Search Results (961)

Domestic donkeys (Equus africanus asinus) are an important livestock genetic resource that is currently considered at risk. The number of donkey breeds worldwide is declining due to their loss of function as working animals in rural communities. Local breeds with small populations, which are threatened by genetic erosion and are at risk of extinction, require urgent action to characterize and preserve their genetic diversity. As microarrays containing thousands of single-nucleotide polymorphisms (SNPs) are not yet available for these species, traditional molecular markers such as microsatellites and mitochondrial DNA (mtDNA) remain valuable tools for genetic monitoring and management. This study uses different molecular markers to assess and manage genetic variability in endangered Sicilian donkey breeds. This information can support breeding plans and mating schemes, as well as in situ and ex situ conservation programs. The practical application of molecular information in the conservation strategies for these breeds is briefly discussed, and the proposed approach is considered transferable to other threatened breeds. Full article

Modern olive breeding points to a plant model characterized by low vigour, high productivity, and resistance to biotic and abiotic stresses, all traits required by the intensive and superhigh-density (SHD) systems of olive tree growing. The Italian Don Carlo and FS-17 Favolosa stand out among the new cultivars that are being tested. They were obtained not by breeding but by mass selection from two seedling populations of the Frantoio cultivar (maternal parent). Here, a multidisciplinary approach was used to determine the paternal parent of Don Carlo and FS-17, and then to investigate the inheritance of interesting traits such as fruit cell dimensions and oil content in these cultivars. Microsatellites were applied in phylogeny and kinship analyses, along with two functional markers previously developed on OeACP1 and OeACP2 genes. Ascolana Tenera cultivar was identified as the paternal parent of both new cultivars. This result was also supported by the analysis of the self-incompatibility group of the new cultivars and their most likely paternal parents. Light and electron microscopy [Cryo Scanning Electronic Microscopy (CRYO-SEM), Electronic Scanning Microscopy (E-SEM), and Transmission Electron Microscope (TEM)] techniques were used to analyze the fruit development concerning oil accumulation. Significant differences in cuticle thickness, size and shape of mesocarp and exocarp cells, and oil content were detected among cultivars. Our results suggested that the rearrangement of the traits studied led to an improved progeny compared to the parents. FS-17 exhibited an oil storage efficiency higher than Frantoio. Don Carlo showed fruit traits and oil content almost intermediate between the parents, making it a dual-purpose cultivar. Full article

Conservation and characterization of germplasm collections are essential for safeguarding agrobiodiversity and supporting breeding programs. A collection of 140 accessions comprising three different Pistacia species, P. integerrima, P. terebinthus, and P. vera, was analyzed using 27 EST-SSR markers. On average, 3.4 alleles per locus, and 28.2% rare alleles were found. Observed heterozygosity (Ho = 0.36) was lower than expected (He = 0.48), while five loci displayed PIC values above 0.50, highlighting their high informativeness. The phylogenetic analysis clearly separated the three species. Among P. vera samples, Nj tree and population structure analysis identified three main sub-groups: Eastern Mediterranean/Middle Eastern accessions, Italian traditional cultivars, and US modern cultivars. The first group showed higher internal variability, reflecting both local diversification and historical genetic exchanges. Through the use of EST-SSR markers, the present study assesses the genetic diversity within the Pistacia collection while highlighting errors due to mislabeling issues. These results confirm the effectiveness of microsatellite markers to provide a framework for the management and exploitation of genetic diversity for breeding and conservation strategies, also in the Pistacia genus. Full article

The genetic diversity and population structure of Tunisian Arabian horses were assessed using highly polymorphic microsatellite markers, which are critical for conservation and breeding programs. Despite the cultural and economic importance of Arabian horses in Tunisia, molecular data supporting their management remain limited. In this study, DNA from 130 horses was genotyped with 17 ISAG-FAO-recommended microsatellites to evaluate diversity within Eastern and Western Arabian lineages and their relationship to Thoroughbreds. Eastern Arabians showed an average of 5.176 alleles per locus, observed heterozygosity of 0.657, expected heterozygosity of 0.677, and a fixation index of 0.028, while Western Arabians displayed 5.941 alleles, heterozygosity values of 0.689 (Ho) and 0.688 (He), and a fixation index of −0.006. Genetic differentiation was low between Eastern and Western Arabians (0.011) but moderate between Eastern Arabians and Thoroughbreds (0.071), with high gene flow within Arabian subpopulations (0.950). Principal component analysis confirmed distinct subpopulations. These findings highlight high genetic diversity in Western Arabians and variable heterozygosity in Eastern Arabians, providing a molecular basis for targeted breeding strategies to preserve genetic traits, control inbreeding, and ensure the long-term sustainability of Tunisian Arabian horse populations. Full article

Rumex crispus L. is a globally distributed invasive species that has naturalized in South Korea, where its use as a medicinal, edible, and ecological restoration resource continues to expand. However, its genetic background remains insufficiently understood, underscoring the need for species-specific molecular markers to enable accurate assessments of intraspecific genetic diversity and population structure. Using 19 newly developed microsatellite markers, we analyzed 120 plants from 6 populations in the riparian zone. A total of 166 alleles were detected, with a mean polymorphism information content of 0.637. Across the six populations, genetic diversity analysis showed mean observed (Ho = 0.304) and expected (He = 0.588) heterozygosity values indicative of heterozygote deficiency (inbreeding coefficient F_IS = 0.456–0.559). Genetic differentiation was low in AMOVA (10%) and F_ST (0.048–0.120) but higher in Jost’s D (0.096–0.342). STRUCTURE analysis identified two major genetic clusters (ΔK = 2), and spatial Bayesian clustering revealed six distinct genetic units (K = 6), suggesting that partial barriers to gene flow may have influenced population structure. These findings provide essential genetic insights that can support the effective control of R. crispus spread and its potential use as a valuable plant resource. Full article

Helichrysum italicum (Roth) G. Don (Asteraceae) is a valuable medicinal and aromatic plant native to a variety of habitats across the Mediterranean region. However, genetic studies of this morphologically diverse species have been limited by the scarcity of species-specific DNA markers. To address this limitation, we generated the first de novo transcriptome assembly comprising 24,806 transcripts from young shoots containing leaves and flowers, developed EST-SSR markers, and evaluated their utility in population genetic analysis. Seventy-eight primer pairs were designed, of which 23 showed successful amplification, polymorphism, and transferability to Helichrysum litoreum Guss. and Helichrysum arenarium (L.) Moench. A subset of 12 EST-SSRs was used to genotype 270 individuals from 12 natural populations of H. italicum in Corsica (France), along with one outgroup population from Croatia. The polymorphic information content ranged from 0.250 to 0.796, and Shannon’s information index ranged from 0.588 to 1.843, indicating the markers’ suitability for population genetic studies. Analysis of molecular variance revealed that 15% of the total genetic variation was attributable to differences among populations. Discriminant analysis of principal components and Bayesian clustering in STRUCTURE identified distinct population clusters corresponding to geographic locations. Notably, the southernmost coastal populations were clearly differentiated from the others. Full article

Objectives: This study presents a comprehensive molecular investigation of Apis cerana cerana populations inhabiting the Lüliang Mountain region, aiming to evaluate their genetic diversity and population structure using polymorphic microsatellite and mitochondrial DNA (mtDNA) markers. Methods: A total of 23 microsatellite loci and three mtDNA fragments (COI–COII, COI, Cytb) were successfully amplified, of which 21 loci were polymorphic and used for subsequent genetic analyses. Measures of genetic variability, population differentiation, and molecular variance were computed to assess intra- and interpopulation diversity. Results: High levels of genetic variation were detected (mean PIC = 0.349), with observed heterozygosity (Ho = 0.827) exceeding expected heterozygosity (He = 0.608). Analysis of molecular variance (AMOVA) revealed that 95.28% of total genetic variation occurred within populations, while 4.72% was attributed to among-population differences. Mitochondrial analyses identified 20 polymorphic sites forming 19 haplotypes, with high haplotype (Hd = 0.884) and nucleotide diversity (π = 0.00157). Conclusions: These results indicate substantial gene flow and interpopulation connectivity among A. c. cerana populations in the Lüliang region. Collectively, the findings provide critical molecular evidence supporting the conservation and sustainable management of A. c. cerana genetic resources in this area. Full article

We studied Lycaena helle (Lepidoptera: Lycaenidae) population genetics in lowlands and mountains of East-Central Europe using the microsatellite markers previously applied in population studies mainly in mountains of Western Europe. As in the West, the East-Central populations are genetically diverse (mean expected/observed heterozygosity 0.67/0.49), affected by drift processes (mean inbreeding coefficient 0.277) and widely differentiated (mean F_ST 0.209). The Polish lowland populations, all of them bivoltine in contrast to mountain populations, are less differentiated than Romanian populations, which are bivoltine in low and univoltine in high altitudes. The lowland Romanian population Vad is extremely genetically impoverished. A transferred CZ population from Western Europe is impoverished relative to its donor population, but the genetic parameters remain within a range of other studied so far. Dendrogram of allelic frequencies suggests that the populations form two branches, one rooted in southeastern Poland and branching towards Carpathians in Romania, one encompassing populations in central and northern Poland. We conclude that the lowland Romanian populations, plus populations in unglaciated southeastern Poland, represent sites where the species survived the glacial cycles in situ, comprising rear edge of subsequent upslope expansion, while northern Poland was colonised from more easterly regions. Full article

Artificial crossbreeding is a critical strategy in the restoration of endangered freshwater fishes with small, fragmented populations, where natural spawning alone cannot reverse genetic erosion. This study examined the genetic diversity and fitness traits of crosses between genetically distant (HGD) and closely related (LGD) broodstock individuals of Pseudopungtungia nigra, an endangered Korean freshwater fish. Using ten microsatellite loci, we evaluated genetic diversity, population structure, and early survival performance among crossbreeds and their broodstock. Both HGD and LGD progenies showed deviations from Hardy–Weinberg equilibrium and exhibited higher observed heterozygosity than expected, indicating the influence of artificial selection. The broodstock and both crossbred groups displayed bottleneck signals, while LD-based effective population size was infinite for the broodstock and HGD but finite for LGD, suggesting estimation bias because the parameter was undeterminable due to small sample size (each group, n = 28–30). STRUCTURE and DAPC analyses revealed that HGD_20 was most genetically similar to the broodstock population, while LGD and HGD_19 formed distinct clusters. Hatching rate was 1.5-fold higher in HGD compared with LGD (p < 0.05), although survival did not differ significantly (p > 0.05). These results highlight that crossbreeding based on genetic distance can enhance genetic diversity and hatching performance without causing excessive genetic divergence from the parental population, offering a practical model for the genetic management of endangered fish restoration. Full article

Background: Colorectal cancer (CRC), particularly the microsatellite-stable (MSS) subtype, remains largely unresponsive to immune checkpoint inhibitors (ICIs) due to immune escape, tumor-associated macrophage (TAM) enrichment, and cytokine-driven suppression that sustain a TAM-dominant tumor microenvironment (TME). To overcome these barriers, a pH-responsive solid lipid nanoparticle (SLN) system was engineered to co-deliver CB-5083 (a VCP/p97 inhibitor), miR-142 (a PD-L1-targeting microRNA), and imiquimod (R, a TLR7 agonist) for spatially confined induction of endoplasmic reticulum stress (ERS) and immune reprogramming in MSS CRC. Methods: The SLNs were coated with PEG–PGA for pH-triggered de-shielding and functionalized with PD-L1- and EGFR-binding peptides plus an ER-homing peptide, enabling tumor-selective and subcellular targeting. Results: The nanoplatform displayed acid-triggered PEG–PGA detachment, selective CRC/TAM uptake, and ER localization. CB-mediated VCP inhibition activated IRE1α/XBP1s/LC3II, PERK/eIF2α/ATF4/CHOP, and JNK/Beclin signaling, driving apoptosis and autophagy, while miR-142 suppressed PD-L1 expression and epithelial–mesenchymal transition markers. R facilitated dendritic cell maturation and M1 polarization. Combined CB + miR + R/SLN-CSW suppressed IL-17, G-CSF, and CXCL1, increased infiltration of CD4⁺ and CD8⁺ T cells, reduced Tregs and M2-TAMs, and inhibited tumor growth in CT-26 bearing mice. The treatment induced immunogenic cell death, reprogramming the TME into a T cell-permissive state and conferring resistance to tumor rechallenge. Biodistribution analysis confirmed tumor-preferential accumulation with minimal off-target exposure, and biosafety profiling demonstrated low systemic toxicity. Conclusions: This TME-responsive nanoplatform therefore integrates ERS induction, checkpoint modulation, and cytokine suppression to overcome immune exclusion in MSS CRC, representing a clinically translatable strategy for chemo-immunotherapy in immune-refractory tumors. Full article

The complex life cycle, high reproductive potential and ability to quickly develop resistance to insecticides are key factors contributing to the destructiveness of the peach–potato aphid (Myzus persicae Sulzer) among pest species. Monitoring its population dynamics at a large scale allows us to better understand M. persicae biology and take relevant measures for pest management. For this purpose, reliable molecular tools are needed. Based on the analysis of 128,362 microsatellite loci, we developed four multiplex assays including 49 comprehensively characterised SSR markers. Internal validation confirmed the species specificity and low genotyping error (e_a = 0.8%, e_l = 0.99%, e_obs = 22.7%) of the assays. A total of 194 alleles were identified (mean = 4 alleles per locus, range = 2–8 alleles per locus) within a group of 365 aphid accessions collected in the Vysočina region (Czechia). The studied aphid population showed the typical characteristics expected of the species with clonal or partially clonal reproduction (heterozygote excess, negative F_IS, moderate-to-high linkage disequilibrium (LD), and distortion of the H-W equilibrium for most of the loci), and did not exhibit any stratification on a spatiotemporal level. Owing to the high discriminatory power of the markers, we discovered that the population sample was founded upon a small number of fundatrices, as only five dominating lineages comprising over 70% of all accessions were identified. In conclusion, this study identified a significant number of new high-quality markers with the high discriminatory power necessary for revealing the population structure and dynamics of M. persicae, which holds considerable potential in both general biological and agricultural research. Full article

Fluconazole-resistant Candida parapsilosis has emerged as a significant nosocomial pathogen, contributing to extensive outbreaks with severe clinical implications. Despite increasing evidence of clonal transmission, the genetic mechanisms that facilitate the persistence of hospital reservoirs remain inadequately characterized. We aimed to characterise the long-term molecular epidemiology of fluconazole-resistant Candida parapsilosis bloodstream isolates (n = 47) collected between 1997 and 2019 at a tertiary centre. All isolates underwent microsatellite analysis using three polymorphic markers (CP1, CP4, B5). Genetic diversity, temporal distribution, and clonal relationships were assessed through phylogenetic analysis and discriminatory power calculations. Microsatellite analysis revealed minimal genetic diversity (combined discriminatory power: 0.7114), with only six distinct genotypes identified. Two dominant clones (Genotype-1: 23.4%, Genotype-2: 46.8%) persisted throughout the study, showing apparent spatiotemporal clustering in surgical and intensive care units. Phylogenetic analysis demonstrated tight genetic clustering, consistent with prolonged clonal persistence across multiple years and clinical departments. Our findings provide strong molecular evidence consistent with persistent, multi-year clonal transmission; however, definitive confirmation will require higher-resolution genomics and epidemiologic linkage. These results underscore the need to strengthen infection-control practices to curtail sustained clonal persistence within the hospital. Full article

Endometrial cancer (EC) is the most common gynecologic cancer. Early detection is one of the most important predictors of survival. The cancer is curable if detected early but the five-year survival rate in advanced cases can be as low as 22%. Microsatellite instability (MSI) testing is used to screen populations for Lynch Syndrome (LS), the most common cause of inherited EC, and to classify EC into distinct groups with unique histological, prognostic, and molecular features. Accurate sample identification is crucial for successful MSI testing because instability is assessed by comparing amplification patterns in markers in the normal and tumor samples that must be taken from the same individual. Penta-C and Penta-D pentanucleotide markers are used widely for sample identification in not only MSI testing but also parentage verification, forensic science, and population genetics studies. The objective of this study was to test 324 pairs of tumor and matched normal DNAs from EC patients for instability in these markers using the Promega MSI Analysis System^TM considered the “gold standard” in MSI testing. Both markers were unstable, and therefore not reliable for MSI testing, in 8.2% of the EC patients with MSI. Instability in both mono- and pentanucleotide markers suggest that the tumors with MSI likely suffer from a “generalized” form of instability also affecting other short tandem repeats. Results from many studies using these markers for various purposes may not be accurate if samples with MSI are involved. Full article

Only about 5% of colorectal cancers are hereditary, which is due to the low carrier rate of pathogenic gene mutations. The typical pattern of these cases is intergenerational aggregation within families and early onset. But public awareness of early diagnosis and intervention of HCRC is insufficient, resulting in most patients being diagnosed only after developing cancer, thereby missing the optimal window for treatment. This article reviews the latest developments in precision screening, treatment, evaluation and prevention strategies for HCRC, including innovative uses of artificial intelligence (AI) in molecular diagnostics, imaging technology advances, and potential application prospects. Regarding precision screening, tests of genomics, transcriptomics, microbiome, etc., combined with personalised risk stratification, can, respectively, effectively detect pathogenic mutations and “cancer-promoting” intestinal environments in the preclinical stage. AI combined with endoscopic and imaging tools has improved the accuracy of polyp detection and tumor profiling. Liquid biopsy and molecular marker detection provide new non-invasive monitoring solutions. In precision treatment, beyond traditional approaches like surgery and chemotherapy, immunotherapy with checkpoint inhibitors may be considered for HCRC patients with mismatch repair deficiency (dMMR). For patients harboring somatic mutations such as KRAS or BRAF V600E, targeted therapy can be guided by these specific mutations. Regarding precision assessment, AI incorporates microsatellite instability (MSI) detection and imaging diagnostic techniques, crucial for integrating genetic, environmental, and lifestyle data in follow-up. This helps assess the risk of recurrence and adjust the long-term medication regimens, as well as provide effective nutritional support and psychological counselling. In summary, the rapid development of precision medicine is driving the clinical management of HCRC into the era of tailored care, aiming to optimise patient outcomes. Full article

Background: Early-onset colorectal cancer (EOCRC), defined as diagnosis before the age of 50, is rising rapidly and disproportionately affects high-risk populations, particularly Hispanic/Latino (H/L) individuals, who experience the steepest increases in incidence and mortality. While prevention and screening strategies have curbed late-onset CRC rates, EOCRC remains outside standard screening guidelines and is projected to become the leading cause of cancer-related death in individuals aged 20–49 by 2030. FOLFOX (folinic acid, fluorouracil, and oxaliplatin) is a standard first-line therapy for microsatellite stable (MSS) CRC lacking actionable driver mutations; however, its efficacy and genomic impact in EOCRC, particularly in underrepresented groups, remain poorly understood. The phosphatidylinositol 3-kinase (PI3K) pathway regulates cell growth, survival, and metabolism, and its alterations have been implicated in therapeutic resistance and adverse outcomes. Yet, the prevalence, clinical relevance, and treatment-specific associations of PI3K pathway alterations in EOCRC remain underexplored. Methods: We analyzed somatic mutation and clinical data from 2515 CRC patients (266 H/L and 2249 Non-Hispanic White [NHW]) across publicly available genomic datasets. Patients were stratified by age at diagnosis (EOCRC < 50 vs. LOCRC ≥ 50), ancestry (H/L vs. NHW), and FOLFOX treatment status. PI3K pathway alterations—including mutations in PIK3CA, PTEN, AKT isoforms, and regulatory genes—were identified using curated pathway definitions. Mutation prevalence was compared across groups using Fisher’s exact or chi-squared tests. AI-HOPE-PI3K, a conversational AI platform, was deployed to automate cohort construction, stratify subgroups, and perform post hoc survival analysis. Results: PI3K pathway alterations were observed across all demographic groups. In EO NHW patients treated with FOLFOX, Kaplan–Meier analysis revealed significantly reduced overall survival among those with PI3K pathway alterations (n = 124) compared with their unaltered counterparts (n = 251; p = 0.0008), identifying alterations as a candidate prognostic biomarker in this subgroup. AI-guided subgroup interrogation further highlighted mutation-specific signals: INPP4B and RPTOR emerged as exploratory candidates in EO H/L patients but did not show significant treatment- or ancestry-specific enrichment upon confirmatory testing. Similarly, ancestry-stratified analysis of PIK3R2 mutations revealed comparable rates in EO H/L (1.37%) and EO NHW (1.6%) FOLFOX-treated patients (p = 1.0). Across ancestry and age groups, mutational landscape analysis revealed diverse molecular events—including missense, nonsense, splice-site, frameshift, and in-frame deletions—underscoring the heterogeneity of PI3K pathway dysregulation. Conclusions: This study identifies PI3K pathway alterations as a potential prognostic marker of poor survival in EO NHW patients receiving FOLFOX and uncovers ancestry- and treatment-specific mutational differences in high-risk CRC populations. By integrating clinical, molecular, and treatment variables, the AI-HOPE and AI-HOPE-PI3K platforms enabled rapid, reproducible, and fine-grained analysis of complex datasets. These findings underscore the need for ancestry-informed molecular profiling to optimize therapeutic strategies and highlight AI-guided interrogation as a powerful tool for advancing precision oncology in underrepresented and disproportionately affected CRC populations. Full article