Search Results (1,533)

(1) Background: Centella asiatica (L.) is a long-lived medicinal plant traditionally recognized for its wound-healing and anti-inflammatory properties. Despite the growing demand for diverse C. asiatica species in Korea, studies on genetic diversity remain limited. (2) Methods: Genome assembly data of C. asiatica from the NCBI database were utilized to develop genomic SSR markers. Genetic diversity and population structure were examined in 30 Korean native C. asiatica accessions using 90 SSR markers. (3) Results: Whole-genome sequencing revealed 376,751 SSR loci, from which 127,528 primer pairs were designed. Among 160 randomly selected primers, 90 showed consistent amplification and displayed high levels of polymorphism. Genetic analyses revealed that the MAF ranged from 0.15 to 1.00 (mean 0.55), the NA ranged from 1 to 15 (mean 5.6), the Ho ranged from 0.00 to 1.00 (mean 0.17), and the PIC values ranged from 0.00 to 0.88 (mean 0.52). Clustering analysis with 90 SSR markers revealed three clusters, whereas population structure analysis indicated two populations among the C. asiatica accessions. Furthermore, two minimum marker sets with five marker combinations were identified and proved useful to differentiate all C. asiatica accessions. (4) Conclusions: The newly developed SSR markers for C. asiatica hold promise for facilitating research endeavors pertaining to variety identification, genetic mapping, and marker-assisted selection. Full article

Multiple sclerosis (MS) is a heterogeneous autoimmune disorder of the central nervous system of polygenic nature. Uncovering the genetic predictors of MS phenotype can help to explain the nature of the disease’s clinical heterogeneity, and contribute to the development of novel tools for precise disease prognosis. We conducted a retrospective genetic association study of 35 polymorphic variants in immune-related genes with MS severity assessed using the Multiple Sclerosis Severity Score (MSSS) in a sample of 548 Russian relapsing-onset MS patients who have not previously received immunomodulatory therapy. Variants in the CXCR5, EOMES, TNFRSF1A, IRF8, PVT1, CCR5, HLA-DRB1, IL6, TCF7, and CD40 genes were identified as MSSS-associated in at least two of the three models analyzed (MSSS > 3.5 versus ≤3.5; MSSS > 5.0 versus <2.5; MSSS as a continuous variable). Among them, variants in CCR5, HLA-DRB1 and IL6 genes were associated with MSSS only in women, while variants in the TCF7 and CD40 genes only in men. The variant in CXCR5 was MSSS-associated both in the total sample and in subgroups of female and male MS patients. Thus, we demonstrate that several GWAS-identified MS risk genes, along with other immunological loci, act as modifiers of the MS phenotype. Full article

Background/Objectives: Popcorn (Zea mays L. var. everta) is an important specialty maize type; however, the genetic variation underlying popping-related quality traits remains insufficiently characterized in breeding. Methods: In this study, 18 popcorn inbred lines were analyzed using 25 simple sequence repeat (SSR) markers distributed across all 10 maize chromosomes, and 16 lines were further evaluated for popping performance and image-based flake morphology. Results: Substantial phenotypic variation was observed among the tested lines, with expansion volume ranging from 173.33 to 343.33 mL and expandability ranging from 16.79- to 32.46-fold. Image-based analysis of 957 popped kernels revealed continuous variation in flake circularity, indicating that flake morphology represents a quantitative trait rather than a strictly discrete classification. SSR analysis detected 2 to 11 alleles per locus, with polymorphism information content values ranging from 0.05 to 0.85, indicating moderate-to-high genetic diversity among the tested lines. Principal component analysis (PCA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and population structure analysis revealed clear genetic differentiation and heterogeneous genetic backgrounds within the germplasm collection. Marker–trait association analysis identified several putative SSR loci associated with expansion efficiency, flake morphology, pericarp retention, and popping dynamics. Notably, marker M18 was putatively associated with both expansion volume and expandability. Conclusions: Based on these results, a conceptual framework was proposed in which popping-related traits were organized into partially independent but interconnected functional modules. Overall, this study provides SSR-based genetic information for popcorn germplasm characterization and offers preliminary marker resources for quality-oriented popcorn breeding. Full article

The active vitamin D metabolite, 1,25-dihydroxycholecalciferol [1,25(OH)₂D], exerts its biological effects through binding to the vitamin D receptor (VDR), a ligand-activated transcription factor regulating the expression of genes involved in calcium and phosphate homeostasis, immune modulation, and cell proliferation and differentiation. In addition to direct transcriptional regulation, 1,25(OH)₂D signaling also involves epigenetic mechanisms. A total of 90 studies were included in this narrative review, comprising experimental studies (n = 45), observational studies (n = 17), population-based studies (n = 8), interventional studies (n = 15), and mixed-design studies (n = 5). Experimental studies in cell cultures and animal models demonstrate that 1,25(OH)₂D may affect several major epigenetic regulatory pathways, including chromatin remodeling, DNA methylation, histone modifications, and the expression of non-coding RNAs, particularly microRNAs. Preclinical evidence suggests that the epigenetic actions of 1,25(OH)₂D are involved in metabolic regulation, immune responses, bone development, fibrotic processes, carcinogenesis, ageing, and fetal programming. However, evidence from observational studies and randomized controlled trials remains limited and inconclusive. Some studies have reported alterations in miRNA expression, methylation of selected loci, and epigenetic age markers. The clinical relevance of 1,25(OH)₂D–mediated epigenetic regulation has not yet been fully established. The interpretation of available findings is limited by substantial heterogeneity in study populations, exposure and intervention protocols, environmental factors, interindividual variability in response to vitamin D supplementation associated with genetic polymorphisms and methylation status, and the restricted range of analyzed cell types. This subject requires randomized controlled trials integrating molecular endpoints with clinically relevant outcomes. Full article

Background/Objectives: Inconsistency of results in genome-wide association studies (GWAS) has been a challenge for animal breeders and geneticists. Understanding how different training subset configurations influence genomic estimated breeding values (GEBVs) and GWAS is essential for optimizing genomic evaluations. This study aimed to evaluate the impact of training population partitioning and QTL architecture on prediction accuracy, GEBV and SNP-effect correlations, and on the consistency of GWAS. Methods: A simulated population consisting of ten breeding generations was partitioned and evaluated on four training scenarios: animal ID, sex, generations, and generation correct.blocks. Moreover, four distinct genetic architectures were simulated, representing combinations of two QTL counts (100 and 1000) and two effect-size distributions (normal and gamma). Phenotypes were available for 10,000 individuals, which were genotyped for 50,000 SNP markers. Results: Across generation blocks, accuracy increased from earlier to more recent generations. GEBV correlations were consistently higher than SNP-effect correlations across scenarios. Adjacent generation blocks showed stronger correlations than distant blocks. Architectures with 1000 QTL yielded higher accuracy than 100 QTL architectures, while effect distribution had limited influence. Manhattan plots showed stable major QTL peaks across subsets. However, reduced peak magnitudes with more noise signals were observed in smaller training sets. Training population size and genetic distance strongly influenced genomic prediction performance. GEBVs were more stable than individual SNP-effect estimates across training configurations. Conclusions: These findings provide insights for interpreting why GWAS results fluctuate more than breeding values due to limited dimensionality of genomic information. Full article

Common forms of migraine are complex disorders characterized by significant clinical diversity. Their genetic basis has been extensively studied but remains unclear. This study represents the first pilot genome-wide association study (GWAS) integrating a polygenic risk score (PRS) in the Portuguese population, designed to identify migraine susceptibility loci through a case–control study and unravel population-specific variants. Genotyping data was acquired with Applied Biosystems Axiom™ PMDA array, producing 12,035,248 single-nucleotide polymorphisms (SNPs) post-imputation, providing a comprehensive scope for GWAS analysis. PRS models were created and tested using a k-folds cross-validation framework and the optimal significance threshold was assessed. We detected 12 potential risk loci corresponding to 12 lead SNPs (RP11-204N11.2, CTA-481E9.4/CTA-481E9.3, RAP1A, TIGD4, CADPS2, RP11-46E17.6, RP4-569D19.5, RP11-398K14.1, PCBP1-AS1, TCF15, IL6R and UNC13A). The top three variants (RP11-204N11.2, CTA-481E9.4/CTA-481E9.3 and RAP1A) were also supported by the PRS model. We highlight that several variants present putative biological relevance to migraine pathophysiology, reinforcing the importance of neurotransmitter release, synaptic transmission and the involvement of vascular components in migraine pathophysiology. Full article

This study evaluated the genetic variability and traceability potential of farmed European sea bass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) populations from a fish farm located in Petrosino (Marsala, Sicily) (FAO 37), using microsatellite markers. A total of 64 D. labrax and 63 S. aurata individuals were genotyped with species-specific multiplex panels (9 and 10 loci, respectively). High levels of polymorphism were observed in both species, with an average of 12 alleles per locus in D. labrax and 9.1 alleles per locus in S. aurata. Mean observed heterozygosity (Ho) was 0.530 in D. labrax and 0.459 in S. aurata, while expected heterozygosity (He) reached 0.762 and 0.702, respectively. The fixation index (F) indicated moderate heterozygote deficiency in both populations (0.320 in D. labrax and 0.352 in S. aurata). Significant deviations from Hardy–Weinberg equilibrium were detected at most loci in both species, suggesting non-random mating, genetic drift, or population substructure. The probability of identity (PI) values across loci confirmed the high discriminatory power of the microsatellite panels, supporting their suitability for individual identification and genetic traceability applications in aquaculture. Overall, the results highlight that, despite substantial genetic variability, the observed heterozygote deficiency and deviations from equilibrium may reflect suboptimal breeding management practices. These findings underline the importance of implementing regular genetic monitoring and integrating molecular tools into broodstock management to maintain genetic diversity, reduce inbreeding, and support sustainable aquaculture production. Full article

Human leukocyte antigen (HLA) loci are highly polymorphic genome regions, with allele frequencies varying significantly across different populations. Population HLA frequency databases may contain biases and make cross-study comparison complicated due to varying data curation protocols, genotyping methodologies, resolution, and inconsistencies in the selection criteria for population samples. This study presents HLA allele frequencies of class I (HLA-A, -B, -C) and class II (HLA-DRB1, -DQB1, -DQA1), as well as their combined haplotypes obtained from over 18,000 whole genome sequencing samples of the Russian population. The cohort was stratified based on PCA and admixture components, providing frequencies for 14 different ethnic groups. For 12 groups cohort size allowed us to reach average saturation of 96% of allele frequencies in groups. Moreover, we demonstrated the utility of composed statistics for disease population study using type 1 diabetes (T1D) as an example. Genetically defined population clusters with similar aggregated genetic risk for T1D demonstrated substantial differences in frequencies of risk and protective HLA alleles. Obtained frequency data were made publicly available through the Allele Frequency Net Database improving previously sparse coverage in HLA frequencies data for the East Europe and North Asia regions. Full article

To investigate the association between polymorphisms in the GABRA5, SOX13, and AGL genes and growth traits in Dongfeng sika deer and to identify potential molecular markers for breeding, this study was conducted based on prior genome-wide association analysis. Based on the previous GWAS analysis of 266 Dongfeng sika deer, the SNP loci of GABRA5, SOX13, and AGL genes were detected in 36 male deer samples. The genetic parameters were calculated, and an association analysis with growth traits was carried out. Phenotypic analysis indicated that body weight and chest circumference had higher coefficients of variation than other growth traits, and body weight showed a strong positive correlation with body-slant length (r = 0.743, p < 0.01) and a moderate correlation with chest circumference (r = 0.709). A total of six SNP loci were identified, including three within GABRA5 (Chr13-8442730, Chr13-9033380, and Chr13-9045819), one within SOX13 (Chr14-5681678), and two within AGL (Chr20-66603370 and Chr20-66618510). The dominant genotypes at these loci include CG (CC), AA, CG, CC (CG), AA, and GG (GC). Linkage disequilibrium analysis revealed a relatively strong association between Chr13-8442730 and Chr13-903380 on chromosome 13. Combined genotype analysis showed that diplotype CCCGGC was associated with higher body weight and larger chest circumference than other genotype combinations. Gene expression analysis showed that the relative expression levels of GABRA5, SOX13, and AGL were lower in the low-growth group than in the high-growth group, and expression variation was also observed within groups. Overall, gene expression levels appeared to be positively associated with growth traits, with higher expression associated with improved growth performance. These findings suggest that GABRA5 and AGL may serve as candidate genes for further investigation and that the identified SNP loci may contribute to the development of molecular markers for the selection of growth traits in Dongfeng sika deer. The results provide a preliminary basis for molecular breeding and genetic improvement strategies in Dongfeng sika deer bucks and serve as an important reference for genetic improvement of growth traits in Cervidae. Full article

Background: Grain length is a key determinant of yield and quality in barley (Hordeum vulgare L.) and is typically governed by complex quantitative traits. Methods: In this study, a diverse natural population comprising 198 barley accessions was evaluated across two years to investigate the genetic basis of grain length. Results: Phenotypic analysis revealed continuous variation with near-normal distribution, indicating polygenic control. Genome-wide association study (GWAS) identified 84 stable single nucleotide polymorphism (SNP) loci significantly associated with grain length, predominantly enriched on chromosome 7. RNA sequencing (RNA-seq) was conducted using two contrasting genotypes at four developmental stages. Differentially expressed genes (DEGs) were mainly enriched in structural constituent of chromatin, protein heterodimerization activity, and the starch and sucrose metabolism. Integration of GWAS and RNA-seq identified 7 key candidate genes seven key candidate genes, including LOC123412467, LOC123408579, LOC123407599, LOC123410619, LOC123410954, LOC123411868, and LOC123426274. Sequence variation analysis further revealed functional polymorphisms, including non-synonymous mutations. The sequencing results show that LOC123412467 and LOC123410619 exhibited consistent allelic variation between long-grain and short-grain accessions, while LOC123426274 displayed stable differential expression across developmental stages, indicating their potential roles as key genes controlling grain length. Conclusions: Collectively, these findings suggest that chromosome 7 contains major regulatory loci controlling barley grain length and demonstrate that integrative multi-omics analysis is an effective strategy for identifying high-confidence candidate genes associated with complex agronomic traits. This study provides valuable insights into the genetic basis of grain length and offers key candidate genes for barley molecular breeding. Full article

Sophora tonkinensis Gagnep. is an important medicinal shrub native to the karst regions of southwestern China, where long-term overharvesting and habitat fragmentation have markedly reduced wild resources. Although recent phytochemical, transcriptomic, and chloroplast genomic studies have improved understanding of this species, its maternally inherited population structure has remained unclear. To address this gap, we developed nine novel chloroplast simple sequence repeat (cpSSR) markers and used them to genotype 274 individuals from eighteen wild populations. A total of 41 alleles were detected, with 2–10 alleles per locus, indicating moderate to high polymorphism at the species level. By combining the nine cpSSR loci, we further identified 25 chlorotypes, including 19 private chlorotypes. Within-population chloroplast diversity was generally low, and five populations were monomorphic, whereas HJSE and LYNG retained comparatively high chlorotype diversity. Genetic differentiation among populations was extremely strong (mean FST = 0.808), whereas historical gene flow was very limited (Nm = 0.112), and AMOVA showed that 85% of total chloroplast variation occurred among populations. Taken together, chlorotype network analysis, chlorotype geographic distribution, UPGMA, PCoA, and exploratory STRUCTURE analysis supported three geographically structured chloroplast groups, indicating long-term restriction of seed-mediated dispersal across the fragmented karst landscape. These newly developed cpSSR markers and the derived chlorotype framework provide a practical basis for tracing maternal lineages, prioritizing conservation units, guiding ex situ germplasm sampling, and informing future breeding of this nationally protected species. Overall, the present results describe chloroplast-based maternal structure rather than total genome-wide diversity in S. tonkinensis. 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

Stem lodging significantly reduces soybean yield stability, particularly under dense planting and intercropping systems. Stem breaking strength is a key component of lodging resistance, but its genetic basis remains incompletely understood. In this study, an F₂ population consisting of 167 individuals derived from a cross between nanxiadou25 (NXD25, high stem breaking strength) and Shiyuehuang (SYH, low stem breaking strength) was analyzed using bulked segregant analysis with whole-genome resequencing (BSA-Seq) to identify loci associated with stem breaking strength. The trait showed broad quantitative variation in the F₂ population, ranging from 20.1 to 673.7 N. Two extreme bulks were constructed using 30 plants with the highest values and 30 plants with the lowest values. QTL-seq detected 21 candidate intervals at the 95% confidence level, among which, three major loci on Chr07, Chr13, and Chr16 exceeded the 99% threshold and were designated qBR7.2, qBR13.1, and qBR16.1. By integrating large-effect SNP/InDel variation, marker development, RNA-seq profiling, and qRT-PCR validation, nine candidate genes were retained for further study, and three marker-linked genes were highlighted as high-priority candidates. RNA-seq identified 9617 differentially expressed genes between the two parents. In addition, three co-dominant InDel markers, Chr07_01, Chr13_17, and Chr16_83, showed phenotype-consistent polymorphism in extreme F₂ individuals. These findings provide valuable loci, candidate genes, and molecular markers for soybean lodging-resistance breeding. Full article

Recurrent pregnancy loss (RPL) is a multifactorial reproductive disorder with important genetic, endocrine, immune, and metabolic determinants. Growing evidence links vitamin D deficiency and vitamin D receptor (VDR) gene polymorphisms to pregnancy complications, including RPL. A narrative review was conducted via a literature search in major databases: PubMed, EMBASE, Scopus, and Web of Science from January 2010 to January 2026, which synthesized observational studies on maternal 25-hydroxyvitamin D [25(OH)D] status and/or VDR polymorphisms in RPL, with predefined eligibility criteria and qualitative risk-of-bias assessment. Most studies focused on FokI (rs2228570) and the 3′ regulatory block BsmI/ApaI/TaqI. FokI is the most extensively studied VDR variant in RPL and showed the most consistent directional association compared with other variants, particularly in Asian and Middle Eastern populations, though the effect varied by study design, ancestry, and covariate adjustment. Contrary to that, investigations of BsmI/ApaI/TaqI loci were not consistent due to ancestry-specific linkage disequilibrium (LD). Genotype and vitamin D interaction effects were scarcely studied, with stratified analyses indicating a more significant genotype effect under vitamin D deficiency. From clinical practice perspectives, VDR polymorphisms may explain why some patients with RPL have a poor response to standard vitamin D supplementation. Women with the FokI f allele polymorphism associated with lower VDR activity require higher vitamin D dosing or earlier immunomodulatory support to achieve adequate endometrial receptivity. VDR variation, particularly FokI, may contribute to RPL susceptibility within an endocrine–immune–metabolic framework. Clinical translation will require standardized RPL definitions, concurrent 25(OH)D assessment, robust control for confounders, and analytical models that account for gene–environment interactions. Full article

To assess the current genetic status of cultured populations of the speckled blue grouper (Epinephelus cyanopodus) in China and to provide a scientific basis for the selective breeding of superior strains, this study utilized single nucleotide polymorphism (SNP) loci screened via whole-genome resequencing technology to analyze the genetic diversity and population genetic structure of 90 E. cyanopodus samples collected from six cultured populations in southeastern China. Comprehensive evaluation of various genetic diversity parameters indicated that all populations exhibited moderate genetic diversity with minor differences among them. Population structure analysis revealed weak genetic differentiation among populations, suggesting that anthropogenic introduction and translocation practices may be the primary factors contributing to the unclear population genetic structure. Additionally, this study identified a number of key genes associated with energy metabolism, muscle development, and environmental adaptation. The findings provide important theoretical foundations for the broodstock selection and scientific aquaculture of E. cyanopodus. Full article