Search Results (5,295)

Several gene-based tests, such as the sequence kernel association test, have been developed to assess associations between rare single nucleotide variants (SNVs) and disease traits. However, these aggregate methods do not distinguish potentially causal variants from null variants within associated regions. To address this limitation, we propose gvClust, a clustering approach that classifies rare variants into null and signal groups using a Gaussian mixture model applied to variant-level summary statistics from multiple-variant models. Signal variants are further partitioned into risk and protective subgroups according to their effect direction and magnitude. We evaluated gvClust in simulation studies using the adjusted Rand index (ARI), mean squared error (MSE), and accuracy of cluster number selection under different sample sizes, effect configurations, outcome types, and linkage disequilibrium (LD) structures. In simulations, gvClust showed improved performance with increasing sample size, achieved high accuracy in determining the number of clusters for continuous traits at large sample sizes, and outperformed both k-means clustering and initialization-only clustering. We then applied gvClust to rare variants in six genes associated with blood pressure traits from a large genome-wide association study and meta-analysis. In the real-data application, gvClust identified distinct null, risk, and protective clusters. These results suggest that gvClust provides a practical framework for classifying rare variants within associated regions and may help improve the biological interpretation of rare variant signals. Full article

Body measurement traits are a direct production indicator reflecting growth status and guiding genetic selection. Identifying molecular markers associated with body measurement traits could accelerate animal breeding programs. The Yanqi horse, an important indigenous breed in Xinjiang, is primarily distributed in the Bayingolin Mongol Autonomous Prefecture. However, molecular markers linked to body measurement traits in Yanqi horses remain uncharacterized. In the present study, whole-genome resequencing was performed on 183 Yanqi horses, yielding 13,366,672 single-nucleotide polymorphisms (SNPs) after quality control. A genome-wide association study on withers height, body length, heart girth, and cannon bone circumference was conducted using a mixed linear model implemented in GEMMA, with population structure and relatedness controlled using principal components and a genomic kinship matrix. Bonferroni-adjusted thresholds (p < 1 × 10⁻⁷ for significant associations; p < 1 × 10⁻⁶ for suggestive associations) were applied to minimize false positives. A total of 185 single-nucleotide polymorphisms were significantly associated with body measurement traits and 359 candidate genes were annotated within 200 kb upstream and downstream of the significant loci. Among these, five genes, GABRB1, FIGN, GABRA4, ENSECAG00000051747, and COX7B2, may be implicated in the growth and development of Yanqi horses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that these genes are primarily involved in cytoskeletal structures within muscle cells, regulation of the actin cytoskeleton, and neuroactive ligand–receptor interaction pathways. In summary, this study presents novel markers and candidate gene sets associated with body measurement traits in Yanqi horses, offering valuable insights for functional gene investigations and presenting substantial potential for accelerating the breeding of Yanqi horses. Full article

Background/Objectives: Serial passage in embryonated eggs is widely used to attenuate the infectious bronchitis virus (IBV) for vaccine production; however, the evolutionary processes underlying attenuation and immunogenicity remain incompletely understood. Here, we analyzed genome-wide viral evolution during serial passages to investigate how mutations emerge, persist, are lost, or become fixed over time and how these dynamics relate to changes in pathogenicity and immunogenicity. Methods: Deep sequencing was performed on 11 representative serial passages (P2–P79) of the UY/11/CA/18 strain, including two derivative lineages: P7 VIR (virulent) and P53 VAC (attenuated and immunogenic). Results: This study identified an early adaptive phase characterized by a limited set of mutations potentially associated with genome replication, viral RNA processing, and virion assembly, including a key change in non-structural protein 14 and variants in M and 3c (E). This phase was followed by a broader expansion of the variant spectrum across replicase genes and delayed accumulation of Spike protein variants. Most Spike changes emerged during later passages and exhibited transient dynamics, and only a subset reached a high frequency after the establishment of early replicase- and structural-associated changes. Consistent with these dynamics, P7 VIR diverged before the late accumulation of Spike variants and retained a pathogenic phenotype, whereas P53 VAC diverged after the emergence of early high-frequency variants but before the extensive late-stage Spike variation observed in P79, which was associated with reduced immunogenicity. Conclusions: These findings support a multi-step model of IBV attenuation in which progressive filtering of genome-wide variation shapes distinct evolutionary outcomes during serial passages. This evolutionary framework provides insight into the relationship between attenuation and immunogenicity and may help guide the rational design of live attenuated vaccines. Full article

For the first time, a regulatory network linking melanin, genes, pathways, and edible quality was constructed for 138 Auricularia cornea strains sourced domestically and internationally. This marks the inaugural study of A. cornea spanning from cellular to physical-mechanical properties. Correlation analysis between melanin and edible quality traits (hardness, springiness, cohesiveness, gumminess, chewiness, and resilience) revealed that hardness, cohesiveness, and gumminess increased with rising melanin content, while springiness correspondingly decreased. Genome-wide association analysis identified 15,597,589 SNP loci. A total of 39 genes related to food quality were annotated, including one melanin-related lacquer enzyme gene, ACW004924. Real-time quantitative PCR validation of key genes identified for melanin and edible quality traits revealed results consistent with those from correlation analysis. The lacquer enzyme genes ACW004736, ACW006232, which regulate melanin synthesis, and the tyrosinase genes ACW001451, ACW002443, and ACW001003 were also identified in edible quality traits. These genes perform similar functions in GO-enriched metabolic processes, catalytic activity, and cellular structural complexes, as well as in KEGG-enriched pathways such as carbon metabolism and polysaccharide synthesis. They catalyze melanin synthesis and promote interactions between melanin and cell wall polysaccharides, chitin, and structural proteins, thereby stabilizing the cellular scaffold structure, jointly mediating the effect of melanin on the edible quality of A. cornea. The results supplement the downstream regulatory chain of catalytic enzymes and edible quality in the γ-L-glutaminyl-3,4-dihydroxybenzene (GDHB) pigment synthesis pathway, and form an information network of melanin synthesis, cell wall structure optimization, and edible quality regulation. Full article

Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness driven by elevated intraocular pressure from compromised aqueous outflow. While genome-wide association studies have identified numerous risk loci, specific candidate proteins and their cellular mechanisms remain elusive. We employed a multi-omics framework integrating UK Biobank plasma proteomics (N = 53,022) and large-scale POAG GWAS summary statistics. We performed a Proteome-Wide Association Study, Mendelian Randomization, and Bayesian colocalization to infer causality. Identified candidates were mapped to human and mouse ocular scRNA-seq atlases to characterize cell-type specificity, followed by druggability assessments. We prioritized five putative causal proteins, with SEL1L and TFPI demonstrating the strongest evidence. Cross-species scRNA-seq revealed that SEL1L and SERPINF1 are robustly expressed in the trabecular meshwork (TM), particularly the juxtacanalicular tissue, implicating them in outflow resistance. Conversely, TFPI and SLC9A3R2 localize to Schlemm’s canal endothelium, suggesting a role in modulating barrier function. Pathway analyses highlighted endoplasmic reticulum protein processing and coagulation cascades. This study maps putative causal POAG proteins to conventional outflow pathway cells, highlighting SEL1L as a novel target for TM homeostasis and TFPI for drug repurposing, thereby providing data-driven hypotheses to facilitate precision glaucoma therapeutics. Full article

Phyllanthus emblica L. is a nutraceutically important medicinal plant; however, the relationship between genetic variation and bioactive potential remains poorly understood. This study integrates genome-wide SNP analysis, phytochemical profiling, and functional bioassays to investigate cross-scale differentiation among fourteen cultivars. Genotyping-by-sequencing (GBS) identified 5644 high-quality SNPs from an initial dataset of 9018 SNPs, revealing moderate but structured genomic divergence (0.0275–0.0845). Phytochemical analysis of five commercial cultivars demonstrated significant variation (p < 0.05) in total phenolic content (6.58–15.53 mg GAE/gDW) and tannin content (284.52–333.81 mg TAE/gDW). Functional assays revealed strong anti-obesity potential, with crude extracts exhibiting superior α-glucosidase inhibition (up to 98.75%), while tannin-enriched extracts showed enhanced pancreatic lipase inhibition (up to 46.26%). Importantly, enzyme inhibition did not correlate directly with total phenolic or tannin content, indicating compound-specific bioactivity. LC-MS/QTOF analysis identified flavonoids (e.g., quercetin and kaempferol), phenolic acids, and other candidate metabolites potentially associated with enzyme inhibitory activity. These findings demonstrate a non-proportional association among genomic variation, metabolite composition, and functional bioactivity, suggesting that bioactivity may be influenced more strongly by compound-specific metabolite composition than by genome-wide similarity alone. Full article

Background/Objectives: To investigate the causal relationships linking body mass index (BMI) and circulating insulin-like growth factor 1 (IGF-1) levels with diabetic maculopathy risk using two-sample Mendelian randomization (MR). Methods: A two-sample MR framework was applied, utilizing genetic instruments for BMI and IGF-1 derived from the UK Biobank. Summary-level diabetic maculopathy data were obtained from the FinnGen consortium. Genome-wide significant single-nucleotide polymorphisms (SNPs, p < 5.0 × 10⁻⁸) independently associated with each exposure were employed as instrumental variables. Primary causal estimates were obtained using the inverse-variance weighted (IVW) method. Sensitivity analyses, including MR-Egger regression, weighted median methods, and the MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO), were conducted to evaluate robustness and potential pleiotropy. Results: Genetically predicted BMI was positively associated with diabetic maculopathy risk in both the IVW analysis (odds ratio [OR] = 1.16 (95% confidence interval [CI]: 1.04–1.30), p = 0.008) and MR-PRESSO (OR = 1.16 (95% CI: 1.04–1.28), p = 0.006). MR-PRESSO exhibited a significant relationship between higher IGF-1 levels and increased diabetic maculopathy risk (OR = 1.09 (95% CI: 1.01–1.18), p = 0.025), whereas the IVW method indicated only a suggestive association (OR = 1.08 (95% CI: 0.99–1.18), p = 0.087). Conclusions: The genetic evidence supports a causal role of insulin resistance-related traits in diabetic maculopathy development, with higher BMI and IGF-1 levels increasing diabetic maculopathy risk. These results underscore the potential contributory role of IGF-1 in disease pathogenesis and suggest that insulin resistance-related traits may represent preventive therapeutic targets. Full article

In this study, we performed the first genome-wide identification and characterization of the cinnamoyl-CoA reductase (CCR) gene family in upland cotton (Gossypium hirsutum), focusing on its potential association with stem strength. We identified 76 GhCCR genes and classified them into four subfamilies. We then analyzed their evolutionary relationships, conserved domains, synteny, promoter cis-elements, and expression patterns. All GhCCR proteins possess the NADB_Rossmann superfamily domain, and family expansion appears to have been driven mainly by segmental and tandem duplications. A small number of GhCCR genes showed relatively high expression in leaf, pistil, and torus tissues, while genes such as GhCCR3/9/10 exhibited elevated transcript levels under abiotic stress conditions. RT-qPCR results indicated that three candidate GhCCR genes (GhCCR25, GhCCR52 and GhCCR64) were significantly more highly expressed in multiple tissues of the stiff-stem line JY-25 than in the soft-stem line JR-15. Together, these findings suggest that GhCCR genes may contribute to the regulation of growth, development, and stress adaptation in G. hirsutum. However, direct biochemical or genetic validation is required to confirm their functional roles in lignin biosynthesis and stem rigidity. Full article

Heat stress (HS) is among the most economically consequential environmental challenges to global dairy production, causing progressive declines in milk yield, compositional quality, and mammary cellular integrity. The temperature–humidity index (THI) is the primary thermal load metric, with performance-impairment thresholds typically beginning at THI 68 in Holstein cattle, with severe impacts manifesting beyond THI 72; breed-specific thresholds for Jersey, Brown Swiss, and Simmental cows differ owing to their lower metabolic heat load and greater inherent thermotolerance. At the molecular level, HS activates heat shock protein networks—notably HSPA1A, HSP90B1, and HSPH1—through HSF1/HSF4 transcriptional activation, while simultaneously suppressing casein genes (CSN1S1, CSN2, CSN3), lipogenic genes (FASN, SCD, CD36), amino acid transporters (SLC7A5, SLC38A2), and mTOR-AKT-STAT5 translational machinery, collectively impairing milk biosynthetic capacity. Pro-apoptotic signaling (BAX, CASP3 upregulation; BCL2 downregulation) and mitochondrial dysfunction further compromise mammary epithelial viability. Post-transcriptional regulation through miRNA, circRNA, and lncRNA competing endogenous RNA networks, alongside epitranscriptomic m6A modifications, adds further regulatory complexity. Genome-wide association studies have identified SNPs in HSP70A1A, HSPA4, TLR4, and PRLR as thermotolerance candidates compatible with sustained milk production. Nutritional supplementation with methionine, arginine, and taurine partially restores cellular synthetic capacity. Integrating multi-trait genomic selection with Bos indicus introgression, precision cooling, and targeted nutrition offers the most viable path toward climate-resilient, high-producing dairy cattle. Full article

Chinese Simmental cattle are a high-quality breed developed through long-term crossbreeding and selection after their introduction into China and have become the main dual-purpose cattle population in the Xinjiang region. To deeply dissect the population structure, characteristics of the population structure, and the genetic basis of the twinning trait, this study focused on Xinjiang Chinese Simmental cattle as the main research subject. It integrated genomic data from global public databases to systematically conduct population structure analysis, genetic relationship analysis, and genome-wide selection signature analysis. Population genetic analysis revealed that the IBS matrix and G matrix indicated that some individuals from different geographical origins exhibited distant genetic relationships; the Xinjiang population showed the fastest LD decay, suggesting abundant genetic diversity; the inbreeding coefficient based on Runs of Homozygosity (ROH) across populations ranged from 0.036 to 0.063; principal component analysis and phylogenetic tree showed that some individuals from different geographical origins had certain genetic interconnections; admixture analysis indicated that K = 5 was the optimal model, with each population exhibiting clear genetic differentiation and admixture characteristics. Furthermore, by combining F_st and θπ analysis (comparing the Xinjiang population with other geographical populations), a total of 89 candidate genes associated with the twinning trait in Xinjiang Chinese Simmental cattle were screened, including CYP19A1, HORMAD1, GRB14, CADM2, CXCR4, and others that have been reported to be closely related to oogenesis and reproductive function. In summary, this study explores genome-wide genetic differences among Simmental cattle populations from different regions, deepens our understanding of their population structures, and offers new candidate genes and molecular markers for high-fecundity breeding in Simmental cattle. Full article

Background: Although emerging evidence indicates that major depressive disorder (MDD) raises the risk of developing ovarian cancer (OC) and worsens survival, the biological mechanisms underlying this relationship remain unclear. This study explores the MDD-OC association using single-cell transcriptomics and genetic approaches. Methods: Using single-cell RNA-seq profiles of peripheral blood from MDD and OC patients, we compared shifts in immune cell subsets and selected the consistently expanded CD8⁺ effector memory (CD8_EM) T cells population for follow-up, validated using flow cytometry. We integrated expression quantitative trait loci (eQTL) data from CD8_EM T cell-specific genes with OC genome-wide association study (GWAS) summary statistics through two-sample Mendelian randomization (MR). In vitro experiments were additionally conducted to assess CLSTN3’s role in OC cell proliferation. Results: Among the 554 differentially expressed genes (DEGs) identified in CD8_EM T cells, MR showed a nominal association between CLSTN3 and ovarian cancer risk (OR 1.21, 95% CI 1.03–1.43), though this did not withstand correction for multiple comparisons. Colocalization analysis confirmed that CLSTN3 expression, regulated by the genetic variant rs3759416, shares a causal variant with the OC GWAS signal (PPH4 = 99.99%). Functionally, siRNA-mediated CLSTN3 silencing in HOC7 cells significantly reduced cell viability (CCK-8 assay). Conclusions: By focusing on CD8_EM T cells shared by MDD and ovarian cancer, we identified CLSTN3 as a candidate molecule through nominated by the convergence of genetic, transcriptomic, and functional evidence. These findings provide preliminary insights into the connection between depression and OC, though further validation is warranted. Full article

Glatiramer acetate (GA) is a first-line disease-modifying therapy for multiple sclerosis (MS) with well-established moderate efficacy and high safety, yet its mechanisms of action remain incompletely understood. DNA methylation plays a significant role in MS development and is modulated by various environmental factors, including therapeutic drugs. In this pilot study, we report the first prospective analysis of genome-wide DNA methylation changes in peripheral blood mononuclear cells (PBMCs) from four female relapsing-remitting MS patients before GA initiation and after approximately four and eight months of therapy. We identified 365 loci that are characterized by differential methylation, distinguishing post-treatment time points from baseline, with significant enrichment in CpG islands, shores, and promoter regions. Two distinct temporal patterns emerged: (1) non-monotonic DNA methylation changes peaking at four months and associated with response to foreign antigenic stimuli, and monotonic changes progressively increasing by eight months and related to mTOR-associated pathways relevant to chronic inflammation and neurodegeneration. Integration of DNA methylation and transcriptomic data revealed significant methylation-expression correlations for eight genes, including HLA-DMA, PDE4A, and SMOX—genes with established roles in MS-associated antigen presentation, immunoregulation, and neuroinflammation. Cell composition of PBMCs remained stable throughout treatment. In general, GA therapy for MS appears to induce dynamic, locus-specific DNA methylation changes in PBMCs, with distinct temporal patterns suggesting a biphasic response of the immune system. However, given that none of the individual DMPs reached genome-wide significance, the results presented in this pilot study strongly require validation in larger independent cohorts. Nevertheless, we believe that our findings provide insights into the immunomodulatory effects of GA and lay the foundation for future hypothesis-driven studies to develop epigenetic biomarkers for therapeutic monitoring and generic GA product assessment. Full article

Background/Objectives: Tree peony (Paeonia suffruticosa) has a short flowering period, and its regulatory mechanisms remain poorly understood. These limitations have severely constrained its industrial development. Expansins (EXPs) are key proteins that mediate cell wall loosening associated with petal expansion, yet they remain uncharacterized in tree peony. Methods: This study utilized gene family identification, key gene screening and functional research, as well as regulatory network analysis to reveal the role of the EXP family in the regulation of flower opening. Results: This study presents the first genome-wide identification of 36 PsEXP genes in tree peony, classifying them into four evolutionarily conserved subfamilies (PsEXPA, PsEXPB, PsEXLA, and PsEXLB). Promoter analysis revealed that 28 out of 36 PsEXP promoters contain gibberellin (GA)-responsive elements. Exogenous GA₃ treatment significantly promoted flower opening and upregulated eight PsEXPs, with PsEXPA4-1 showing the highest expression level and promoter GA-responsive element abundance. Subcellular localization confirmed that PsEXPA4-1 was targeted to the cell wall. Overexpression of PsEXPA4-1 in Arabidopsis led to early flowering and enlarged petals, indicating that PsEXPA4-1 had the potential to promote cell expansion, consistent with its proposed role in tree peony flower opening. Mechanistically, we identified a bHLH transcription factor, PsbHLH25, whose expression was induced by GA. Y1H and dual-luciferase assays indicated that PsbHLH25 can bind to the PsEXPA4-1 promoter. Conclusions: This study systematically characterized the EXP gene family in tree peony, revealed PsEXPA4-1 as a key effector downstream of GA promoting flower opening, and discovered PsbHLH25 as a transcriptional activator linking GA signaling to PsEXPA4-1. These findings provided important insights into GA-mediated floral opening and genetic resources for understanding the molecular mechanisms and enabling precise flowering time regulation in tree peony. Full article

Staphylococcus aureus (S. aureus) bovine mastitis is a significant public health issue. Despite enormous efforts, important gaps remain regarding host–microenvironmental factors. How intramammary reduced oxygen modulates S. aureus transcription in bovine mammary epithelial cells (MECs) remains unclear. We examined oxygen-associated transcriptional changes in a bovine-mammary adapted S. aureus clone following internalization into MECs and identified functional category enrichments under Normal-O₂ and Reduced-O₂ exposures. Bovine MAC-T monolayers were infected with a dominant bovine mastitis isolate under Normal-O₂ or Reduced-O₂ conditions. Triplicate infection experiments were performed for each oxygen condition. Each condition included matched non-reacted bacterial controls maintained under the same gas condition but without MAC-T exposure serving as the reference condition for expression calling. RNA was extracted and profiled using a high-throughput qRT-PCR platform covering genome-wide loci. Expression calls were mapped to curated BioQT roles and interpreted descriptively. Results indicated 211 loci were upregulated and 99 were downregulated under Normal-O₂ conditions, versus 53 upregulated and 35 downregulated under Reduced-O₂ conditions, relative to their non-reacted controls. Under Normal-O₂ conditions, regulated loci covered multiple functional roles, including cellular processes, transport/binding proteins, regulatory functions, and energy metabolism with downregulated loci enriched in transport/binding and cell-envelope categories. Under Reduced-O₂ conditions, upregulated loci were abundant in cellular process annotations dominated by pathogenesis/toxin-related functions, whereas downregulated loci were enriched in nucleotide biosynthetic and DNA/cell division categories. Thus, this reveals oxygen-associated shifts in the transcriptional response of intramammary S. aureus in MAC-T cells. Normal-O₂ conditions were associated with broader category representation, whereas Reduced-O₂ conditions yielded a narrower distribution enriched for selected toxin/pathogenesis- and iron/cation-associated annotations. These oxygen-linked transcriptional-shifts highlight candidate pathways for the intramammary adaptation of S. aureus, potential diagnostic markers, anti-virulence strategies, and targeted therapeutics. Full article

The innate immune system, particularly the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling pathway, is a major early defense barrier against influenza A virus infection. However, excessive immune responses can trigger lethal cytokine storms and severe immune-mediated pathology. In this study, we performed a genome-wide CRISPR/dCas9 gene activation screen in human lung epithelial (A549) cells by using an A/Puerto Rico/8/1934 (H1N1) reporter virus, and identified the ubiquitin-specific protease USP17L13 as a novel negative regulator of innate immunity that promotes influenza virus replication. Overexpression of USP17L13 significantly enhanced the replication of multiple subtypes of influenza viruses in A549 cells, including a human pandemic H1N1 virus, seasonal H3N2 viruses, as well as a globally circulating clade, 2.3.4.4b, of the highly pathogenic avian H5N1 virus. Transcriptomic analysis demonstrated that USP17L13 suppresses host antiviral defenses by downregulating nuclear factor kappa B (NF-κB) signaling and arachidonic acid metabolism, while upregulating pathways associated with ribosomal translation and oxidative phosphorylation to facilitate viral production. Mechanistically, USP17L13 attenuates the host interferon (IFN) response by promoting the degradation of the key viral RNA sensors, RIG-I, and melanoma differentiation-associated protein 5 (MDA5). Further analysis revealed that USP17L13 is inducible by type I and type II interferons as well as inflammatory cytokines, suggesting that it may act as a negative-feedback regulator to limit excessive inflammation. Collectively, our findings identify USP17L13 as a previously unrecognized proviral host factor and provide new insight into how host deubiquitinases shape influenza virus-host interactions, with potential implications for host-directed approaches to controlling excessive inflammation during viral infection and improving influenza vaccine production. Full article