 contains 90 TATA-box elements, the highest number among the StCRY genes, suggesting a potentially strong transcriptional efficiency. Additionally, the promoter sequence of StCRY3 harbors multiple cis-elements responsive to abiotic stress, including three G-Box elements, one W-box, one ERE, four ABREs, five MYC, and three MYB elements, among others. Consistently, its expression was significantly upregulated under both cold and salt stress conditions. These findings highlight the potential of StCRY genes not only in stress adaptation but also as candidate genes for breeding programs aimed at improving potato resilience and productivity. Future studies could focus on functional validation and the incorporation of specific StCRY genes into breeding strategies to enhance stress tolerance.

5. Conclusions

Potato, as a multifunctional crop, is rich in starch as well as various vitamins and minerals. Its advantages include efficient water use and relatively low environmental dependence, making it suitable for cultivation in resource-limited areas. In this study, 7 StCRY genes were identified from the potato genome, unevenly distributed across four chromosomes and exhibiting conserved structures during evolution. Their promoter sequences contain a variety of cis-regulatory elements related to light, growth and development, hormones, and stress responses. GO enrichment analysis indicated that StCRY genes respond to blue light. Gene expression profiling revealed that StCRY3 and StCRY7 showed significant upregulation at 12 h and 24 h under cold and salt stress, while StCRY1 exhibited a notable increase under drought stress, suggesting that abiotic stresses can influence plant blue-light receptors and thereby affect growth and development. These findings provide a theoretical foundation for further studies on the roles of StCRY genes in potato growth, development, and responses to abiotic stress.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/genes16101234/s1. Table S1: Physicochemical characteristics of StCRY; Table S2: Ka/Ks analysis of StCRY; Table S3: Primers of StCRY.

Author Contributions

K.L. and Y.G. (Yuliang Gao) designed the research strategy and conceived and supervised the project; Y.G. (Yan Gao) wrote the manuscript; Y.G. (Yan Gao), X.Y., X.L. and Y.L. analyzed the data. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by The National Natural Science Foundation of China (No. 32160702) and Jilin Province Science and Technology Development Plan (No. 20210202114NC).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The original contributions presented in this study are included in the article/Supplementary Materials. Further inquiries can be directed to the corresponding authors.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Chromosomal distribution of StCRY gene family members in potato. Blue vertical bars represent potato chromosomes, with the scale on the left indicating chromosome length (Mb).
Figure 1. Chromosomal distribution of StCRY gene family members in potato. Blue vertical bars represent potato chromosomes, with the scale on the left indicating chromosome length (Mb).
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Figure 2. Phylogenetic tree of CRY gene family members from potato (Solanum tuberosum, St), tomato (Solanum. lycopersicum, Sl), A. thaliana (At), and rice (O. sativa, Os). Red circles indicate potato, blue triangles indicate tomato, blue stars indicate Arabidopsis, and pink squares indicate rice. Bootstrap values are shown at each node.
Figure 2. Phylogenetic tree of CRY gene family members from potato (Solanum tuberosum, St), tomato (Solanum. lycopersicum, Sl), A. thaliana (At), and rice (O. sativa, Os). Red circles indicate potato, blue triangles indicate tomato, blue stars indicate Arabidopsis, and pink squares indicate rice. Bootstrap values are shown at each node.
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Figure 3. Conserved motifs and gene structures of StCRY family members. The left panel shows the distribution of conserved motifs in StCRY proteins, with different colored boxes representing distinct motifs (Motif 1–15). The right panel illustrates the exon–intron structures of StCRY genes, where pink boxes indicate coding sequences (CDS), blue boxes represent untranslated regions (UTRs), and black lines denote introns.
Figure 3. Conserved motifs and gene structures of StCRY family members. The left panel shows the distribution of conserved motifs in StCRY proteins, with different colored boxes representing distinct motifs (Motif 1–15). The right panel illustrates the exon–intron structures of StCRY genes, where pink boxes indicate coding sequences (CDS), blue boxes represent untranslated regions (UTRs), and black lines denote introns.
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Figure 4. Cis-acting elements in StCRY promoters. The number of each element is indicated within the corresponding grid, and the background color of the grids represents the abundance of the elements. The red labels denote the four different categories of promoter cis-acting elements.
Figure 4. Cis-acting elements in StCRY promoters. The number of each element is indicated within the corresponding grid, and the background color of the grids represents the abundance of the elements. The red labels denote the four different categories of promoter cis-acting elements.
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Figure 5. Collinearity among StCRY homologous genes. Gray lines in the background represent the collinearity of genes across the whole genome, while red lines connect StCRY gene pairs with collinear relationships. The outer red rectangles indicate the gene density across the genome.
Figure 5. Collinearity among StCRY homologous genes. Gray lines in the background represent the collinearity of genes across the whole genome, while red lines connect StCRY gene pairs with collinear relationships. The outer red rectangles indicate the gene density across the genome.
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Figure 6. Comparative collinearity of StCRY genes across multiple plant species. Gray lines in the background connect collinear genes across the genomes of different species. Blue lines indicate collinear StCRY gene pairs between potato and tomato, green lines indicate collinear pairs between potato and rice, and red lines indicate collinear pairs between potato and Arabidopsis.
Figure 6. Comparative collinearity of StCRY genes across multiple plant species. Gray lines in the background connect collinear genes across the genomes of different species. Blue lines indicate collinear StCRY gene pairs between potato and tomato, green lines indicate collinear pairs between potato and rice, and red lines indicate collinear pairs between potato and Arabidopsis.
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Figure 7. GO enrichment of StCRY genes. The horizontal axis shows the proportion of genes associated with each GO term. Circle size represents the number of genes, and color indicates the −log10 (p-value).
Figure 7. GO enrichment of StCRY genes. The horizontal axis shows the proportion of genes associated with each GO term. Circle size represents the number of genes, and color indicates the −log10 (p-value).
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Figure 8. Potential regulation of StCRY genes by miRNAs. Purple circles represent StCRY genes, and blue triangles represent miRNAs. Black dashed lines connect miRNAs and StCRY genes showing regulatory correlations.
Figure 8. Potential regulation of StCRY genes by miRNAs. Purple circles represent StCRY genes, and blue triangles represent miRNAs. Black dashed lines connect miRNAs and StCRY genes showing regulatory correlations.
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Figure 9. Interaction network of StCRY proteins. Purple circles represent gene popularity, with circle size indicating the level of popularity. Lines connect genes showing correlations, and gradient colors indicate the strength of these correlations.
Figure 9. Interaction network of StCRY proteins. Purple circles represent gene popularity, with circle size indicating the level of popularity. Lines connect genes showing correlations, and gradient colors indicate the strength of these correlations.
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Figure 10. Heatmap of StCRY genes expression in potato under abiotic stresses. (A) Cold stress (CK: control; Cold: cold treatment). (B) Drought stress (CK: control; Drought: drought treatment). (C) Salt stress (CK: control; 3 h, 6 h, 12 h, and 24 h represent different time points of salt treatment). _1, _2, and _3 indicate three biological replicates.
Figure 10. Heatmap of StCRY genes expression in potato under abiotic stresses. (A) Cold stress (CK: control; Cold: cold treatment). (B) Drought stress (CK: control; Drought: drought treatment). (C) Salt stress (CK: control; 3 h, 6 h, 12 h, and 24 h represent different time points of salt treatment). _1, _2, and _3 indicate three biological replicates.
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Figure 11. RT-qPCR validation of StCRY gene expression under abiotic stresses in potato. Purple bars represent cold stress, blue bars represent drought stress, and red bars represent salt stress, with samples collected at 0 h, 1 h, 3 h, 6 h, 12 h, and 24 h. Different lowercase letters indicate significant differences (p < 0.05).
Figure 11. RT-qPCR validation of StCRY gene expression under abiotic stresses in potato. Purple bars represent cold stress, blue bars represent drought stress, and red bars represent salt stress, with samples collected at 0 h, 1 h, 3 h, 6 h, 12 h, and 24 h. Different lowercase letters indicate significant differences (p < 0.05).
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Gao, Y.; Yang, X.; Lv, X.; Li, Y.; Li, K.; Gao, Y. Genome-Wide Identification of the CRY Gene Family in Solanum tuberosum and Response to Abiotic Stresses. Genes 2025, 16, 1234. https://doi.org/10.3390/genes16101234

AMA Style

Gao Y, Yang X, Lv X, Li Y, Li K, Gao Y. Genome-Wide Identification of the CRY Gene Family in Solanum tuberosum and Response to Abiotic Stresses. Genes. 2025; 16(10):1234. https://doi.org/10.3390/genes16101234

Chicago/Turabian Style

Gao, Yan, Xueying Yang, Xin Lv, Yuxuan Li, Kuihua Li, and Yuliang Gao. 2025. "Genome-Wide Identification of the CRY Gene Family in Solanum tuberosum and Response to Abiotic Stresses" Genes 16, no. 10: 1234. https://doi.org/10.3390/genes16101234

APA Style

Gao, Y., Yang, X., Lv, X., Li, Y., Li, K., & Gao, Y. (2025). Genome-Wide Identification of the CRY Gene Family in Solanum tuberosum and Response to Abiotic Stresses. Genes, 16(10), 1234. https://doi.org/10.3390/genes16101234

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