Search Results (5,131)

The Kazakh horse represents a significant genetic resource within China’s equine population, characterized by notable resilience and an ability to thrive on coarse forage. Nevertheless, a decline in its numbers has been observed recently, making the improvement of its reproductive performance crucial for the preservation of this breed and the advancement of the related industry. In this study, testicular tissues from 1-year-old (pre-pubertal) and 2-year-old (post-pubertal) Kazakh horses were analyzed. miRNA sequencing was conducted on tissues from these age groups, followed by bioinformatics analyses to elucidate the functions of differentially expressed miRNAs (DEmiRNAs). The reliability of the sequencing data was subsequently verified using RT-qPCR. Analysis revealed 165 differentially expressed miRNAs (DEmiRNAs) in the testicular tissues between the two age groups. Of these, 118 DEmiRNAs (e.g., eca-miR-206 and eca-miR-2483) were significantly up-regulated (p < 0.05), and 47 DEmiRNAs (e.g., eca-miR-196a and eca-miR-211) were significantly down-regulated (p < 0.05). These DEmiRNAs were mainly implicated in biological processes including lipid metabolism and signal transduction. Their predicted target genes are potentially involved in key reproductive processes, notably testicular development and spermatogenesis. This study identifies candidate miRNAs and potential regulatory pathways associated with sexual maturation in Kazakh horses, providing a preliminary molecular basis for future functional validation and improvement of equine reproductive performance. Full article

Hepatitis C virus (HCV) infection is still a major worldwide health concern. It is distinguished by a high degree of genetic variation that affects the course of the illness and the effectiveness of treatment. The epidemiological profile of HCV is prone to rapid change in areas where there is significant human migration, like Turkey. The purpose of this study was to evaluate the impact of long-term migration on local viral diversity by analyzing the distribution and temporal trends of HCV genotypes among Turkish citizens and asylum seekers in Kayseri, Turkey, over an eight-year period. From January 2014 to December 2021. 1173 HCV RNA-positive patients at Kayseri City Training and Research Hospital were the subject of a retrospective analysis. Genotypes were determined using the Abbott RealTime HCV Genotype II assay and Montania 4896 assay (Anatolia Geneworks, Türkiye). The most prevalent genotypes were Genotype 1b (48.3%, 95% CI: 45.5–51.2%), Genotype 4 (25.0%, 95% CI: 22.5–27.5%), and Genotype 1a (10.3%, 95% CI: 8.6–12.1%). Turkish patients exhibited the highest prevalence of Genotype 1b (98.2%), while asylum seekers demonstrated greater relative burdens of Genotype 4 (8.5% of total GT4) and Genotype 5 (83.3% of total GT5). Genotype 3a emerged in 2018, with a predominance in males (73.9%). The Cochran–Armitage trend test revealed statistically significant increasing trends for Genotype 3 (Z = 3.572, p = 0.0004) and Genotype 3a (Z = 2.600, p = 0.009). This eight-year retrospective study demonstrates that the HCV genotype distribution in Kayseri has undergone significant changes in the context of migration and demographic shifts. The statistically significant increasing trends of Genotypes 3 and 3a, particularly among younger male populations, suggest evolving transmission dynamics. These findings underscore the necessity of demographically targeted and culturally appropriate screening and treatment strategies for both resident and migrant populations to achieve HCV elimination goals. Full article

To clarify the genetic background and biological characteristics of grape germplasm resources and provide theoretical support for germplasm innovation and new-variety breeding, we conducted systematic morphological identification and SSR molecular-marker analysis on 38 core grape germplasms (29 fresh-eating cultivars, 1 local cultivar, and 8 wild germplasms) from the National Southeast Mountainous Crop Germplasm Repository (Jiangxi·Yichun) and other regions. For morphological identification, 14 quantitative traits and 5 descriptive traits of leaves, floral organs and fruits were determined in strict accordance with the NY/T 2932-2016 Descriptors for Grape Germplasm Resources. For SSR molecular-marker analysis, eight pairs of internationally universal core primers were used for PCR amplification and fluorescence detection referring to the NY/T 3640-2020 Identification of Grape Cultivars Using SSR Markers, and genetic diversity analysis was conducted on 11 local and wild grape germplasms. The results revealed abundant phenotypic diversity among the tested germplasms: the functional leaves of cultivars were predominantly pentagonal and cuneate, while those of wild germplasms were mostly reniform and cordate, with 3–5 lobes for most germplasms; all germplasms were hermaphroditic, except for two wild accessions with unisexual flowers. Significant variations were observed in fruit traits, with the coefficient of variation (CV) of cluster weight and berry weight reaching 67.64% and 50.53%, respectively. The genetic plasticity of weight-related traits was much higher than that of shape- and length-related traits, and the average Shannon–Wiener index (H′) of 19 morphological traits was 3.47, indicating a high level of overall phenotypic diversity. SSR analysis showed that the eight primer pairs amplified a total of 42 genotypes (5.25 per primer pair on average). The population had a mean observed number of alleles (Na) of 5.28, a mean effective number of alleles (Ne) of 7.25, and a mean polymorphism information content (PIC) of 0.74, demonstrating rich genetic diversity and high polymorphism of the tested loci. Cluster analysis divided the 11 local germplasms into four groups, which clearly reflected the genetic relationships among them, and genetic admixture was found in some germplasms due to unclear introduction traceability. In this study, fresh-eating grape cultivars suitable for the climatic conditions of Jiangxi Province were screened, the utilization value of local germplasm resources was clarified, and a two-dimensional evaluation system based on phenotypic traits and SSR molecular markers was constructed. The findings provide basic data and a scientific basis for the precise evaluation, elite gene mining, and new-variety breeding of grape germplasm resources in Jiangxi Province. Full article

Maize is one of the most widely cultivated crops worldwide and is extensively used for animal feed and industrial applications. Plant height (PH) and ear height (EH) are critical determinants of lodging resistance and tolerance to high planting density, and coordinated regulation of these traits is essential for yield improvement. In this study, 479 maize inbred lines from Northeast and North China were genotyped using 7861 single-nucleotide polymorphism (SNP) markers to perform a genome-wide association study (GWAS). After controlling for population structure and relatedness, the mixed linear model (MLM) identified 20 loci significantly associated with PH on chromosomes 2, 4, 5, 6, 7, and 8, and 8 loci associated with EH on chromosomes 2, 3, 4, and 7. A total of 23 candidate genes were identified, including PLATZ8, pectin methylesterase 36, and leucine-rich repeat extensin 14. Gene Ontology (GO) enrichment analysis revealed significant enrichment in biological and molecular functions such as DNA binding, pectinesterase activity, zinc ion binding, ATP binding, and uniporter activity. Bioinformatic characterization of the two most likely candidate genes, Zm00001d002726 and Zm00001d015394, showed that both possess a typical compact four-exon structure. Functional prediction indicated that Zm00001d002726 encodes a pectinesterase/pectinase, potentially regulating cell elongation through pectin degradation and remodeling of the cell wall. Pectinesterase activity may influence PH and EH by mediating pectin demethylation within the cell wall. In contrast, Zm00001d015394 encodes a PLATZ family transcription factor that may regulate downstream gene expression through DNA-binding activity. These findings provide insight into the genetic architecture and potential molecular mechanisms underlying PH and EH in maize and offer a foundation for future breeding efforts. Full article

Wild relatives of cultivated legumes represent valuable genetic resources for crop improvement, ecosystem resilience, and sustainable agriculture. This study presents a comparative ecological and metagenomic assessment of three biogeographically distinct regions in Bulgaria—Kaliakra, Strandzha, and the Eastern Rhodopes—where populations of wild legumes, including Pisum elatius, Cicer montbrettii, Vicia incisa, and Lupinus spp., occur. Field expeditions were conducted during flowering and seed maturation stages, followed by rhizosphere soil sampling and high-throughput sequencing targeting bacterial 16S rRNA and fungal ITS regions. Soil physicochemical properties, microbial diversity indices, and taxonomic composition were analysed and compared among regions. Distinct microbial community structures were identified. Kaliakra soils were dominated by Firmicutes (26–58%) and Proteobacteria (20–25%), while Strandzha soils showed higher abundance of Actinobacteriota (12–68%) and Proteobacteria (10–35%). The Eastern Rhodopes exhibited more balanced communities, with Proteobacteria (30–45%), Firmicutes (7–43%), and Actinobacteriota (3–11%). Fungal communities also differed significantly, with Nectriaceae dominating in Kaliakra, higher evenness in Strandzha, and intermediate diversity in the Eastern Rhodopes. Alpha diversity revealed the highest bacterial richness in Kaliakra, whereas the Eastern Rhodopes showed the greatest community evenness. Beta diversity analysis demonstrated clear regional separation driven by environmental filtering. These findings highlight the ecological and microbiological differentiation of wild legume habitats and support their conservation and utilisation in sustainable agriculture and breeding programs. Full article

Background: Early-onset Alzheimer’s disease (EOAD) caused by autosomal dominant mutations provides a deterministic framework for investigating genetic modifiers of neurodegeneration. Telomere biology has emerged as a central regulator of genomic stability, cellular ageing, and stress response integration, yet its role in EOAD, particularly in under-represented populations, remains poorly defined. Methods: We conducted a cross-sectional case–control study to evaluate the genetic distribution, disease association, and predicted regulatory consequences of common variants in the telomere maintenance genes TERT and TERC in individuals from Western Mexico. The EOAD group comprised genetically confirmed carriers of the PSEN1 p.Ala431Glu (A431E) founder mutation with clinical EOAD (n = 69), and controls were unrelated individuals without dementia (n = 179). Five common variants were analyzed: rs2242652, rs2853677, rs2736100, and rs10069690 (TERT), and rs12696304 (TERC). Results: Genotype distributions in controls conformed to the Hardy–Weinberg equilibrium. Single-variant analyses showed no significant allele-level associations. Most TERT variants did not show significant allele-level associations with EOAD. However, a preliminary genotype-level enrichment for the GC allele at rs12696304 (TERC) was observed among EOAD cases compared with controls; allele-level associations were not significant. Linkage disequilibrium analysis revealed low r² values (<0.20), supporting variant independence. Population-level allele frequency comparisons revealed ancestry-dependent divergence across loci; in silico functional annotation localised all variants to non-coding regulatory regions. GTEx-based analyses indicated that rs12696304 acts as an eQTL for ACTRT3 in whole blood and pituitary, as well as for LRRC34 in the cerebellar hemisphere, suggesting a potential regulatory network within the TERC locus (3q26.2). Conclusions: Overall, common regulatory variants in TERT did not show strong independent effects on EOAD susceptibility in PSEN1 A431E carriers. However, the convergence of association patterns, functional annotation, and regulatory evidence provides hypothesis-generating support for the TERC locus (3q26.2), particularly rs12696304, as a candidate region for further investigation. Additional studies integrating telomere dynamics, functional validation, and multi-omics analyses are needed to clarify the role of telomere biology in the pathogenesis of autosomal dominant EOAD. Full article

Fanconi anemia (FA) is a rare inherited disorder characterized by genomic instability, congenital anomalies, and progressive bone marrow failure; such manifestations may vary across populations, partly due to differences in genetic background. This study aims to describe the clinical and molecular spectrum of FA in Mexican patients. A total of 14 patients with clinical suspicion of FA were evaluated; cytogenetic and molecular analyses were successfully performed using MLPA and NGS. Clinically, short stature was present in 100% (n = 14) of the patients, followed by upper limb abnormalities, which were present in 78.6% (n = 11) of the patients, and microphthalmia, which was present in 71.4% (n = 10) of the patients. Molecular analysis identified pathogenic variants in FANCA (78.6%, n = 11), FANCC (14.3%, n = 2), and FANCE (7.1%, n = 1), with a relatively balanced distribution of homozygous (57.1%, n = 8) and compound heterozygous variants (42.9%, n = 6). Notably, the FANCA:c.3931_3932del variant was recurrent in six patients from the same geographic region (Michoacan), suggesting possible regional enrichment. Our findings expand the clinical and molecular characterization of FA in Mexican patients and underscore the importance of integrating phenotypic and genomic data to better understand population-specific patterns of this disorder. Full article

Bougainvillea (Bougainvillea glabra) is a perennial woody species belonging to the Nyctaginaceae family, native to South America. It is widely recognized for its brightly colored bracts and strong adaptability, and is widely cultivated as a major ornamental plant in tropical and subtropical regions. However, QTL mapping studies on morphological traits remain limited in the genus Bougainvillea, and the genetic basis underlying its key ornamental traits is still largely unclear. In this study, an F₁ segregating population was constructed using the cultivars ‘Mrs Eva White’ and ‘Formosa’ as parents, and was used for high-density genetic map construction and quantitative trait locus analysis. Fourteen leaf and thorn-related traits were investigated, with coefficients of variation ranging from 8.16% to 64.54%. Based on specific-locus amplified fragment sequencing (SLAF-seq), a total of 1,133,206 SLAF markers were developed, among which 479,488 were polymorphic. Using the inclusive composite interval mapping (ICIM) algorithm in the GACD 1.2 software, a high-density genetic linkage map was constructed for B. glabra, consisting of 17 linkage groups and 3256 markers. The genetic map spanned 1797.64 cM, with an average marker interval of 0.55 cM. A total of 22 QTLs were detected for the measured leaf and thorn traits, including 16 major QTLs with a PVE ≥ 8%. Collectively, this study identified stable genetic loci for important morphological traits and provides a valuable theoretical foundation for marker-assisted selection and genetic improvement of ornamental traits in Bougainvillea. Full article

Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with leaf color using SPAD values as a phenotypic indicator. Methods: An ${\mathrm{F}}_2$ population derived from a cross between the dark green line YSG1go and the light green line Asagikei-KUJYO was used. A linkage map was constructed based on RNA-seq-derived SNP markers, and SPAD values were measured for QTL analysis. Results: The linkage map consisted of eight linkage groups with a total length of 2103.0 cM and 765 mapped markers. SPAD values showed significant differences between the parental lines, with high broad-sense heritability ($H^2$ = 0.76), indicating a strong genetic contribution to this trait. Multiple significant QTLs were detected on chromosomes 4 and 5, each explaining 27.4–38.1% of the phenotypic variance. The direction of allelic effects differed among QTLs, suggesting that favorable alleles are distributed between the parental lines. In addition, genes related to chloroplast protein translation were identified within the QTL regions. Conclusions: SPAD values are a suitable indicator for genetic analysis of leaf color in bunching onion, and the QTLs identified in this study provide valuable information for molecular breeding aimed at improving dark green leaf color. Full article

Indigenous pig breeds represent valuable reservoirs of genetic diversity but face increasing risks of genetic erosion due to uncontrolled crossbreeding with commercial lines. The Ashanti Dwarf Pig (ADP) of Ghana is an important local genetic resource well-adapted to tropical environments but poorly characterised at the genomic level. Using high-density SNP data from the ADPs and publicly available datasets from other African, European, and Asian pig populations, we examined genetic diversity, population structure, inbreeding, and selection signatures. After quality control, 59,124 SNPs across 875 individuals were retained. ADPs exhibited high polymorphism (~99%) and moderate heterozygosity but also elevated inbreeding (FIS = 0.15; FROH = 0.40), indicating recent inbreeding under free-range management. Population structure revealed that ADPs cluster closely with other African pigs and European breeds more than Chinese breeds. ADMIXTURE analysis, however, indicated recent introgression from both European and Chinese lines. Selection scans revealed candidate genes linked to metabolism-Zinc Finger Ran-Binding Protein 3 (ZRANB3), growth-Sortilin Related VPS10 Domain Containing Receptor 1 (SORCS1), reproduction–Sus Scrofa Chromosome 9 quantitative trait loci (SSC9 QTLs), and immunity-Tudor Domain-Containing Protein 3 and CKLF-like MARVEL transmembrane Domain Containing 7 (TDRD3, CMTM7), reflecting adaptation to tropical production systems. Our results provide a comprehensive genomic characterisation of the ADP within a global context, revealing both genetic richness and vulnerability to genetic erosion. These findings underscore the importance of structured breeding and conservation strategies in preserving this unique African genetic resource and supporting sustainable pig production under changing climatic conditions. Full article

Soil salinization severely restricts rice growth and global grain production, posing a serious threat to food security. Dongxiang wild rice serves as an important genetic resource for improving salt tolerance in rice. In this study, a backcross inbred line (BIL) population derived from Dongxiang wild rice DY80 and an indica restorer line R974 were used to detect QTLs for salt tolerance at the germination and seedling stages. Four QTLs related to germination-stage salt tolerance and three QTLs for seedling-stage salt tolerance were identified, among which qSTS5 on chromosome 5 showed the largest effect with a LOD score of 8.0 and a phenotypic contribution rate of 14.8%. An F_2:3 population was further constructed to validate qSTS5, which increased its LOD value to 10.4 and phenotypic variation explanation rate to 18.5%, and the locus was finally delimited to a 2.3 Mb interval. Transcriptome analysis identified eight differentially expressed genes (DEGs) within the qSTS5 region under salt stress. Sequence comparison between the parents revealed that three DEGs had no coding-region variations, while the other five showed nucleotide polymorphisms leading to amino acid changes. Among them, Os05g0349800 encodes a LEA protein, a typical stress-responsive gene, and harbors a frameshift mutation in DY80. Combined with its induced expression pattern under salt stress, this gene was considered the most promising candidate for qSTS5. This study not only provides a stable major QTL for rice breeding for salt tolerance but also lays a foundation for dissecting the molecular mechanism of salt tolerance in Dongxiang wild rice. Full article

Background: Non-syndromic retinitis pigmentosa (RP) is characterized by rod–cone degeneration, resulting in night blindness, visual field constriction, and eventual blindness. Recessively inherited RP is predominantly exacerbated in consanguineous populations, such as Pakistan. This study aimed to perform the genetic analysis of sixteen non-syndromic RP segregating Pakistani families, and to summarize the mutation spectrum of non-syndromic RP in our population by reviewing related literature. Methods: We screened 16 non-syndromic RP families using targeted capture panel sequencing of 344 genes related to inherited retinal dystrophies. Variants were prioritized based on rarity (minor allele frequency (MAF) < 0.001 in the gnomAD South Asian subset), pathogenicity assessments using ACMG/AMP criteria, and REVEL scores (>0.5). Candidate variants were validated for familial segregation through Sanger sequencing. Results: We identified 15 distinct variants across 14 genes associated with non-syndromic retinitis pigmentosa, comprising 6 missense, 7 nonsense, 1 frameshift, and 2 splice-site variants, including 4 novel variants, i.e., p.(Val220Met) and p.(Pro1282SerfsTer2) in RP1, 1 each in PDE6B (c.2021+5G>A), and PRCD p.(Ser38Ter). Homozygosity predominated, underscoring the impact of consanguinity on the burden of autosomal recessive disease in the present cohort, while the CERKL disease-causing mutation, i.e., p.(Arg257Ter), recurred in two families. Conclusions: This study expands Pakistan’s non-syndromic RP mutational spectrum by identifying novel variants in RP1, PDE6B, and PRCD, alongside recurrent CERKL and RHO mutations of the local population. The literature review suggests that RP1, TULP1, and PDE6B are among the most mutated genes in our population, supporting the value of population-specific genetic panels to enhance diagnostics and carrier screening. Full article

Background/Objective: Sesame (Sesamum indicum L.) is a nutritionally and economically important oilseed crop that is grown predominantly by smallholder farmers in Mozambique. However, its breeding process is constrained by a limited understanding of the genetic diversity in sesame germplasm. Therefore, this study determined the genetic diversity and population structure of a panel of 109 sesame accessions from Instituto de Investigação Agrária de Mocambique (IIAM) using DArTseq SNPs. Methods: The generated 14,763 SNPs were filtered, retaining 11,502 high-quality SNPs for this study. Results: Overall genetic diversity was moderate (mean He = 0.30, Ho = 0.30, MAF = 0.21, PIC = 0.25). Population structure analysis using sparse non-negative matrix factorization identified eight subpopulations, consistent with principal component analysis implemented via the Latent factor mixed model. Discriminant analysis of principal components (DAPC) and Ward’s hierarchical clustering based on Nei’s distance resolved the same eight clusters, although DAPC revealed overlap among clusters, consistent with extensive admixture. Analysis of molecular variance showed that 85.85% of total molecular variation was within subpopulations and 14.15% among the subpopulations. Pairwise fixation indices (ranging from 0.02 to 0.10) identified divergent subpopulations 7 and 1 as suitable candidates for hybridization. Within subpopulations, observed heterozygosity exceeded expected heterozygosity, likely reflecting residual heterozygosity in sesame landraces, admixture, reverse Wahlund effect and scoring of paralogs as heterozygous SNPs. Conclusions: Overall, this study provided insights into sesame’s genetic diversity in Mozambique, contributing to germplasm conservation and informed parental selection. Full article

Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid for which the genetic basis of fruit appearance traits has not been comprehensively elucidated. This study investigated the genetic architecture of fruit color and morphological traits using integrated digital phenotyping and genome-wide association analysis of a core collection of diverse strawberry germplasm maintained for Korean breeding programs. A 108-accession core collection was assembled, genotyped, and phenotyped for 12 fruit quality traits. Population structure analysis identified K = 10 genetic clusters, and a Mantel test confirmed significant genotype–phenotype correspondence (r = 0.38, p < 0.001). Genome-wide association studies (GWAS) using BLINK and MLMM identified 15 significant marker–trait associations across six traits. Pleiotropic loci on chromosomes 15 (4C) and 22 (6B) were consistently associated with fruit lightness (L*) and red channel intensity (R) in both models, and the 6B locus explained approximately 18% of the phenotypic variance for each trait. Gene Ontology enrichment implicated transcriptional regulation, SUMOylation, and plastid-to-chromoplast transition, suggesting that the identified loci influenced fruit coloration through cellular regulatory mechanisms rather than direct pigment biosynthesis. These findings provide a genomic foundation for dual-trait marker-assisted selection targeting light and vividly red fruits for strawberry breeding. Full article

This scientometric review examines the evolution and scope of invasive (blood and tissue) and non-invasive (faeces, hair, and saliva) sampling in terrestrial mammal population genetics, with particular emphasis on the comparability of observed heterozygosity (Ho), expected heterozygosity (He), and the inbreeding coefficient (Fis) between studies published from 1985 to 2026. Searches in Web of Science and Scopus, filtered under PRISMA/PRISMA-S criteria, yielded a compendium of articles analysed with Bibliometrix and VOSviewer 1.6.20 to quantify temporal production, keyword evolution, collaborative networks, and publication outlets. Searches in Web of Science and Scopus, filtered under PRISMA/PRISMA-S criteria, yielded a broad corpus of 145 articles for general scientometric analyses, of which 85 met the eligibility criteria for the focused analysis of Ho, He, and Fis. The field shows steady growth (annual rate ≈ 6.1%), substantial authorship and international collaboration, and increasing thematic diversity. Adoption of non-invasive sampling has accelerated, broadening spatial and taxonomic coverage, but also increasing exposure to DNA degradation and genotyping error when laboratory quality control is insufficient. Across the literature, reporting of quality control practices (e.g., extraction blanks, negative PCR controls, multi-tube replication, and error-rate estimation) has improved over time but remains inconsistent. Comparisons indicate that differences in Ho, He, and Fis between invasive and non-invasive sampling are generally modest once marker system and species are taken into account. These findings indicate that quality control and transparency in reporting, rather than invasiveness per se, are the main factors determining comparability among studies. The scientometric patterns also reveal a methodological transition from microsatellites to SNP-based and reduced representation approaches, with implications for synthesis across marker types. Overall, this review identifies geographic and taxonomic biases in research effort and highlights the need for standardised reporting of DNA quality indicators, inclusion thresholds, and validation protocols to strengthen genetic monitoring in mammalian conservation. Full article