Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plants, little is known about PEBP genes in pears. In this study, a total of 24 PEBP genes were identified, in which 10, 5 and 9 were from Pyrus bretschneideri genome, Pyrus communis genome and Pyrus betuleafolia genome, respectively. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, promoter regions, collinearity and expression were determined with these PEBP genes. It was found that only PbFT from PEBP genes of P. bretschneideri was relatively highly expressed in leaves during flower bud differentiation. Whereas, expression patterns of TFL1 homologues, gene23124 and gene16540, were different from PbFT in buds. The expression pattern and the treatment of reduction day-length indicated that the expression of PbFT in leaves were regulated by day-length and circadian clock. Additionally, the phenotype of transgenic Arabidopsis suggested that PbFT played a role in not only promoting flower bud differentiation, but also regulating the balance between vegetative and reproductive growth. These results may provide important information for further understanding of the evolution and function of PEBP genes in pears.

Light-harvesting chlorophyll a/b binding (Lhc) proteins play a key role in the efficiency of the photosynthetic system of plants and participate in the regulation of plant growth, development, and the response to abiotic stress. In this study, 28 PbrLhc genes of the family were identified in the pear Pyrus bretschneideri genome database, which were distributed on 25 of the 27 chromosomes. Phylogenetic relationship analysis demonstrated that PbrLhc proteins could be divided into five subfamilies. Using MEME Suite, PlantRegMap, and Softberry, the conserved motifs, transcription binding sites, and predicated location of all PbrLhc proteins, respectively, were determined. A collinearity relationship using MCScanX software showed that there was a collinearity relationship between different PbrLhc genes. Using the hierarchical clustering method to develop a heat map of gene expression, five genes were found to be down-regulated under irrigation treatment and up-regulated under drought treatment; seven genes were up-regulated under irrigation treatment and down-regulated under drought treatment. Finally, the results of these analyses will provide theoretical basis for future study on the function and differential expression of PbrLhc genes in response to drought stress.

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

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.

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.