Members of the glycogen synthase kinase 3 (GSK3) family in plants, as a class of serine/threonine protein kinases, have been demonstrated to play crucial roles in a wide range of biological processes and environmental stresses. However, the GSK3 gene family has not been analyzed in pears. In this study, 12 GSK3 gene family members were identified in the Pyrus bretschneideri genome. These genes were located on 10 chromosomes and phylogenetically classified into four subfamilies. All 12 PbGSK3 proteins possessed highly conserved domains. The results demonstrated the structural characteristics of all 12 PbGSK3s and the evolutionary processes of their putative proteins. The presence of several cis-acting elements in the promoter region of the PbGSK3s associated with hormonal and stress responses suggested that the PbGSK3s might be involved in the growth and development of pears and in stress response. The expression profiles of PbGSK3s under drought stress were also analyzed. When the pears were subjected to drought stress for different durations, the expression patterns of 12 PbGSK3s exhibited variations. The findings would provide a scientific foundation for further exploration of the potential functions of the GSK3 genes in pears.

Fatty acid desaturase (FAD) is a rate-limiting enzyme catalyzing the biosynthesis of unsaturated fatty acids (UFAs) and participates in key physiological processes such as plant growth and development, fruit ripening, and stress responses by regulating membrane lipid composition. Using pear genome data, this study systematically identified FAD gene family members through bioinformatic analysis and characterized their drought-responsive expression patterns. Results revealed that 34 FAD family members were identified in pear, unevenly distributed across 12 chromosomes and classified into six subfamilies. Members within the same subfamily exhibited similar conserved domains and gene structures. Promoter element analysis demonstrated that pear FAD promoters contain cis-acting elements associated with plant growth and development, hormone responses, and abiotic stress responses. qRT-PCR expression profiling showed that PbrFAD23 and PbrFAD30 were significantly upregulated during the early stages of drought stress, followed by suppressed expression levels, suggesting their potential crucial regulatory roles in the initial drought response. Genome-wide identification of 34 PbrFAD family members highlighted that PbrFAD23 and PbrFAD30, with marked upregulation under early drought stress, exhibit prominent drought responsiveness. This study provides valuable resistance gene resources for molecular breeding of stress-tolerant pear varieties and establishes a theoretical foundation for functional characterization of key drought-resistant candidate genes in pear.

Drought stress severely restricts the growth of pear trees. As a widely used drought-tolerant rootstock, Pyrus betulifolia exhibits stable growth performance; however, the molecular mechanisms underlying its drought tolerance remain to be elucidated. In this study, we investigated the molecular responses of P. betulifolia leaves to osmotic stress induced by 20% PEG-4000 using time-series RNA-seq technology. A total of 3745 differentially expressed genes were identified, with transcriptional changes peaking at 6 h, indicating a critical phase of transcriptional reprogramming during drought response. Genes associated with osmotic adjustment (e.g., P5CS) and oxidative stress responses (e.g., SOD and POD) were significantly upregulated between 6 and 12 h. Weighted gene co-expression network analysis (WGCNA) identified three distinct temporal modules and screened out NF-Y, RVE1, COL9, COL6, C2C2 zinc finger proteins, and Pseudo ARR-B as putative key regulators, whose expression patterns were validated using qRT-PCR. Collectively, these results provide a comprehensive view of the temporal transcriptional dynamics of drought response in P. betulifolia and offer valuable candidate gene resources for further functional studies and drought tolerance breeding.

Biogas residue is a valuable by product of organic waste recycling with potential to enhance soil quality. However, its long-term effects on root-zone soil microbial communities, leaf physiology, and fruit quality in perennial fruit crops such as pear remain poorly understood. In this study, a ‘Huangguan’ pear orchard managed with five consecutive years of biogas digestate application (Z) was compared against a treatment without digestate history (CK) in North China. Soil organic matter, bacterial (16S) and fungal (ITS) community profiles, fruit quality traits, and leaf physiological and anatomical parameters were comprehensively evaluated. Compared with CK, long-term biogas digestate application significantly increased soil organic matter content by 16.45% and 18.27% at soil depths of 20 cm and 40 cm, respectively. Principal coordinate analysis revealed pronounced structural divergence in both bacterial and fungal communities between orchards. At 20 cm depth, the bacterial Chao1 and Shannon diversity indices in Z were significantly higher by 15.23% and 3.98%, respectively, accompanied by a 479.59% surge in the relative abundance of Bacillus. In the 40 cm layer, fungal OTU richness increased by 45.34%. The application of biogas digestate promoted the enrichment of functional microbial taxa, including Solicoccozyma aeria, Sphingomonas, Chaetomiaceae, Lophotrichus, Bacillus, Streptomyces, and Acinetobacter pittii. Fruit soluble solids content in Z consistently exceeded CK by 22.36% in 2024 and 7.56% in 2025. Single fruit weight was 10.21% greater in 2024. Leaf water content increased by 23.08% in 2024 and 97.22% in 2025, alongside a 28.57% enhancement in the leaf effective quantum yield of the photosystem in 2025. Overall, long-term biogas digestate application reshapes the root-zone soil microbial community and augments soil fertility; meanwhile, fruit quality and leaf physiological function were improved in pears.

C2H2-type zinc finger transcription factors play crucial roles in regulating plant growth and responses to abiotic stresses. Although pear is an economically important fruit crop with available genomic resources, the comprehensive analyses of its C2H2 gene family remain limited. In this study, we performed a genome-wide identification of C2H2 genes in pear, identifying 52 members that were unevenly distributed across 17 chromosomes. The predicted PyC2H2 proteins ranged from 343 to 1764 amino acids in length, with molecular weights between 12.4 and 62.7 kDa. Phylogenetic analysis classified these 52 PyC2H2 proteins into 10 classical clades, where genes with closer evolutionary relationships shared more similar conserved motifs. Collinearity analysis identified 37 collinear gene pairs between Arabidopsis thaliana and pear, suggesting evolutionary conservation. Promoter analysis revealed the presence of various cis-acting elements associated with hormone and stress responses, including Box 4, G-box, and GT1-motif. Additionally, the expression patterns of PyC2H2 genes differed among pear organs. These results provide valuable insights into the potential roles of PyC2H2 genes in drought stress responses and offer a foundation for future molecular breeding of drought-tolerant pear cultivars.