Search Results (1,721)

Topmouth culter (Culter alburnus) is one of the most economically important freshwater fish in China, but intensive aquaculture has caused germplasm degradation and reduced growth performance, while the genetic basis underlying growth variation in this species remains poorly understood. This study aimed to identify major-effect loci and candidate genes associated with growth-related traits to support molecular breeding. Whole-genome resequencing (average depth 11.44×) was performed on 300 individuals derived from random mating among three geographic populations (Danjiangkou, Taihu, and Poyang Lake); 239 individuals with complete phenotypic records were retained for a genome-wide association study (GWAS) of five growth-related traits, including body weight (BW), body weight without viscera (BWW), total length (TL), body length (BL), and body height (BH). After stringent filtering, 7,597,008 high-quality single-nucleotide polymorphisms (SNPs) were obtained, and association analysis was conducted using a linear mixed model, followed by Benjamini–Hochberg false discovery rate correction and 1000-permutation testing for BW and BL. Six genome-wide significant SNPs and 473 suggestive SNPs were identified, with individual significant SNPs explaining over 11% of phenotypic variance, indicating candidate loci of putatively moderate-to-large effect. Significant SNPs were predominantly clustered on chromosomes 16 and 19. Four candidate genes—aig1, cacna1b, pgm5, and bcr—were identified, with functions related to lipid metabolism, muscle structure, and cell proliferation. This first population-level GWAS in topmouth culter provides valuable molecular markers for marker-assisted selection and lays a foundation for accelerated genetic improvement of this species. Full article

CLEC3B (C-type lectin domain family 3 member B), also known as tetranectin (TN), is a secreted trimeric protein containing a C-type lectin-like domain (CTLD). Located on chromosome 3p21.31. CLEC3B maintains organismal homeostasis through roles in immune regulation, angiogenesis, and musculoskeletal biology. Genetic studies demonstrate that CLEC3B deficiency impairs tissue repair, bone mineralization, and fibrinolytic balance. Altered CLEC3B expression is linked to cardiovascular disease progression, autoimmune susceptibility, and cancer prognosis. This review synthesizes CLEC3B’s biological functions and evaluates its translational potential: circulating CLEC3B as a prognostic and diagnostic biomarker; tissue-resident CLEC3B as a predictive marker for therapeutic response; and CLEC3B-related pathways as candidate therapeutic targets for potential amenable to replacement or inhibition strategies. We identify critical research gaps to guide future investigations, including limited structural data, ambiguous glycan specificity, incomplete proteolytic network mapping, and lack of validated disease models. Collectively, these gaps currently preclude definitive therapeutic claims. Full article

Background/Objectives: Y chromosome microdeletions in the azoospermia factor (AZF) regions are a major genetic cause of severe male infertility, yet their relationship with hormonal profiles in azoospermic men remains unclear. This study aimed to investigate AZF microdeletions and associated hormonal parameters in azoospermic patients. Methods: Azoospermic patients were screened for AZFa, AZFb, and AZFc microdeletions using multiplex real-time PCR targeting sequence-tagged site (STS) markers (sY84, sY127, and sY254). Patients were categorized into AZF-negative and AZF-positive groups, with the latter further stratified according to their deletion subtype. Serum follicle-stimulating hormone (FSH), testosterone, and inhibin B levels were measured. Hormonal parameters were compared between groups using the Mann–Whitney U test, and a logistic regression analysis was performed to evaluate associations between hormonal variables and AZF deletion status. Results: AZF microdeletions were detected in 18.7% (17/91) of patients. Patients without AZF deletions showed a median FSH level of 17.40 (7.12–31.27) IU/L. In contrast, AZFc deletion carriers exhibited an intermediate median FSH level of 21.10 (16.11–26.10) IU/L and lower median inhibin B concentrations (25.50 [25.25–26.00] pg/mL) compared with AZF-negative patients (56.00 [33.50–106.50] pg/mL). Median testosterone levels in AZFc patients (3.61 [2.87–4.35] ng/mL) remained within the expected physiological range. However, no statistically significant differences were observed between the AZF subgroups for age (p = 0.262), FSH (p = 0.506), testosterone (p = 0.615), or inhibin B (p = 0.524). The logistic regression analysis also showed no significant association between hormonal parameters and AZF deletion status. Conclusions: Hormonal parameters alone are insufficient to predict the presence of AZF microdeletions in azoospermic men. These findings highlight the importance of routine genetic screening for accurate diagnosis, clinical management, and reproductive counseling in male infertility. Full article

Background/Objectives: Sex estimation is a cornerstone of research and practice in bioarchaeology and forensic anthropology. However, morphological and metric methods are often hampered by population-specific variation, subjectivity in assessment, and taphonomy. This study compares morphological analysis and ancient DNA (aDNA)-based sex assessment in a 19th-century Portuguese sample to evaluate the accuracy of osteological (anthropological) criteria. Methods: This study analysed 37 skeletons from the Venerável Ordem Terceira da Nossa Senhora do Carmo burial grounds in Porto. Sex estimation was based on (1) the bioanthropological assessment of morphological traits of the os coxae and the skull (2) through aDNA analysis using a multi-marker approach, including real-time PCR (qPCR) targeting autosomal loci, the amelogenin locus, a Y-chromosomal INDEL, and Y-STRs. aDNA was extracted via a non-destructive protocol. Results: Whilst anthropological analysis was possible on all 37 individuals, estimation of sex through aDNA analysis was possible for 26 individuals. A 20% discordance rate was found between morphological and aDNA results. Many individuals morphologically classified as “possible female” or “indeterminate” were genetically identified as male. Genetic analysis resolved most cases that biological anthropologists concluded were “indeterminate”. Conclusions: The high discordance in the Carmo sub-sample may indicate reduced skeletal sexual dimorphism, with males exhibiting skeletal traits typically associated with females, suggesting a sample-specific reduction in sexual dimorphism likely influenced by environmental, nutritional, and/or genetic stressors. A limitation of this study is its small sample size: only 26 of 37 individuals yielded usable genetic results, and only a portion of these individuals provided sufficient data for a direct comparison between morphological and genetic data. Nevertheless, these findings highlight the risk that applying generalised osteological standards relying solely on morphology can lead to systematic misclassification, emphasising the need for a critical, multidisciplinary approach to sex estimation. Full article

The einkorn wheat group, comprising ancient diploid species (2n = 14, AA), including Triticum monococcum, Triticum boeoticum, and Triticum urartu, represents a valuable source of genetic variation for improving disease resistance in wheat. To develop a practical platform for introgressing powdery mildew resistance into bread wheat, we screened 21 einkorn accessions with Blumeria graminis f. sp. tritici (Bgt) race E09 and identified seven resistant donors. Because direct hybridization between diploid einkorn (AA) and hexaploid wheat (AABBDD) is constrained by genomic divergence and poor cross-compatibility, we crossed resistant einkorn accessions with susceptible durum wheat and induced chromosome doubling in the F₁ hybrids to generate synthetic durum–einkorn amphiploids. Nine amphiploids were obtained. Chromosome counts and genomic in situ hybridization confirmed the expected genomic constitution (AABBAA) in most lines, with limited variation in chromosome number in two amphiploids. Phenotyping against Bgt race E09 showed that three amphiploids retained high resistance, four showed moderate resistance, and two were moderately susceptible. Marker analysis identified five einkorn accessions contain known Pm genes such as Pm60, Pm60b, and PmNCA6/Pm37, as well as their derived amphipliods. Two einkorn accessions and their derived amphiploids may harbor novel Pm genes. Field evaluation of the agronomic traits of these amphiploids indicated some improvement in tillering, spike length, and seed weight. Moreover, these amphiploids had better seed-setting rates in crosses and backcrosses with common wheat. These synthetic durum–einkorn amphiploids thus offer a new bridging platform for transferring alien genes from diploid einkorn to hexaploid common wheat, providing valuable genetic resources for wheat-breeding programs. Full article

Soil salinity is a major constraint on global wheat productivity, yet the genetic and molecular determinants of root system architecture (RSA) adaptation under salt stress remain poorly characterized. We integrated a genome-wide association study (GWAS) of 566 wheat accessions with comparative RNA-seq transcriptomics to identify the genetic and transcriptional determinants of RSA adaptation under 200 mM NaCl. GWAS identified a candidate locus on chromosome 7B harboring TaIAO, which encodes a protein with predicted aldehyde oxidase-like activity consistent with a role in tryptophan-dependent auxin biosynthesis. Accessions carrying the favorable CC allele exhibited significantly greater root volume retention than those carrying the GG genotype (p < 0.001). Comparative RNA-seq revealed that the salt-tolerant Sarajevo 1 exhibited coordinated transcriptional repression of three distinct modules—cell wall expansion (TaExpansin), auxin redistribution (TaPIN-like), and stress-associated ROS defense (TaPOD1)—whereas the sensitive genotype CI 17260 aberrantly induced or incompletely repressed these modules under stress. ELISA-based IAA quantification, ROS imaging, and qRT-PCR analysis provided independent physiological and transcriptional support for these patterns. These findings support a two-tier adaptive model in which constitutive genetic variation at the TaIAO locus may contribute to a developmental baseline, coupled with coordinated stress-responsive transcriptional repression of energy-consuming modules, providing promising targets for marker-assisted breeding of salt-tolerant wheat. Full article

Climate change is intensifying soil salinization, posing a major threat to crop establishment and productivity, particularly in arid and semi-arid regions. Barley (Hordeum vulgare L.), one of the most salt-tolerant cereals, offers valuable genetic resources for improving salinity resilience at early growth stages. This study exploited the genetic diversity of the Nested Association Mapping (NAM) population Halle Exotic Barley-25 (HEB-25) to dissect salinity tolerance during germination and seedling developmental stages. First, the HEB-25 parental lines (25 wild barley genotypes and cv. Barke) were evaluated under salinity treatment to identify contrasting responses. Based on this screening, four HEB families (01, 04, 09, and 22) were selected out of 25 HEB families for detailed phenotypic and genomic analysis. Seeds of the selected HEB families were subjected to 40% seawater salinity stress and control treatments to assess germination percentage and seedling traits, including shoot length, root length, fresh weight (FW), dry weight (DW), DW/FW ratio, root–shoot ratio, and salt tolerance index (STI). Substantial variation was observed among families for all measured traits under salinity stress. STI values enabled clear differentiation among families: Family 01 exhibited the most consistent overall tolerance profile, Family 22 showed the strongest sensitivity in biomass traits, and Family 04 displayed a trait-specific response with sensitivity at the family-mean level but exceptional within-family diversity, harboring some of the highest individual TI values across the population. A genome-wide association study was conducted using 32,995 SNP markers. A total of 27 significant SNPs were identified, corresponding to 20 quantitative trait loci (QTLs). Of these, 12 QTLs were detected under control conditions, 16 under seawater treatment, and 21 based on tolerance indices, indicating both constitutive and stress-responsive genetic effects. Gene annotation within these regions revealed approximately 23 candidate genes associated with abiotic stress tolerance, including genes involved in ion transport, osmotic adjustment, kinases and stress signaling pathways. HEB_22_003, HEB_04_087, and HEB_01_013 represent the most promising genotypes for salinity breeding. These findings highlight the effectiveness of combining precise phenotyping with high-resolution genomic analysis in the HEB-25 population to uncover the genetic architecture of salinity tolerance at early developmental stages. We identified 20 salinity-responsive QTLs, including five major-effect loci on chromosomes 2H, 4H, 5H, and 7H that consistently explained the largest share of phenotypic variation. These loci co-localized with candidate genes linked to ion homeostasis, Ca²⁺-mediated signaling, protein glycosylation, epigenetic regulation, and root system plasticity, revealing key mechanisms underlying early-stage salt adaptation in barley. The strong and contrasting responses of Family 01 and Family 04 provide an excellent genetic framework for functional validation of tolerance alleles. Collectively, these genomic resources establish a robust foundation for QTL pyramiding, marker-assisted breeding, and the development of climate-resilient barley cultivars for saline agroecosystems. Full article

Indigenous goat populations are valuable genetic resources for livestock production in arid and semi-arid environments, yet many remain insufficiently characterized at the phenotypic and genomic levels. This study investigated phenotypic variation and genome-wide associations in two local Ardi goat lines in Bahrain: Ardi Bahraini and Ardi Mu’atar, the latter being distinguished by a characteristic facial marking pattern. A total of 280 goats were phenotypically characterized for qualitative traits and body measurements, and 76 animals were genotyped using the Illumina Caprine 60K single nucleotide polymorphism (SNP) BeadChip. After quality control, 49,716 autosomal SNPs were retained for genome-wide association analysis. Phenotypic analysis showed that the two lines differed significantly in body weight, body length, hip height, face width, tail length, ear width, and tail circumference, while discriminant analysis identified tail length, ear width, tail circumference, and facial patterns differentiating the lines. Principal component analysis (PCA) showed partial genomic clustering of the two lines, and genome-wide significant and suggestive SNPs based on Bonferroni and false discovery rate (FDR) thresholds on chromosomes 6, 13, 14, and 29. The strongest association was observed for rs268277393 on chromosome 13, located near DOK5 (Docking Protein 5) and TRNAC-GCA (transfer RNA cysteine, anticodon GCA), and was associated with the Ardi Mu’atar facial pattern. Additional candidate regions were located near genes with possible roles in pigmentation, development, or morphological variation. These findings provide preliminary genomic evidence supporting the phenotypic distinctiveness of Ardi Mu’atar goats and identify candidate markers that may contribute to future conservation and breeding programs. Further validation in larger populations and functional studies will be required to confirm the biological role of these candidate regions. Full article

Objectives: Noninvasive prenatal testing relies on the analysis of total cell-free DNA (cfDNA) in maternal plasma, where fetal-derived DNA constitutes only a minor fraction. This study aimed to preliminarily compare a modified TPY cfDNA extraction protocol with two commercial extraction kits for the downstream detection of Y-chromosome-specific markers in pregnancies carrying male fetuses. Methods: Plasma samples were obtained from 52 singleton pregnancies between 10 and 30 weeks of gestation with male fetal sex confirmed by ultrasonography. Total cfDNA was extracted from aliquots of the same maternal plasma samples using the modified TPY protocol, the QIAamp DSP Virus Kit, and the MagMAX™ Cell-Free DNA Isolation Kit. Quantitative real-time PCR was performed for the Y-chromosome-specific markers SRY and DYS14. At the same time, GLO was used as a reference marker to reflect the total cfDNA background. Extraction performance was assessed primarily using total cfDNA concentration and Ct values obtained from amplification of fetal-specific Y-chromosome markers. Results: Total cfDNA concentrations varied among the extraction methods, with the commercial kits yielding higher total cfDNA concentrations than the modified TPY protocol. In contrast, the TPY protocol yielded slightly lower mean Ct values for SRY and DYS14 than the commercial kits. SRY and DYS14 amplification was detected in 90.4% and 94.2% of samples, respectively. However, these Ct differences should be interpreted cautiously because fetal fraction, maternal DNA contamination, extraction recovery, and fragment size distribution were not directly measured. Conclusions: The modified TPY protocol showed preliminary technical feasibility for extracting total cfDNA from maternal plasma and enabling downstream amplification of Y-chromosome-specific markers in male pregnancies. Nevertheless, the observed lower Ct values do not establish selective fetal DNA enrichment, reduced maternal DNA contamination, or clinical superiority over commercial methods. Further analytical validation using standardized fetal fraction measurement, recovery efficiency testing, fragment size analysis, fetal-to-maternal DNA ratio assessment, and larger cohorts including both male and female pregnancies is required before broader clinical applicability can be determined. Full article

Background: Extrachromosomal DNA (ecDNA) amplification represents a distinct mechanism of genomic instability in cancer, increasingly recognized for its role in aggressive disease progression. This review examines how ecDNA drives tumour evolution and assesses its potential as both a prognostic marker and therapeutic target. Methods: The authors integrate findings from multiple detection platforms—including FISH, whole-genome sequencing, and specialized reconstruction algorithms—and present data across diverse cancer types; no preregistration is noted, and no animal studies are included. Results: ecDNA consists of circular, acentric DNA elements carrying high-copy oncogene amplifications (such as EGFR, MYC, MDM2, and CDK4). Unlike chromosomal DNA, ecDNA segregates unevenly during cell division, generating intratumoral heterogeneity, accelerating adaptation to selective pressures, and promoting resistance to therapy. Pan-cancer surveys summarized here reveal ecDNA in a significant subset of tumours, with particularly high frequencies in liposarcoma, glioblastoma, and HER2-positive breast cancer, and consistent associations with worse clinical outcomes. Conclusions: The authors conclude that ecDNA amplification serves as a credible adverse prognostic indicator and holds promise for refining risk stratification and guiding treatment strategies. However, they stress that clinical adoption remains constrained by the absence of standardized, scalable, and reproducible detection. 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

Hybridization between sugarcane (Saccharum spp.) and its wild relative Erianthus rockii offers a promising route to broadening the narrow genetic base of modern cultivars, but the authenticity and chromosome inheritance patterns of such hybrids remain poorly understood. In this study, we combined molecular marker (tetra-primer ARMS-PCR) and cytogenetic (genomic in situ hybridization, GISH) approaches to verify hybridity and track chromosome transmission in 24 F₁ and 12 BC₁ progeny. The F₁ hybrids exhibited a strict n + n transmission pattern, receiving exactly 15 chromosomes from E. rockii. When F₁ plants were used as the male parent in backcrosses, no BC₁ seeds were obtained due to complete pollen sterility. Remarkably, when F₁ plants served as the female parent, all 12 BC₁ clones retained the entire set of 15 E. rockii chromosomes intact, following an unconventional 2n + n pattern. These findings reveal a strong parent-of-origin effect and, for the first time, demonstrate that the whole E. rockii chromosome complement can be stably transmitted into backcross progeny without loss or recombination. This opens a direct route for introgressing complete wild genomes into sugarcane breeding lines, preserving complex polygenic traits and guiding rational crossing strategies. Full article

Early and late leaf spot (ELS and LLS), caused by Passalora arachidicola and Nothopassalora personata, are major constraints to peanut (Arachis hypogaea L.) production. Durable resistance in cultivated germplasm remains limited due to the crop’s narrow genetic base. Wild Arachis species represent an important but underutilized source of resistance. This study aimed to identify and prioritize wild introgressions associated with foliar disease resistance in advanced peanut backcross lines derived from the induced allotetraploid BatSten1 (Arachis batizocoi × A. stenosperma)^4x. A population of advanced backcross lines carrying reduced wild genome content (~5% to ~1% across advancement) was evaluated through four years of field trials for LLS severity and yield, complemented by detached-leaf bioassays to dissect resistance components for both ELS and LLS. Genome-wide SNP genotyping, combined with mixed-model analysis and association mapping, identified introgressed regions influencing disease response. Genome-wide association studies (GWAS) detected loci on chromosomes A06 and A09 associated with LLS resistance, explaining approximately 25% and 11% of phenotypic variation, respectively, with evidence of additive effects between loci. Component-level analyses further revealed both resistance- and susceptibility-associated introgressions. Although tomato spotted wilt virus (TSWV) incidence was evaluated in field trials, exploratory GWAS did not detect significant marker–trait associations, indicating that genetic components associated with this trait were not resolved under the conditions tested. Overall, these results expand the understanding of the genetic architecture of leaf spot resistance beyond traditional donor sources and provide a framework for prioritizing beneficial wild introgressions while minimizing linkage drag in peanut pre-breeding programs. Full article

The genetic architecture of wheat yield-related traits is complex due to their polygenic control, relatively low heritability, and strong genotype–environment interactions. Commonly used characteristics of wheat productivity include thousand-grain weight (TGW), grain weight per ear (GWE), and grain number per ear (GNE). To identify stable loci associated with productivity-related traits in common wheat, we performed QTL analysis using two mapping populations derived from crosses between contrasting cultivars. The populations were phenotyped for GNE, GWE, and TGW over two years. In addition, GWAS was conducted using a cultivar panel phenotyped for yield and GWE over ten years, and for GNE, GWE, and TGW over two years. The most reproducible loci were located on chromosomes 2D, 4A, 5A, 5B, 6A, 6B, and 7A. From these regions, 16 SNPs were selected for KASP marker development. Validation in an independent panel of 296 spring common wheat varieties phenotyped over three years identified three most informative markers: wsnp_Ex_c16175_24619793 (4A), wsnp_Ex_c2171_4072995 (5A), and BS00034554_51 (6B), all consistently associated with TGW and additionally associated with GWE, GNE, or yield in individual years. These markers may be useful for marker-assisted selection of wheat productivity-related traits. 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