The dirigent (DIR) gene is a key player in environmental stress response and has been identified in many multidimensional tube plant species. However, there are few studies on the StDIR gene in potato. In this study, we used genome-wide identification to identify 31 StDIR genes in potato. Among the 12 potato chromosomes, the StDIR gene was distributed on 11 chromosomes, among which the third chromosome did not have a family member, while the tenth chromosome had the most members with 11 members. 22 of the 31 StDIRs had a classical DIR gene structure, with one exon and no intron. The conserved DIR domain accounts for most of the proteins in the 27 StDIRs. The structure of the StDIR gene was analyzed and ten different motifs were detected. The StDIR gene was divided into three groups according to its phylogenetic relationship, and 22 duplicate genes were identified. In addition, four kinds of cis-acting elements were detected in all 31 StDIR promoter regions, most of which were associated with biotic and abiotic stress. The findings demonstrated that the StDIR gene exhibited specific responses to cold stress, salt stress, ABA, and drought stress. This study provides new candidate genes for improving potato’s resistance to stress.

Cucumber wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), is a major threat to cucumber production, especially in greenhouses. This study used a fermentation product derived from a new strain of Streptomyces rochei (G-6) to investigate the potential for biocontrol of cucumber wilt disease and the effect on promoting cucumber growth. In the first experiment, the inhibitory effect of S. rochei G-6 fermentation product (SGFP) on FOC growth was evaluated, then the effect of SGFP on wilt incidence and severity, as well as cucumber growth, antioxidant system, and soil nutrient conversion capacity were investigated. The results showed that SGFP inhibited FOC growth by 85.3% in the antimicrobial experiment. In the potting experiment, the incidence rate in the FOC group reached 88.7%, but it was only 56.0% in the SGFP1 group and 64.7% in the SGFP2 group, indicating the efficient inhibitory effect of SGFP on cucumber wilt, with the biocontrol effect of SGFP1 being higher than that of SGFP2. In addition, the disease index decreased significantly (p < 0.05) in both SGFP treatments, which was significantly (p < 0.05) lower in the SGFP1 group than in the SGFP2 group, indicating that pre-treatment was better than post-treatment in reducing the disease severity. In addition, SGFP promoted the growth of cucumber seedlings, as indicated by indicators related to the growth of aboveground and underground parts. Furthermore, the activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) in the cucumber seedlings increased after SGFP treatment and the malondialdehyde level was decreased, indicating a reduction in oxidative stress. SGFP also improved the soil nutrient conversion capacity by increasing the activities of urease, phosphatase, and sucrase, which may enhance nutrient uptake by cucumber seedling. The findings of this study suggest that SGFP is an effective biocontrol agent against cucumber wilt and also promotes cucumber growth by regulating the antioxidant system and soil environment, and its application is a promising solution to reduce wilt incidence in cucumber production.

Anthocyanins, flavonoid pigments, are responsible for the purple and red hues in potato tubers. This study analyzed tubers from four potato cultivars—red RR, purple HJG, yellow QS9, and white JZS8—to elucidate the genetic mechanisms underlying tuber pigmentation. Our transcriptomic analysis identified over 2400 differentially expressed genes between these varieties. Notably, genes within the flavonoid biosynthesis pathway were enriched in HJG and RR compared to the non-pigmented JZS8, correlating with their higher levels of anthocyanin precursors and related substances. Hierarchical clustering revealed inverse expression patterns for the key genes involved in anthocyanin metabolism between pigmented and non-pigmented varieties. Among these, several MYB transcription factors displayed strong co-expression with anthocyanin biosynthetic genes, suggesting a regulatory role. Specifically, the expression of 16 MYB genes was validated using qRT-PCR to be markedly higher in pigmented HJG and RR versus JZS8, suggesting that these MYB genes might be involved in tuber pigmentation. This study comprehensively analyzed the transcriptome of diverse potato cultivars, highlighting specific genes and metabolic pathways involved in tuber pigmentation. These findings provide potential molecular targets for breeding programs focused on enhancing tuber color.

A comprehensive genome-wide identification of SET-domain-containing genes in Solanum lycopersicum (tomato) has revealed 46 members. Phylogenetic analysis showed that these SET genes, along with those from Arabidopsis thaliana and Oryza sativa, are divided into five subfamilies, with Subfamilies II and V being the largest. Motif and domain analyses identified 15 conserved motifs and revealed the presence of pre-SET and post-SET domains in several genes, suggesting functional diversification. Gene structure analysis further demonstrated variation in exon–intron organization, likely contributing to differential gene regulation. Promoter analysis identified cis-acting elements related to light responsiveness, plant growth, hormones, and stress, implicating SET genes in various biological processes. RNA-seq and qRT-PCR data revealed distinct expression patterns of SlSET genes under salt stress, with several genes showing significant upregulation, indicating their potential role in stress tolerance. In particular, SlSET6 silencing using VIGS reduced tomato’s tolerance to salt stress, leading to higher lipid peroxidation, reduced antioxidant enzyme activity, and decreased proline content, further confirming its critical role in salt stress response. These findings provide valuable insights into the functional diversity, evolutionary history, and stress-related roles of SET domain genes in tomato, with potential applications for crop improvement strategies.

Sulfur is an intermediate element in plants. It plays an important role in the growth and development of plants. Plant roots absorb sulfate from their external environment and produce cysteine under the catalysis of cysteine synthase. Cysteine is a synthetic precursor of sulfur-containing metabolites and critical molecules including glutathione (GSH), methionine, vitamins, coenzymes, and antioxidants. It also plays a central role in plant stress resistance. In this study, we identified the Cys family genes in tomato and analyzed the expression of SlCys genes under cold stress. A bioinformatics analysis showed that the SlCys gene promoters were rich in cis-acting elements related to stress response. Transcriptome data analysis and qRT-PCR (real-time fluorescent quantitative polymerase chain reaction) experiments showed that SlCys5 may be the key gene in the Cys gene family for cold tolerance in tomato. After cold stress treatment, the SlCys5-silenced tomato plants were more sensitive to cold stress, and wilting was more severe than in control plants. Thus, SlCys5 is a positive regulator of cold tolerance in tomato. In this study, we elucidated the evolutionary pattern and functional differentiation of the Cys gene family in tomato, deepening our understanding of the regulatory mechanism of cold stress tolerance in plants.

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.