Search Results (230)

The root-knot nematode (Meloidogyne incognita) poses a major threat to global agriculture by impairing root function, reducing nutrient uptake, and ultimately limiting seed development and crop productivity. This study investigated the molecular and metabolic defense responses of Cucumis metuliferus (prickly pear) to M. incognita infection. Gene expression and metabolic pathway reprogramming in M. incognita-infected roots were examined using integrated transcriptomics and metabolomics approaches. The identified genes were involved in stress responses and defense activation. Furthermore, metabolite profiling revealed significant shifts in secondary metabolite production, with an upregulation of defense-related compounds like jasmonic acid, salicylic acid, and prostaglandins. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis highlighted critical pathways such as biotin metabolism and nucleotide metabolism, underscoring the adaptive metabolic responses of C. metuliferus plants. GO (Gene Ontology) analysis from the integrated transcriptomics and metabolomics data highlighted significant upregulation of enzymatic pathways, transporter activities, and reorganization of cellular structures. Furthermore, KEGG pathway analysis revealed activation of secondary metabolite biosynthesis, immune-related signaling pathways, and metabolic reprogramming including increased carbon metabolism and nucleotide biosynthesis. This study provides a valuable molecular framework for breeding of M. incognita-resistant cultivars, ultimately supporting more stable seed distribution and agricultural productivity in M. incognita-prone regions. Full article

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. Full article

Fruit shape is an important quality and yield trait of pear, and the fruit shape of ‘Laiyang Cili’ presents a spindle shape which seriously affects its commercial value. Calyx excision treatment could change the fruit shape, while the underlying genes and their regulatory mechanism remain poorly understood. In this study, we constructed RNA-seq libraries of pear treated with calyx excision to explore underlying regulatory mechanisms. At the early stage of the calyx excision treatment, the numbers of differentially expressed genes (DEGs) between each comparison group were relatively high and gradually decreased along with fruit development. The expression pattern of the DEGs ranked in the top 30 of the six groups had obvious divergence, and DEGs were mainly distributed in the “after calyx excision treatment (0 days)” (AC0d) and AC2d groups. The DEGs were mainly enriched in plant hormone signal transduction and plant defense response. We identified 17 candidate genes related to fruit shape and tested their expression patterns along with fruit development. Among them, nine candidate genes expression trends were consistent with fragments per kilobase of exon model per million mapped fragment (FPKM) values, including MYB62, outer envelope pore protein 62 (OEP62), auxin response factor 3 (ARF3), auxin-responsive protein 50 (SAUR50), protein phosphatase 2C 51 (PP2C 51), major allergen Pyr c 1 (PYRC1), aquaporin TIP1-3 (TIP1-3), transcription factor TGA4 (TGA4) and auxin-responsive protein 17 (IAA17). And then, weighted gene co-expression network analysis (WGCNA) analysis revealed that the OVATE family protein (OFP) and SUN domain-containing protein (SUN) were divided into the MEblue model, which had a positive correlation with calyx excision treatment, and the expression trend of LOC103960706 (OFP8) appeared cohesive with FPKM values. Pbr014104.1 and Pbr016952.1, which were the ortholog genes of LOC103960706, were further identified from the pear genome, and were found to be highly expressed in pear fruit through RT-PCR analysis. Taken together, the key stage determining the development of fruit shape was in the early stage after calyx excision treatment, and fruit shape regulation and development were co-regulated by multiple genes. Full article

Recurrent pregnancy loss (RPL) is defined as the occurrence of two or more pregnancy losses before 20 weeks of gestation. RPL is a common medical condition among reproductive-age women, with approximately 23 million cases reported annually worldwide. Up to 5% of pregnant women may experience two or more consecutive pregnancy losses. Previous studies have investigated risk factors for RPL, including maternal age, uterine pathology, genetic anomalies, infectious agents, endocrine disorders, thrombophilia, and immune dysfunction. However, RPL is a disease caused by a complex interaction of genetic factors, environmental factors (e.g., diet, lifestyle, and stress), epigenetic factors, and the immune system. In addition, due to the lack of research on genetics research related to RPL, the etiology remains unclear in up to 50% of cases. Platelets play a critical role in pregnancy maintenance. This study examined the associations of platelet receptor and ligand gene variants, including integrin subunit beta 3 (ITGB3) rs2317676 A > G, rs3809865 A > T; fibrinogen gamma chain (FGG) rs1049636 T > C, rs2066865 T > C; glycoprotein 1b subunit alpha (GP1BA) rs2243093 T > C, rs6065 C > T; platelet endothelial cell adhesion molecule 1 (PECAM1) rs2812 C > T; and platelet endothelial aggregation receptor 1 (PEAR1) rs822442 C > A, rs12137505 G > A, with RPL prevalence. In total, 389 RPL patients and 375 healthy controls (all Korean women) were enrolled. Genotyping of each single nucleotide polymorphism was performed using polymerase chain reaction–restriction fragment length polymorphism and the TaqMan genotyping assay. All samples were collected with approval from the Institutional Review Board at Bundang CHA Medical Center. The ITGB3 rs3809865 A > T genotype was strongly associated with RPL prevalence (pregnancy loss [PL] ≥ 2: adjusted odds ratio [AOR] = 2.505, 95% confidence interval [CI] = 1.262–4.969, p = 0.009; PL ≥ 3: AOR = 3.255, 95% CI = 1.551–6.830, p = 0.002; PL ≥ 4: AOR = 3.613, 95% CI = 1.403–9.307, p = 0.008). The FGG rs1049636 T > C polymorphism was associated with a decreased risk in women who had three or more pregnancy losses (PL ≥ 3: AOR = 0.673, 95% CI = 0.460–0.987, p = 0.043; PL ≥ 4: AOR = 0.556, 95% CI = 0.310–0.997, p = 0.049). These findings indicate significant associations of the ITGB3 rs3809865 A > T and FGG rs1049636 T > C polymorphisms with RPL, suggesting that platelet function influences RPL in Korean women. Full article

Potassium fertilizer management is critical for achieving high yields of Korla fragrant pear, yet current practices often overlook or misuse potassium inputs. In this study, a two-year field experiment (2023–2024) was conducted with 7- to 8-year-old pear trees using four potassium levels (0, 75, 150, and 225 kg/hm²). Metagenomic sequencing was employed to assess the effects on soil microbial communities, sulfur cycle functional genes, and fruit yield. Potassium treatments significantly altered soil physicochemical properties, the abundance of sulfur cycle functional genes, and fruit yield (p < 0.05). Increasing application rates significantly elevated soil-available potassium and organic matter while reducing pH (p < 0.05). Although alpha diversity was unaffected, NMDS analysis revealed differences in microbial community composition under different treatments. Functional gene analysis showed a significant decreasing trend in betB abundance, a peak in hpsO under K150, and variable patterns for soxX and metX across treatments (p < 0.05). All potassium applications significantly increased yield relative to CK, with K150 achieving the highest yield (p < 0.05). PLS-PM analysis indicated significant positive associations between potassium rate, nutrient availability, microbial abundance, sulfur cycling, and yield, and a significant negative association with pH (p < 0.05). These results provide a foundation for optimizing potassium fertilizer strategies in Korla fragrant pear orchards. It is recommended that future studies combine metagenomic and metatranscriptomic approaches to further elucidate the mechanisms linking potassium-driven microbial functional changes to improvements in fruit quality. Full article

Pear (Pyrus pyrifolia) is an important deciduous fruit tree that requires a specific period of low-temperature accumulation to trigger spring flowering. The warmer winter caused by global warming has led to insufficient winter chilling, disrupting floral initiation and significantly reducing pear yields in Southern China. In this study, we integrated targeted phytohormone metabolomics, full-length transcriptomics, and proteomics to explore the regulatory mechanisms of dormancy in ‘Mixue’, a pear cultivar with an extremely low chilling requirement. Comparative analyses across the multi-omics datasets revealed 30 differentially abundant phytohormone metabolites (DPMs), 2597 differentially expressed proteins (DEPs), and 7722 differentially expressed genes (DEGs). Integrated proteomic and transcriptomic expression clustering analysis identified five members of the dormancy-associated MADS-box (DAM) gene family among dormancy-specific differentially expressed proteins (DEPs) and differentially expressed genes (DEGs). Phytohormone correlation analysis and cis-regulatory element analysis suggest that DAM genes may mediate dormancy progression by responding to abscisic acid (ABA), gibberellin (GA), and salicylic acid (SA). A dormancy-associated transcriptional regulatory network centered on DAM genes and phytohormone signaling revealed 35 transcription factors (TFs): 19 TFs appear to directly regulate the expression of DAM genes, 18 TFs are transcriptionally regulated by DAM genes, and two TFs exhibit bidirectional regulatory interactions with DAM. Within this regulatory network, we identified a novel pathway involving REVEILLE 6 (RVE6), DAM, and CONSTANS-LIKE 8 (COL8), which might play a critical role in regulating bud dormancy in the ‘Mixue’ low-chilling pear cultivar. Furthermore, lncRNAs ONT.19912.1 and ONT.20662.7 exhibit potential cis-regulatory interactions with DAM1/2/3. This study expands the DAM-mediated transcriptional regulatory network associated with bud dormancy, providing new insights into its molecular regulatory mechanisms in pear and establishing a theoretical framework for future investigations into bud dormancy control. Full article

Pear buds exhibit inherent dormancy, during which carbohydrates play a pivotal role in dormancy release and germination. In this study, Pyrus pyrifolia ‘Cuiguan’ was employed as the experimental material to investigate the molecular mechanisms underlying flower bud dormancy release. The results revealed that the dynamic balance between starch and soluble sugar is critical for promoting dormancy release and germination in P. pyrifolia ‘Cuiguan’ flower buds. Through transcriptomic and proteomic profiling, a total of 4035 differentially expressed genes (DEGs) and 1596 differentially expressed proteins (DEPs) were identified, which were predominantly associated with carbohydrate metabolism, particularly sugar metabolism pathways. Their changes were coordinately regulated at both transcriptional and translational levels. Key structural genes involved in maltose and sucrose biosynthesis, including BAM (LOC103949270), AAM (LOC125479337, LOC103940334, and LOC103941903), SPS (LOC125475683), and INV (LOC125478747), were significantly upregulated during the germination stage, facilitating flower bud sprouting. Integrated multi-omic analysis demonstrated that starch–sugar interconversion may govern dormancy release and sustained bud growth by modulating sugar metabolism-related genes and proteins. These findings provide novel insights into the molecular mechanisms of carbohydrate biosynthesis and associated protein regulation during dormancy release and development of P. pyrifolia ‘Cuiguan’ under natural conditions. Full article

Phytopythium vexans is a plant pathogen responsible for a variety of destructive diseases in crops worldwide. This includes patch canker, damping-off, root, and crown rots in economically important crops, such as apple, pear, grapevine, citrus, avocado, and kiwi. The pathogen has a global distribution, and a recent report confirmed its presence in southern Ontario, Canada. This study presents the first genome sequencing, assembly, and annotation of the Canadian P. vexans strain SS21. To explore how variation in secreted protein repertoires may relate to infection strategies and host adaptation, we compared the predicted secretome of SS21 with reference strains from Iran (CBS 119.80) and China (HF1). The analysis revealed that HF1 harbors a larger set of CAZymes, sterol-binding proteins, and predicted effectors, which may suggest broader adaptive potential. In contrast, strain SS21 appears to have adapted to a niche-specific strategy, with fewer necrosis-inducing proteins, glucanase inhibitors, and effectors, possibly indicating adaptation to specific hosts or ecological conditions. Comparative genome data highlight distinct evolutionary trajectories that may have shaped each strain’s infection strategy, with SS21 potentially serving as a robust additional reference for future studies on P. vexans biology and host interactions. While this analysis identifies key candidate effectors, gene expression studies are required to validate their functional roles in infection and host manipulation. Full article

This study investigated the impact of slow cooling on browning and fruit quality at three maturity stages (early, mid and late). Slow cooling reduced core browning in early/mid-harvest pears, as the browning indexes of early-, middle- and late-harvested ‘Yali’ pears at 60 d were 0.13, 0 and 0.1, respectively, preserving firmness and soluble solids. Transcriptomic analysis revealed that upregulated genes in ‘Yali’ pears facilitated stress adaptation via enhanced catalytic activity and phosphorylation. Mid-harvested pears exhibited activation of phosphorus metabolism and DNA repair mechanisms to maintain cellular homeostasis, whereas the late-harvested counterparts showed significant suppression of photosynthesis-related pathways and pyrimidine metabolism, which collectively accelerated senescence progression. Universal downregulation of hormone-response pathways such as ethylene and auxin revealed systemic stress adaptation decline. Then, the PbRAV transcription factors’ role was also studied. EMSA confirmed that GST-PbRAV2 binds to the PbLAC15 promoter, linking RAV2 to laccase regulation. Overripe pears showed PbRAV2 dysregulation, impairing LAC15 suppression and accelerating browning. Findings provide a theoretical basis for using slow cooling to mitigate browning in pear storage. Full article

Pear (Pyrus communis L.) is a widely cultivated fruit tree species, valued for its significant economic impact and cultural relevance. The rise in commercial cultivars, characterized by genetic uniformity and high yield, is increasingly displacing traditional landraces. However, traditional varieties are highly adapted to local environmental conditions, having resulted from centuries of selection. In this study, 51 pear (Pyrus communis L.) accessions conserved in the Greek national germplasm collection were genotyped using eight SSR markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). A total of 44 alleles were detected, including several private alleles, indicative of localized adaptation or potential genetic isolation. Analyses of population structure and genetic diversity, using Principal Coordinate Analysis (PCoA), UPGMA clustering, and Bayesian inference via STRUCTURE, uncovered distinct genetic groupings within the collection. The results revealed moderate genetic variability among the 51 accessions and identified some accessions with significant genetic divergence. These findings underscore the importance of conserving Greek pear germplasm, as it represents an ideal source of desirable traits, such as stress tolerance and fruit quality, which can be utilized in breeding programs. Full article

Pyrus bretschneideri ‘Xinli No.7’, a progeny of Pyrus sinkiangensis ‘Korla Fragrant Pear’, is an early-maturing, high-quality pear (Pyrus spp.) cultivar. As a dominant variety in China’s pear-producing regions, it holds significant agricultural importance. Investigating its male sterility (MS) mechanisms is critical for hybrid breeding and large-scale cultivation. Integrated cytological, physiological, and transcriptomic analyses were conducted to compare dynamic differences between male sterility (MS, ‘Xinli No.7’) and male-fertile (MF, ‘Korla Fragrant Pear’) plants during anther development. Cytological observations revealed that, compared with ‘Korla Fragrant Pear’, the tapetum of ‘Xinli No.7’ exhibited delayed degradation and abnormal thickening during the uninucleate microspore stage. This pathological alteration compressed the microspores, ultimately leading to their abortion. Physiological assays demonstrated excessive reactive oxygen species (ROS) accumulation, lower proline content, higher malondialdehyde (MDA) levels, and reduced activities of antioxidant enzymes (peroxidase and catalase) in MS plants. Comparative transcriptomics identified 283 co-expressed differentially expressed genes (DEGs). Functional enrichment linked these DEGs to ROS-scavenging pathways: galactose metabolism, ascorbate and aldarate metabolism, arginine and proline metabolism, fatty acid degradation, pyruvate metabolism, and flavonoid biosynthesis. qRT-PCR validated the expression patterns of key DEGs in these pathways. A core transcriptome-mediated MS network was proposed, implicating accelerated ROS generation and dysregulated tapetal programmed cell death. These findings provide theoretical insights into the molecular mechanisms of male sterility in ‘Xinli No.7’, supporting future genetic and breeding applications. Full article

Cysteine-rich polycomb-like protein (CPP) transcription factors play critical roles in plant growth, development, and responses to stresses and hormone signaling. However, the research on the CPP gene family remains unexplored in apple. In this study, a total of 10 CPP genes (MdCPP1–MdCPP10) were identified and unevenly distributed across seven scaffolds. Phylogenetic and conserved motif analyses revealed that these 10 CXC domain-containing MdCPPs could be classified into three subfamilies. Evolutionary tree and synteny analyses demonstrated that apple shared the highest number of orthologous gene pairs with white pear compared to Arabidopsis. By analyzing the MdCPP gene promoter, a large number of cis-acting elements related to hormone and stress response were discovered. In addition, transcriptomic data demonstrated tissue-specific expression patterns of MdCPP genes, with MdCPP5 and MdCPP8 showing the highest expression in buds and leaves. The qRT-PCR results indicated that MdCPP genes have different expression responses to SA, GA, JA, and IAA treatments. Notably, MdCPP4, MdCPP6, MdCPP8, and MdCPP9 were significantly upregulated under different hormone treatments. Among them, the upregulation of MdCPP6 was the most significant. These findings establish a foundation for further functional characterization of MdCPPs and provide theoretical support for their potential applications in apple genetic improvement and agricultural production. Full article

Fire blight, caused by Erwinia amylovora, is a devastating bacterial disease threatening apple, pear, and other Rosaceae species. In our prior study, transcriptome analysis identified a fire blight-resistant variety, Duli (Pyrus betulifolia Bunge), and highlighted the PR1 gene as a key resistance factor. Using Duli’s genomic data, we systematically identified and characterized the Pb-PR-1 gene family through bioinformatics analysis. A total of 31 Pb-PR-1 genes were found, encoding proteins of 123–341 amino acids. Phylogenetic analysis grouped these genes into four subfamilies, with 27 genes distributed across seven chromosomes, all contain a conserved CAP superfamily domain. Their promoter regions were enriched in hormone and stress-responsive elements. After inoculation with E. amylovora, susceptible Duli showed lesion development by day 2, with rapid disease progression, while resistant plants exhibited slower disease advancement and smaller lesions. Enzyme activity assays revealed that in resistant plants, PPO (polyphenol oxidase) and CAT (catalase) activities peaked on day 6, showing a 2.4-fold and 3.81-fold increase compared to susceptible Duli. At the same time, MDA (malondialdehyde) content decreased by 16.6%. The activities of SOD (superoxide dismutase) and PAL (phenylalanine ammonia-lyase) peaked on day 4, with increments of 34.32% and 47.1% over susceptible Duli. qRT-PCR showed significant differences in Pb-PR-1 gene family expression between resistant and susceptible plants post-inoculation. Notably, Pb-PR-1-11, Pb-PR-1-21, and Pb-PR-1-26 expression increased with infection duration, aligning with PPO and CAT activity trends. Other genes showed high early infection expression but declined by day 6. Pb-PR-1-3, Pb-PR-1-6, Pb-PR-1-8, Pb-PR-1-16, and Pb-PR-1-30 were upregulated 13.17-fold on average by day 2. In summary, the Pb-PR-1 family exhibited elevated expression during early infection and enhanced defense-related enzyme activities, improving plant resistance. This study provides a foundation for understanding the PR-1 family’s role in Duli and advancing fire blight resistance in Pyrus species. Full article

Fire blight, a devastating bacterial disease caused by Erwinia amylovora, has posed significant challenges to apple and pear production for over a century. This study introduces a gliding filamentous bacterium, the strain NSD29, isolated from natural forest soil in Xinjiang, China, as a biological control agent for managing this disease. Comprehensive characterization based on morphological, physiological, biochemical, 16S rRNA gene, and whole-genome analyses identified the strain NSD29 as Herpetosiphon llansteffanensis. The train NSD29 demonstrated potent predatory activity against E. amylovora in vitro. Its biocontrol efficacy was subsequently evaluated on detached leaves, inflorescences, young fruit, and shoots of fragrant pear under controlled greenhouse conditions. Results indicated that applying H. llansteffanensis NSD29 significantly inhibited lesion expansion on pear leaves and young fruit, achieving protective efficacies of 75.2% and 72.0%, respectively. Furthermore, pre-treatment spraying with NSD29 effectively reduced the incidence of blossom blight, with a control efficacy of 61.2%. On detached pear shoots, the application of NSD29 fermentation broth suppressed lesion expansion, demonstrating substantial protective (86.8%) and curative (75.6%) efficacies. This research provides the first evidence for the potential of Herpetosiphon species in the biological control of plant diseases, highlighting H. llansteffanensis NSD29 as a promising candidate for developing strategies to combat fire blight. Full article

Pear psylla (Cacopsylla chinensis), a major pear tree pest widely distributed in China, is increasingly affecting the productivity of orchards. This species exhibits seasonal polyphenism with two distinct forms, namely, a summer form and a winter form. Through topically applying Beauveria bassiana conidial suspensions to the abdominal cuticle of C. chinensis, we demonstrated that the entomopathogenic fungus B. bassiana exhibits significant yet phenotypically divergent virulence against these two forms. Using PacBio SMRT sequencing and Illumina RNA-seq, we analyzed transcriptomic changes post-infection, revealing form-specific immune responses, with 18,232 and 5027 differentially expressed genes identified in summer- and winter-form pear psylla, respectively, and a total of 3715 DEGs shared between the two seasonal phenotypes. In summer-form individuals, B. bassiana infection disrupted oxidative phosphorylation and downregulated immune recognition genes, cellular immune-related genes, and signaling genes, along with the upregulation of the immune inhibitor serpin, indicating immunosuppression. Conversely, in winter-form individuals, immune-related genes and glycolytic rate-limiting enzymes were upregulated after infection, suggesting that the winter-form immune system normally responds to B. bassiana infection and supports efficient defense through metabolic reprogramming to fuel energy-demanding defenses. These findings advance our understanding of C. chinensis/B. bassiana interactions, providing a basis for elucidating immune regulation in seasonally polymorphic insects. The results also inform strategies to optimize B. bassiana-based biocontrol, contributing to sustainable pear psylla management. Full article