Search Results (894)

Background/Objectives: The Chinese dwarf cherry (Cerasus humilis) is an endemic shrub fruit tree species in China. Its fruit is flavorful, nutrient-rich, and has considerable research and utilization potential. However, most currently cultivated varieties of C. humilis are highly acidic and primarily used for processing. Consumer-preferred, low-acid, fresh-eating varieties are scarce, limiting industrial development. We used 208 F₁ individuals derived from a cross between high-acid “Nongda 4” and the low-acid “DS-1”. Methods: Restriction site-associated DNA sequencing (RAD-seq) was used to develop single-nucleotide polymorphism (SNP) markers and construct a high-density genetic linkage map. Using two years of fruit titratable acidity phenotypic data, quantitative trait locus (QTL) mapping and candidate gene screening were performed. Results: The genetic map contained 2491 SNP markers, assigned to eight linkage groups. The total genetic distance was 672.71 cm, with an average distance of 0.27 cm between markers, indicating high map quality. QTL mapping identified 18 loci associated with fruit titratable acidity, including 11 major-effect QTLs (logarithm of odds, LOD ≥ 3.5). These major-effect QTLs were concentrated on linkage groups LG2 and LG5, with an explained phenotypic variation of 8.6–31.13%. Two candidate genes were identified within QTL intervals: phosphoester phosphatase and MATE transmembrane transporter. The phosphatase gene’s expression showed a strong correlation with titratable acid content (p < 0.01, correlation coefficient 0.93), suggesting that it plays an important role regulating fruit acidity in C. humilis. Conclusions: This study supports marker-assisted breeding of low-acid, fresh-eating varieties, aiding commercial promotion of C. humilis. Full article

To identify molecular markers associated with wool traits in fine-wool sheep, we examined genetic polymorphisms in the NOTCH2 and CD1A genes in 944 Subo Merino sheep in this study. Subsequently, we performed association analyses between mutation sites in the NOTCH2 and CD1A genes and wool traits using SAS 9.4 software, followed by linkage disequilibrium (LD) analysis of different mutation sites using Haploview 4.2 software. Additionally, bioinformatics tools were employed to predict the potential impacts of missense mutations on protein secondary and tertiary structures. Finally, quantitative PCR (qPCR) was used to assess the expression levels of the NOTCH2 and CD1A genes. Genetic analysis revealed six polymorphic sites in NOTCH2 and CD1A, all of which were missense mutations. Two SNPs in NOTCH2 (SNP1 and SNP2) showed significant associations with the coefficient of variation of fibre diameter, and SNP1 was also associated with greasy fleece weight. Four SNPs in CD1A (SNP3–SNP6) were significantly associated with fibre diameter standard deviation, and SNP3, SNP4, and SNP5 were additionally associated with crimp number. LD analysis revealed that SNP3, SNP4, and SNP5 were closely linked. Bioinformatics analysis indicated that the mutations caused alterations in the secondary and tertiary structures of the NOTCH2 and CD1A proteins. qPCR results showed that the CD1A gene was highly expressed in the fine wool fibre group compared with the ultra-fine wool fibre group. In conclusion, this study revealed a genetic association between NOTCH2 and CD1A and wool traits. The results are expected to provide a theoretical foundation for breeding wool traits in Subo Merino sheep, thereby enhancing the economic value of fine wool. Full article

Biological invasions threaten biodiversity worldwide. The American blue crab Callinectes sapidus Rathbun, 1896, among the Mediterranean’s most damaging invaders, takes up the challenge to transform this threat into gain. To turn its impact into economic value and guide control efforts, we analysed separately the meat composition and exoskeleton biopolymers of adult crabs from three Moroccan protected Sites of Biological and Ecological Interest: Marchica Lagoon (S₁), Moulouya Estuary (S₂), and Al Hoceima National Park (S₃). Marchica specimens exhibited the highest protein content (21.87 ± 1.15 g 100 g⁻¹, p < 0.001) and an elevated lipid fraction, yielding nutrient-dense meat suitable for premium markets. Moulouya crabs were noted for their taste potential, with a higher concentration of fat (1.73 ± 0.09%) and carbohydrates (0.91 ± 0.1%). Al Hoceima individuals displayed markedly mineralised exoskeletons producing lean and low-fat meat, valued in dietary applications. Exoskeleton organic-to-mineral (OM/MM) ratios and proximate composition revealed three adaptive profiles, opportunistic (S₁), acclimatory (S₂), and conservative (S₃), presumably correlated to local salinity, productivity, and substrate conditions, underscoring the species’ phenotypic plasticity. X-ray diffraction confirmed the α-chitin polymorph, while FTIR analysis indicated degrees of deacetylation consistent with high-purity chitosan. These findings support the development of a site-specific circular economy framework and may contribute to the ecological resilience of Morocco’s protected coastal areas. Full article

Background/Objectives: The diagnosis of melanocytic lesions on the trunk is challenging due to a high frequency of atypical features in benign nevi, leading to a high rate of unnecessary excisions. This study aimed to identify robust dermoscopic predictors of cutaneous melanoma on the trunk and to evaluate a novel diagnostic criterion: the orientation of lesions relative to Langer’s skin tension lines. Methods: We conducted a retrospective analysis of 321 melanocytic lesions (227 nevi and 94 melanomas) excised from the trunk. Dermoscopic features were systematically evaluated. A chi-square test and an age- and sex-adjusted multivariate logistic regression were performed to calculate odds ratios (OR) and identify independent predictors of malignancy. A subgroup analysis was also conducted on “critical” versus “non-critical” anatomical sites. Results: Non-adherence to Langer’s lines was the most powerful predictor of melanoma (OR 5.55, 95% CI 3.22–9.81; p < 0.001). Other significant predictors included blue-white veil (OR 5.09) and polymorphous vessels (OR 4.06). Notably, 70% of melanomas did not align with Langer’s lines, whereas 72% of nevi did. Classic features such as scar-like regression were not statistically significant predictors in this cohort. In the subgroup analysis, color asymmetry was a significant predictor of melanoma only in non-critical sites (p for interaction = 0.026). Conclusions: The orientation of a melanocytic lesion relative to Langer’s lines is a powerful and independent predictor of melanoma on the trunk. This simple morphological feature, which may reflect differences in growth patterns between malignant and benign lesions, could serve as an additional clinical cue to support decision-making and improve diagnostic accuracy in this challenging anatomical location. Full article

Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC I plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and dN/dS analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC I polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand. Full article

Malaria persists as a paradigmatic model of co-evolutionary complexity, emerging from the dynamic interplay among a human host, Anopheles vectors, and Plasmodium falciparum parasites. In human populations, centuries of selective pressures have sculpted an intricate and heterogeneous immunogenetic landscape. Classical adaptations, such as hemoglobinopathies, are complemented by a diverse array of genetic polymorphisms that modulate innate and adaptive immune responses. These genetic traits, along with the acquisition of functional immunity following repeated exposures, mitigate disease severity but are continually challenged by the parasite’s highly evolved mechanisms of antigenic variation and immunomodulation. Such host adaptations underscore an evolutionary arms race that perpetually shapes the clinical and epidemiological outcomes. Intermediaries in malaria transmission have evolved robust responses to both natural and anthropogenic pressures. Their vector competence is governed by complex polygenic traits that affect physiological barriers and immune responses during parasite development. Recent studies reveal that these mosquitoes exhibit rapid behavioral and biochemical adaptations, including shifts in host-seeking behavior and the evolution of insecticide resistance. Mechanisms such as enhanced metabolic detoxification and target site insensitivity have emerged in response to the widespread use of insecticides, thereby eroding the efficacy of conventional interventions like insecticide-treated bed nets and indoor residual spraying. These adaptations not only sustain transmission dynamics in intervention saturated landscapes but also challenge current vector control paradigms, necessitating the development of innovative, integrated management strategies. At the molecular level, P. falciparum exemplifies evolutionary ingenuity through extensive genomic streamlining and metabolic reconfiguration. Its compact genome, a result of strategic gene loss and pruning, is optimized for an obligate parasitic lifestyle. The repurposing of the apicoplast for critical anabolic functions including fatty acid, isoprenoid, and haem biosynthesis highlights the parasite’s ability to exploit host derived nutrients efficiently. Moreover, the rapid accumulation of mutations, coupled with an elaborate repertoire for antigenic switching and epigenetic regulation, not only facilitates immune escape but also accelerates the emergence of antimalarial drug resistance. Advanced high throughput sequencing and functional genomics have begun to elucidate the metabolic epigenetic nexus that governs virulence gene expression and antigenic diversity in P. falciparum. By integrating insights from molecular biology, genomics, and evolutionary ecology, this study delineates the multifaceted co-adaptive dynamics that render malaria a recalcitrant global health threat. Our findings provide critical insights into the molecular arms race at the heart of host–pathogen vector interactions and underscore promising avenues for the development of next generation therapeutic and vector management strategies aimed at sustainable malaria elimination. Full article

Fat volume and obesity-related genes (e.g., the FTO gene) are important candidate genes affecting energy metabolism. Single nucleotide polymorphisms (SNPs) in the FTO gene are associated with carcass, growth and meat quality traits of pigs, cattle, sheep, rabbits and ducks. The purpose of this study was to detect the single nucleotide polymorphisms in the chicken FTO gene coding region by DNA sequencing and analyze its association with the carcass and growth traits of Heying black chickens. We detected polymorphisms in exons 5, 7, 8 and 9, respectively, g.57337C>A, g.64757T>G, g.97213G>A and g.220985G>A, which are synonymous mutations. g.57337C>A mutation site CA and AA genotype individuals were significantly higher than CC genotype individuals in live weights, head weights, breast muscle weights and leg muscle weights (p < 0.05), AA genotype individuals were significantly higher than CC genotype individuals in slaughter live weights and liver weights (p < 0.05) and CA and AA genotype individuals were significantly higher than CC genotype individuals in heart weights (p < 0.01). In terms of growth traits, the weights of individuals with genotype CA at 8 weeks were significantly higher than that of individuals with genotype CC (p < 0.05), and the weights of individuals with genotype AA and CA at 10 weeks and 16 weeks were significantly higher than that of individuals with genotype CC (p < 0.05). For the g.64757T > G mutation, individuals with the TT genotype exhibited significantly higher values (p < 0.05) than those with the TG genotype across multiple traits, including slaughter weight, live weight, eviscerated weight and semi-eviscerated weight. Individuals with GG genotypes were significantly higher than individuals with TG genotypes (p < 0.05) in slaughter weights and wing weights. In terms of growth traits, the 16-week-old body weight of individuals with TT genotype was significantly higher than that of individuals with TG genotype (p < 0.01). The GA genotype exhibited significantly higher slaughter weights in the g.97213G>A variant compared to the GG genotype (p < 0.01), and in live weights, eviscerated weights, semi-eviscerated weights, leg muscle weights and wing weights, GA genotype was significantly higher than in GG genotype (p < 0.05). In terms of growth traits, GA genotype was significantly higher in individuals 8 weeks old, 10 weeks old and 16 weeks old than GG genotype (p < 0.05). g.220985G>A was significantly higher in individuals with GG genotype than GA genotype (p < 0.05). In terms of growth traits, the weight of GG genotype was significantly higher than that of GA genotype (p < 0.05). The results showed that the FTO gene may be a candidate gene related to chicken growth and slaughter traits and lays a foundation for Heying black chicken assisted breeding. Full article

The Xinglong buffalo is a local swamp buffalo breed adapted to tropical regions in China. To facilitate the protection and utilization of valuable genetic resources, we first developed the breed-specific single nucleotide polymorphism (SNP) liquid-phase chip based on genotyping-by-target-sequencing (GBTS) technology. Whole-genome resequencing data from 143 buffaloes, resulting in 34,757,694 SNPs, were used to identify 1208 breed-specific and 2889 background sites. This chip also incorporates 965 functional SNP sites derived from literature, including SNPs significantly associated with immunity, reproduction, growth, and production. A total of 5062 SNP sites were successfully identified for the development of a 5K liquid-phase genome-wide breeding chip for the Xinglong buffalo. The validation of the chip using 93 samples showed a high detection rate with good repeatability and consistency. In addition, the chip exhibits strong capabilities in clustering and kinship analysis. Results of kinship analysis underscored the importance of a breed-specific chip for the Xinglong buffalo. These results highlight the advantages of a low-density, cost-effective, and breed-specific SNP chip for accurate genotyping. This chip will support future endeavors in molecular breeding, conservation, and genetic evaluation of Xinglong buffalo, thereby facilitating the sustainable utilization of this valuable indigenous germplasm resource. Full article

Brain-derived neurotrophic factor (BDNF) plays a crucial role in cognitive functions and dementia. In individuals with mild cognitive impairment (MCI) and dementia, we have investigated BDNF Val66Met genotype distribution, peripheral BDNF DNA methylation, mRNA and protein levels, and cognitive performance using the Mini-Mental State Examination (MMSE) and Clock Drawing Test (CDT). Lower BDNF_IV1 methylation had predictive value for dementia. Patients with mild-to-moderate dementia had lower levels of BDNF_IV2 methylation, whereas patients with severe dementia had higher levels than the MCI group, while BDNF_IV2 methylation positively correlated with CDT scores. An insignificant decline in BDNF mRNA levels in dementia patients positively correlated with significantly lower BDNF plasma levels, especially pronounced in severe dementia patients. BDNF mRNA and protein levels were positively correlated with CDT and MMSE scores, respectively. BDNF Val66Met polymorphism was associated with methylation of the BDNF_IX amplicon, but not with methylation in BDNF promoters I and IV, peripheral BDNF gene and protein expression, MMSE and CDT scores, or dementia. Methylation at the BDNF Val66Met site was positively correlated with overall BDNF_IX methylation and methylation at 5 BDNF_IX CpG loci but negatively correlated with methylation of BDNF_IV1, BDNF_IV3, and BDNF_I1 amplicons. Further studies should evaluate the translational potential of these peripheral BDNF-based biomarkers for dementia. Full article

Fatty acid binding proteins FABP3 and FABP4 act as intracellular lipid chaperones that influence fatty acid transport and metabolism in mammary tissue, and genetic variation in these genes may affect milk composition. We examined the associations between FABP3 and FABP4 polymorphisms and milk composition and fatty acid profiles in 200 lactating Native Southern Yellow (NSY) cows. DNA from each cow was PCR-amplified and Sanger-sequenced for FABP3 and FABP4; genotypes were tested for their association with milk fatty acid concentrations and standard composition traits using linear models adjusted for relevant covariates. We detected a missense variant in FABP3 (c.3656G > A; p.Val45Met) and an intronic SNP in FABP4 (g.3509T > C). The FABP3 p.Val45Met AA genotype was associated with higher concentrations of butyric, palmitic, oleic, and α-linolenic acids. Cows with the FABP4 TC genotype exhibited elevated levels of myristoleic, γ-linolenic, conjugated linoleic, and arachidic acids, along with increased fat-free dry matter, protein, and lactose. In silico analyses provided mixed evidence for the structural effects of p.Val45Met, molecular docking suggested altered ligand affinity for several fatty acids, and splice site prediction implicated g.3509T > C in possible transcript processing changes. These variants constitute candidate markers for milk fatty acid composition in NSY cattle; replication in independent cohorts and functional validation are recommended to confirm their utility for milk quality improvement. Full article

This study investigated interspecific and intraspecific polymorphism in Rheum (Polygonaceae) from Kazakhstan using the inter-primer binding site (iPBS) retrotransposon marker system. The results revealed considerable variation in the level and nature of genetic polymorphism both within and among Rheum species and ecopopulations across different regions of Kazakhstan. Rh. compactum and the ecopopulation Rh. tataricum from the Zhambyl Region (ZH) exhibited the lowest levels of polymorphism, supporting their designation as conservation priorities. Genetic differentiation analysis among species and ecopopulations identified clear distinctions, resulting in the formation of well-defined clusters with high bootstrap support. Minimal genetic distances were observed between the two ecopopulations of Rh. tataricum, along with a high degree of intraspecific genetic homogeneity in Rh. compactum and Rh. nanum. A distinct genetic divergence between Rh. compactum and the other taxa was detected, reinforcing its status as a separate species rather than a synonym of Rh. altaicum. The iPBS markers proved effective for investigating genetic variation in Rheum, offering valuable insights for future studies aimed at understanding the evolutionary history of the genus. Full article

Enhancing the failure tolerance ability of networks is crucial, as node or link failures are common occurrences on-site. The current fault tolerance schemes are divided into reactive and proactive schemes. The reactive scheme requires detection and repair after the failure occurs, which may lead to long-term network interruptions. The proactive scheme can reduce recovery time through preset backup paths, but requires additional resources. Aiming at the problems of long recovery time or high overhead of the current failure tolerance schemes, the Polymorphic Network adopts field-definable network baseline technology, which can support diversified addressing and routing capabilities, making it possible to implement a more complex and efficient failure tolerance scheme. Inspired by this, we propose an efficient Multi-topology Failure Tolerance mechanism in Polymorphic Network (MFT-PN). The MFT-PN embeds a failure recovery function into the packet processing logic by leveraging the full programmable characteristics of the network element, improving failure recovery efficiency. The backup path information is pushed into the header of the failed packet to reduce the flow table storage overhead. Meanwhile, MFT-PN introduces the concept of multi-topology routing by constructing multiple logical topologies, with each topology adopting different failure recovery strategies. Then, we design a multi-topology loop-free link backup algorithm to calculate the backup path for each topology, providing extensive coverage for different failure scenarios. Experimental results show that compared with the existing strategies, MFT-PN can reduce resource overhead by over 72% and the packet loss rate by over 59%, as well as effectively cope with multiple failure scenarios. Full article

The Atlas cedar Cedrus atlantica is a relict and endemic conifer from Morocco and Algeria, although plantations may be found in several locations aside from its natural range. Recurrent droughts have been widely related to Atlas cedar dieback, growth decline, and mortality, but the genetic basis of potential adaptive capacity is unknown. We used the double digest restriction-site associated DNA sequencing technique (ddRAD-seq) to describe the genetic structure and variability of Atlas cedar along an aridity gradient in Morocco. Furthermore, we investigated the potential genetic origin of three Spanish plantations, also along an aridity gradient. The obtained single nucleotide polymorphisms (SNPs) were used to perform genotype–environment associations (GEAs) to define SNPs related to bioclimatic variables of temperature and precipitation. The vulnerability of this species to environmental variations was also estimated by its risk of non-adaptedness (RONA). Population structure showed a divergence between the Moroccan natural stands and some of the Spanish plantations, with each Moroccan nucleus being genetically distinct. The genetic variability was significantly lower in plantations than in natural populations. The drier Spanish plantations (easternmost) were genetically very similar to the driest Moroccan population (southernmost), suggesting that as its origin. A total of 41 loci under selection were obtained with the Moroccan dataset. In relation to temperature and precipitation variables, isothermality showed the highest number of associated loci (10) in GEA studies, and genotype–phenotype associations (GPAs) showed one locus associated with the Specific Leaf Area. RONA value was higher in the southernmost High Atlas population, where rising temperature was the main driver of expected genetic offset by allele frequency changes under the worst emissions scenario. In contrast, Spanish plantations would need smaller genetic changes to cope with the expected climate change. Likely gene flow from southern to northern areas suggests a latitudinal heading, where Spanish plantations might operate as an assisted migration. Moreover, one locus showed a northern/southern pattern in saplings but not in adults, suggesting a potential latitudinal pattern of selection. Our results are discussed on the basis of their management and conservation. Full article

European black pine (Pinus nigra Arn. subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbour genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci being polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece. Full article

In this study, 944 Subo Merino sheep, a high-quality fine wool breed, were selected as research subjects. The SNP typing of the FAT3 gene was performed using the Fluidigm BiomarkTM HD system, and 11 missense mutation sites were identified. The analysis of population polymorphism of single-nucleotide polymorphisms was conducted. It is noteworthy that a substantial strong linkage disequilibrium was identified between SNP 5 and SNP 6 (r² > 0.8). The association between SNPs of the FAT3 gene and wool traits showed that multiple SNPs were significantly correlated with several different wool traits (p < 0.05). Furthermore, the investigation delved into the impact of the FAT3 gene on wool fiber through the utilization of quantitative polymerase chain reaction (qPCR), which yielded findings that this gene was notably expressed in fine wool fiber (FW) (p < 0.001). To predict the subcellular localization and protein transmembrane structure of FAT3, we employed the PSORT II Prediction and TMHMM online software. It was determined that the protein contains a transmembrane domain. This study provides molecular markers for the improvement of the selection and breeding of ultrafine-wool sheep and offers experimental evidence for accelerating the genetic breeding of sheep. Full article