Search Results (461)

Fruit size and pungency are key yield and quality traits in chili. This study combines high-throughput genotyping with bulk segregant analysis (BSA) to identify candidate SNPs and quantitative trait loci (QTLs) by analyzing extreme phenotypes from a Ghotki × Chakwal-4 F2 population. The traits were fruit length, diameter, length-to-diameter ratio, and weight, along with capsaicin content. Significant correlations were observed among length, diameter, and length-to-diameter ratio. A total of 534 single nucleotide polymorphisms (SNP) markers were used to develop genetic maps from 4315 to 6607 cM long. The SNP frequency data was pooled for the 25% of individuals showing extreme values for each measured trait, and bulk segregant analysis (BSA) was performed. BSA identified high-scoring SNPs associated with pungency (SNP 1_41308232; SNP 12_104377148), fruit length (SNP 1_92509300; SNP 6_218780813), and fruit weight (SNP 6_100989762 and SNP 6_138660974). Genetic mapping identified twelve pungency QTLs, three for fruit length, two for fruit diameter, two for the length-to-diameter ratio, and thirteen for fruit weight. Overlapping QTL regions on chromosome 6 influence fruit length, fruit width, and capsaicin content, indicating potential pleiotropy and offering promising targets for multi-trait selection in chili breeding. The study identifies key SNPs and QTLs that simultaneously influence chili fruit size and pungency, providing valuable targets for multi-trait breeding. Full article

Background: Vitamin D receptor (VDR) gene polymorphisms are linked to muscle and bone physiology, yet their influence on individual differences in resistance training adaptations, especially between sexes, is not well understood. Methods: In total, 191 healthy Chinese Han adults (94 men, 97 women) completed a 12-week, twice-weekly resistance training program (squat and bench press). Key indicators of strength, power, body composition, and muscle morphology were assessed before and after the intervention. Participants were genotyped for VDR polymorphisms (rs731236/TaqI, rs7975232/ApaI, rs1544410/BsmI, rs2228570/FokI). Data were analyzed to compare responses across genotype groups. Results: Training induced significant improvements in multiple outcomes. Overall, the AG genotype of rs731236 and the CT genotype of rs1544410 were associated with greater gains in bone mineral content. Sex-specific analyses revealed distinct patterns: in women, the rs731236-AA genotype correlated with better strength and power gains, while the AG genotype linked to greater body composition improvements. In men, the rs1544410-CC genotype was associated with superior lower-limb muscle growth. The rs7975232 showed no significant overall effect, and rs2228570 deviated from Hardy–Weinberg equilibrium. Conclusions: VDR gene polymorphisms, particularly rs731236 and rs1544410, are associated with inter-individual variability in resistance training responses among Chinese Han adults, demonstrating clear sex and phenotype specificity. These findings offer preliminary support for genotype-informed personalized training. Full article

Background: Catechol-O-methyltransferase (COMT) catalyzes catecholamine O-methylation and contributes to dopamine turnover, potentially influencing levodopa requirements in Parkinson’s disease (PD). We evaluated whether the Gothelf COMT haplotype—and its constituent variants rs2075507, rs4680 (Val158Met), and rs165599—differ in frequency between PD cases and controls. We then tested associations between these variants and clinical phenotypes, with a prespecified focus on levodopa equivalent daily dose (LEDD). Finally, we examined whether haplotype structure and allele-specific context (e.g., background-dependent effects) help explain observed genotype–phenotype relationships in the PD cohort. Aim: Analysis of the rs2075507, rs4680 and rs165599 at individual and haplotype level between control and diseased groups. Furthermore, analysis of association of individual SNPs or haplotype level with clinical outcomes. Subjects and methods: Fifty-five individuals with Parkinson’s disease (PD) and fifty-three neurologically healthy controls were enrolled at a single center. Genomic DNA was isolated from peripheral blood, and three COMT variants—rs2075507 (promoter), rs4680/Val158Met (coding), and rs165599 (3′UTR)—were genotyped by Sanger sequencing. Allele, genotype, and tri-marker haplotype frequencies were estimated, and case–control differences were evaluated. Within the PD cohort, associations with clinical outcomes—primarily levodopa equivalent daily dose (LEDD)—were analyzed using multivariable linear models. Statistical tests were two-sided, with multiplicity control as specified in the corresponding tables. Results: The rs2075507 polymorphism showed a robust additive association with LEDD; each A allele predicted higher dose (LEDD ≈ +1331 mg/day, p = 0.001) after adjusting for age and sex. The tri-haplotype test did not show significant association with LEDD. Nevertheless, rs2075507 SNP strongly marked downstream backgrounds: in AA carriers, rs4680–rs165599 haplotypes were enriched for Val (G) and rs165599-G; in GG carriers, for rs165599-A with mixed Val/Met; and GA was A-loaded at both loci. Exact tests confirmed that AA and GG differed in rs4680–rs165599 composition, whereas GA vs. GG was not significant. Conclusions: The promoter variation at rs2075507 may represent the genetic contributor to levodopa dose requirements when modeled with SNP–SNP interactions, with its effect is modified mostly by rs165599 polymorphism. Tri-haplotypes do not independently predict LEDD. The rs4680 (coding) and rs165599 (3′UTR) context appears to fine-tune rather than determine dosing needs, mainly via interaction with rs2075507 SNP. Full article

Improving wheat processing quality is a crucial objective in modern wheat breeding. Among various quality parameters, grain protein content (GPC) and wet gluten content (WGC) significantly influence the end-use quality of flour. These traits are controlled by multiple minor effect genes and highly influenced by environmental factors. Identifying stable and major-effect genetic loci and developing breeder-friendly molecular markers are of great significance for breeding high-quality wheat varieties. In this study, we evaluated the GPC and WGC of 310 diverse wheat varieties, mainly from China and Europe, across four environments. Genotyping was performed using the wheat 100K SNP chip, and genome-wide association analysis (GWAS) was employed to identify stable loci with substantial effects. In total, four loci for GPC were identified on chromosomes 1A, 3A, 3B, and 4B, with explained phenotypic variation (PVE) ranging from 6.0 to 8.4%. In addition, three loci for WGC were identified on chromosomes 4B, 5A, and 5D, which explained 7.0–10.0% of the PVE. Among these, three loci coincided with known genes or quantitative trait loci (QTL), whereas QGPC.zaas-3AL, QGPC.zaas-4BL, QWGC.zaas-4BL, and QWGC.zaas-5A were potentially novel. Seven candidate genes were involved in various biological pathways, including growth, development, and signal transduction. Furthermore, five kompetitive allele specific PCR (KASP) markers were developed and validated in a natural population. The newly identified loci and validated KASP markers can be utilized for quality improvement. This research provides valuable germplasm, novel loci, and validated markers for high-quality wheat breeding. Full article

Micronutrients, particularly boron (B), iron (Fe), manganese (Mn), and zinc (Zn), are pivotal for cotton (Gossypium spp.) growth, reproductive success, and fiber quality. However, their critical roles are often overlooked in fertility programs focused primarily on macronutrients. This review synthesizes recent advances in the physiological, molecular, and agronomic understanding of B, Fe, Mn, and Zn in cotton production. The overarching goal is to elucidate their impact on cotton nutrient use efficiency (NUE). Drawing from the peer-reviewed literature, we highlight how these micronutrients regulate essential processes, including photosynthesis, cell wall integrity, hormone signaling, and stress remediation. These processes directly influence root development, boll retention, and fiber quality. As a result, deficiencies in these micronutrients contribute to significant yield gaps even when macronutrients are sufficiently supplied. Key genes, including Boron Transporter 1 (BOR1), Iron-Regulated Transporter 1 (IRT1), Natural Resistance-Associated Macrophage Protein 1 (NRAMP1), Zinc-Regulated Transporter/Iron-Regulated Transporter-like Protein (ZIP), and Gossypium hirsutum Zinc/Iron-regulated transporter-like Protein 3 (GhZIP3), are crucial for mediating micronutrient uptake and homeostasis. These genes can be leveraged in breeding for high-yielding, nutrient-efficient cotton varieties. In addition to molecular hacks, advanced phenotyping technologies, such as unmanned aerial vehicles (UAVs) and single-cell RNA sequencing (scRNA-seq; a technology that measures gene expression at single-cell level, enabling the high-resolution analysis of cellular diversity and the identification of rare cell types), provide novel avenues for identifying nutrient-efficient genotypes and elucidating regulatory networks. Future research directions should include leveraging microRNAs, CRISPR-based gene editing, and precision nutrient management to enhance the use efficiency of B, Fe, Mn, and Zn. These approaches are essential for addressing environmental challenges and closing persistent yield gaps within sustainable cotton production systems. Full article

Chromosome dynamics, recombination, and nucleolar organization intersect during meiotic prophase I, yet how the recombination context influences nucleolar architecture remains unclear. We analyzed the nucleolar pool of Cdc14 in Saccharomyces cerevisiae under matched prophase I gating and a uniform, frame-based operational definition of transient two-focus episodes. In a prophase-arrest reference, Cdc14–mCherry formed a predominant single nucleolar focus with occasional, reversible two-focus episodes that Nop56–GFP placed within the nucleolar compartment (nucleolar splitting). Splitting rose sharply when interhomolog recombination was compromised and remained elevated when Spo11 catalytic activity was abolished, indicating that increased DSB formation is not required and pointing instead to the homolog engagement state as a key variable. Population checkpoint readouts did not map onto the phenotype: Hop1 phosphorylation differed strongly across genotypes, yet splitting remained high in recombination-defective and DSB-free contexts and low in the reference. Timing analyses showed that events concentrated early and declined in the reference, whereas recombination-defective and DSB-free backgrounds retained activity into later windows across thresholds. We propose that nucleolar splitting reflects a rheological response of the nucleolus to chromosome-scale forces that vary with homolog engagement, consistent with contributions from DSB-independent chromosome dynamics such as telomere clustering, telomere-led rapid prophase movements, and centromere coupling/pairing. Together, these data support the nucleolus as a mesoscale, mechanically sensitive readout of meiotic chromosome dynamics. Full article

The spoilage phenotype of microorganisms is a key mechanism leading to food spoilage, but how their metabolic environment affects the spoilage phenotype remains unclear. This study utilized metabolomics and spoilage phenotype analysis to reveal metabolic differences between different quorum sensing (QS) genotypes of Hafnia. alvei H4 and their impact on spoilage phenotypes. Ultra-high performance liquid chromatography–fluorescence detection revealed that the QS system participated in the differential metabolic regulation of eight amino acids, with serine exerting the most significant influence on the spoilage phenotype. Subsequent studies demonstrated that QS-promoted serine inhibited bacterial motility by affecting the biosynthesis of rhamnolipid (rather than c-di-GMP) and inhibiting flagellar/chemotactic genes expression. Moreover, QS-promoted serine induced the difference of bacterial inner membrane, further inhibiting bacterial motility. These findings provided fundamental information for the control of biofilms conformation within complex food nutritional background. Full article

Peaches are a fruit crop with global importance due to their economic value. Fruit quality (e.g., weight, soluble solids content (SSC)) and phenology traits (e.g., maturity date) are essential for generating novel varieties. Nevertheless, modern germplasm’s narrow genetic diversity hampers breeding efforts to enhance these traits. To identify genetic markers helpful for marker-assisted breeding, this work leveraged a diverse panel of 140 peach commercial cultivars and advanced breeding lines phenotyped across three harvest seasons for the maturity date (MD), chlorophyll absorbance (IAD), SSC, and fruit weight (FW). Genotypic data were generated via ddRADseq, identifying 5861 SNPs. A rapid linkage disequilibrium decay (critical r² = 0.308 at 950 kb) was determined, and a population structure analysis revealed two admixed genetic clusters, with phenotypic distributions influenced by seasonal environmental factors. A total of 599 marker–trait associations were detected by using single and multi-year analysis, and for each trait the surrounding genomic regions explored to identify potential candidate genes annotated with functions related to the trait under study, and expressed in peach fruits. This study highlights multiple loci potentially responsible for phenotypic variations in plant phenology and fruit quality, and provides molecular markers to assist peach breeding for fruit quality. Full article

Background: Variants in the GBA gene represent the most common genetic risk factor for Parkinson’s disease and are associated with a more aggressive disease course. Deep brain stimulation is an established therapy for advanced Parkinson’s disease, yet the influence of GBA status on postoperative outcomes remains incompletely defined. This review aims to summarize the clinical relevance of GBA genotyping prior to DBS and to evaluate its potential contribution to decision-making, risk stratification, and long-term management. Methods: A structured narrative review was conducted. The literature on sequencing methodology, variant interpretation, and postoperative outcomes in GBA-positive and GBA-negative patients was examined. Particular focus was placed on motor, cognitive, and neuropsychiatric outcomes, and on studies comparing trajectories across variant classes. Results: Across all study designs, patients with GBA-associated Parkinson’s disease demonstrated robust motor improvement after DBS, with outcomes comparable to those in non-carriers. Cognitive and neuropsychiatric decline occurred more rapidly in GBA carriers. Recent evidence indicates that cognitive and neuropsychiatric decline is influenced more by the genetic profile than the stimulation procedure. Variant severity appears to influence postoperative trajectories. Long-read sequencing improves detection of recombinant alleles and may refine genotype–phenotype associations. Genotyping provides additional value in counseling, expectation management, and postoperative planning. Conclusions: DBS remains an effective motor therapy for patients with GBA-associated Parkinson’s disease. Current findings indicate GBA genotyping should inform, and not limit, candidate selection. Integration of clinical, cognitive and genetic data supports more individualized management. Methodological advances in sequencing and the development of prediction models may further enhance personalized DBS planning. Full article

This review integrates molecular, clinical, and translational data to provide an updated understanding of GJB2-related deafness and its emerging treatment landscape. Truncating mutations in GJB2 typically cause severe-profound hearing loss (HL) phenotypes, whereas non-truncating alleles are often associated with milder or progressive phenotypes. Geographic variation in variant prevalence contributes to regional differences in disease burden. Beyond the coding region, deletions and cis-regulatory mutations within the DFNB1 locus, including GJB6 and CRYL1, can influence HL severity when compounded with other pathogenic GJB2 variants. DFNB1 hearing loss generally presents as symmetric, bilateral, and flat to gently sloping across frequencies, with preserved cochlear neurons that support excellent cochlear implant (CI) outcomes. Early implantation CI in GJB2-positive children yields superior speech and language development compared with non-GJB2 etiologies. Emerging therapies include dual-AAV (AAV1 + AAV-ie/ScPro) delivery, achieving cell-specific Cx26 restoration, adenine base-editing for dominant-negative variants, and allele-specific suppression using RNA interference or antisense oligonucleotides. Concurrent progress in human iPSC-derived cochlear organoids provides a physiologic model to advance toward clinical trials. By integrating genotype-phenotype correlations, natural history insights, and advances in molecular therapeutics, this review presents a comprehensive update on GJB2-related HL and highlights how gene-based strategies are poised to change the treatment of this condition. Full article

Atopic eczema and asthma frequently co-occur, forming a distinct complex phenotype that likely arises from shared genetic pathways and early-life environmental influences. We aimed to investigate whether variants in TNS1 and NRXN1—previously identified in a genome-wide interaction study—influence susceptibility to atopic eczema and the asthma–eczema phenotype and whether early-life environmental tobacco smoke (ETS) exposure modifies these genetic effects. A total of 188 Caucasian children under 2 years at recruitment were prospectively followed up to 6 years of age. Eligibility of all participants for the study or control group was based on a questionnaire and a physician-confirmed diagnosis of eczema and asthma. Early-life ETS exposure was assessed by parental questionnaire. All participants were genotyped for TNS1 and NRXN1 SNPs. The TNS1 rs918949 [T] allele was associated with the combined asthma–eczema phenotype but not with eczema alone. Synergistic gene–environment interactions were identified for both TNS1 and NRXN1, with the highest risk of the combined asthma–eczema phenotype observed among ETS-exposed carriers of risk alleles. Our findings provide the first independent replication of evidence suggesting that TNS1 and NRXN1 may contribute to the asthma–eczema comorbidity through mechanisms that could be substantially modified by early-life ETS exposure. Full article

Background: Mucopolysaccharidosis type IIIC (MPS IIIC) is a rare lysosomal storage disorder caused by pathogenic variants in the HGSNAT gene. Data from large patient cohorts remain scarce, particularly in Latin America. Methods: We retrospectively analyzed clinical, biochemical, and genetic data from patients diagnosed with MPS IIIC through the MPS Brazil Network. Diagnosis was based on reduced activity of acetyl-CoA:α-glucosaminide N-acetyltransferase (HGSNAT), elevated urinary glycosaminoglycans (uGAGs), and/or molecular genetics tests. Results: A total of 101 patients were confirmed with MPS IIIC, representing one of the largest cohorts worldwide. Females accounted for 60% of cases. The mean age at symptom onset was 5.4 ± 3.9 years, while the mean age at diagnosis was 11.7 ± 6.9 years, reflecting a 6-year diagnostic delay. Most patients initially presented with developmental delay (82%) and facial dysmorphism (80%), whereas behavioral manifestations were less frequently identified (25%), suggesting a milder phenotype than previously reported. Genetic information was available for 28% of patients, showing recurrent alleles (c.372-2A>G, c.252dupT) and several novel mutations, which expand the mutational spectrum of the disease. Genotype–phenotype similarities with Portuguese, Italian, and Chinese cases suggest shared ancestry contributions. Regional differences included earlier diagnoses in the North of Brazil and high consanguinity rates in the Northeast region. Conclusions: This study describes the largest Brazilian cohort of MPS IIIC, documenting novel variants and regional heterogeneity. Findings highlight diagnostic delays, ancestry influences, and the urgent need for disease-modifying therapies. Full article

Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in the CRTC2 and ELOVL6 genes on intramuscular fat content and to evaluate their associations with growth and meat quality traits in 18-month-old Kalmyk heifers raised under different environmental conditions. Methods: A total of 400 clinically healthy Kalmyk heifers (200 from LLP “Qazaq Asyldary” and 200 from LLP “Agrofirma Turikpen”) were examined. All animals originated from closed breeding herds, and only unrelated individuals without common ancestors to the third generation were included. Zootechnical measurements— live weight, withers height, chest depth, chest girth, and body length—were performed twice by a trained specialist. Backfat thickness and musculus longissimus dorsi depth were measured postmortem. Blood samples were collected for genomic DNA extraction using the GeneJET purification kit, and DNA quality was assessed by Nanodrop, Qubit, and agarose gel electrophoresis. Target fragments of CRTC2 and ELOVL6 were amplified (150–200 bp) and sequenced on an ABI 3500 system. SNP identification, allele frequencies, and genotyping were performed by alignment to the Bos taurus ARS-UCD1.2 reference genome. Statistical analyses were conducted in RStudio using linear and mixed models with “farm” as a random effect. Results: Only one informative polymorphism, g.133528A>G in ELOVL6, was detected. Three genotypes (AA, AG, GG) were observed, with the heterozygous AG genotype showing significantly higher live weight, greater body length, and improved linear measurements compared to AA and GG. No significant associations were detected with backfat thickness or muscle depth. The g.133528A>G polymorphism in ELOVL6 positively influences growth traits without increasing fatness, aligning with the naturally lean phenotype of Kalmyk cattle. Conclusions: The AG genotype may serve as a promising marker for selecting faster-growing animals in marker-assisted breeding programs. Full article

TANGO2 deficiency disorder is a rare autosomal recessive disease (~100 cases reported worldwide). Despite being caused by loss-of-function variants in the TANGO2 gene, patients exhibit marked phenotypic variability, including intrafamilial differences among individuals carrying identical variants. To uncover potential modifier mechanisms influencing disease severity, we developed an integrative Systems biology framework, combining exome sequencing, transcriptomics, variant effect prediction, and Human Phenotype Ontology mapping. This approach was applied to two siblings carrying identical compound heterozygous TANGO2 variants but opposite clinical outcomes: one severely affected and one asymptomatic. Personalized protein–protein interaction networks and combined univariate and multivariate analyses were employed to maximize specificity in this single-family comparison. In the affected sibling, a cumulative burden of common APOB variants, together with altered VLDLR, NTN1, and LDHA expression, implicated disrupted lipid metabolism and neurodevelopmental pathways. The asymptomatic sibling harbored a potentially protective 3′-UTR variant in EP300 and no APOB variant burden, supporting enhanced post-transcriptional regulation within developmental biology networks. These findings highlight lipid metabolism as a key pathway in TANGO2 deficiency pathophysiology and suggest autophagy and mitophagy as additional modifier mechanisms influencing phenotypic variability. Our integrative multi-omics framework provides a valuable strategy for elucidating genotype-phenotype relationships in rare diseases and supports personalized therapeutic approaches. Full article

Photosynthesis (PS) is the cornerstone of crop productivity, directly influencing yield potential. Photosynthesis remains an underexploited target in soybean breeding, partly because field-based photosynthetic traits are difficult to measure at scale. Also, it is unclear which reproductive stage(s) provide the most informative physiological signals for yield. Few studies have evaluated soybean PS in elite germplasm under field conditions, and the integration of chlorophyll fluorescence (CF) with UAV imaging for PS traits remains largely unexplored. This study evaluated genotypic variation in photosynthetic and canopy traits among elite soybean germplasm across environments and developmental stages using CF and UAV imaging. Linear mixed-model analysis revealed significant genotypic and G×E effects for yield, canopy and several photosynthetic parameters. Broad-sense heritability (H²) estimates indicated dynamic genetic control, ranging from 0.12 to 0.77 at the early stage (S1) and 0.20–0.81 at the mid-reproductive stage (S2). Phi2, SPAD and FvP/FmP exhibited the highest heritability, suggesting their potential as stable selection targets. Correlation analyses showed that while FvP/FmP and SPAD were modestly associated with yield at S1, stronger positive relationships with Phi2, PAR and FvP/FmP emerged during S2, underscoring the importance of sustained photosynthetic efficiency during pod formation. Principal component analysis identified photosynthetic efficiency and leaf structural traits as key axes of physiological variation. UAV-derived indices such as NDRE, MTCI, SARE, MExG and CIRE were significantly correlated with CF-based traits and yield, highlighting their utility as high-throughput proxies for canopy performance. These findings demonstrate the potential of integrating CF and UAV phenotyping to enhance physiological selection and yield improvement in soybean breeding. Full article