DNA Analysis Research Articles

P-505 Clinical rescue rate of abnormally fertilized oocytes and the relationship with patient, embryo and laboratory features

Abstract Study question Which are the main patient, embryonic and laboratory variables associated with a diploid result in abnormally fertilized embryos? Summary answer Embryo diploid constitution is associated with maternal age, trophectoderm and inner cell mass quality as well as pronuclear (PN) number predicted by time-lapse incubator. What is known already In conventional in vitro fertilization cycles, morphological PN evaluation can identify proper fertilization and predict embryo ploidy constitution. Atypical PN patterns like 0PN, 1PN or more than 2PN are associated with ploidy abnormalities. However, we have previously shown that PN number is insufficient to predict embryo ploidy composition, and advanced single nucleotide polymorphism (SNP)-based methodologies for preimplantation genetic testing (PGT) detect a significant number of genetically diploid embryos from presumed abnormally fertilized oocytes. In this study, we characterized the diploid rescue rate associated with abnormal PN configurations, uncovering the link between ploidy results and relevant patient, embryonic and clinical/laboratory parameters. Study design, size, duration Retrospective observational study evaluating the association between diploid rescue rate of abnormally fertilized embryos and different patient, embryonic and laboratory features. Embryos were cultured in conventional or EmbryoScope™ time-lapse incubator (Vitrolife) until blastocyst stage and classified according to Gardner embryo grading system. Ploidy assessment was performed on 343 euploid trophectoderm (TE) biopsies collected between January 2021 and November 2023. Results were stratified according to patients age, embryo quality parameters and different laboratory procedures. Participants/materials, setting, methods Multi-center international study involving consenting patients using autologous gametes and undergoing PGT for aneuploidies (PGT-A) combined with ploidy analysis. Ploidy protocol was performed using a validated targeted NGS approach composed of a custom panel of 357 SNPs and a proprietary pipeline of analysis. Reliable ploidy classification was obtained using a combined algorithm strategy based on SNPs allele frequencies. Categorical variables were expressed in percentages. Nominal variables were analysed using the Cochran-Armitage test to detect trends. Main results and the role of chance Among 343 euploid embryos, diploidy rates obtained for 0PN, 1PN, 2.1PN and 3PN groups were 86.8% (n = 118/136;95%CI=79.89-91.96) 43.7% (n = 59/135;95%CI=35.19-52.50), 65.0% (n = 13/20;95%CI=40.78-84.61) and 26.9% (n = 14/52;95%CI=15.57-41.02) respectively. Regarding patient parameters, advanced maternal age, but not paternal age, was significantly associated with lower diploid rescue rates, with a decreasing trend from 72.5% (n = 79/109;95%CI=63.10-80.60) below age 35 to 42.9% (n = 30/70;95%CI=31.09-55.25) above age 40 (p < 0.01). When considering embryo morphological evaluations, Cochran Armitage test revealed a significant link between diploidy rates and TE quality with a decreasing trend going from 72.1% (n = 80/111;95%CI=62.76-80.17) to 52.7% (n = 79/150;95%CI=44.36-60.87) and 45.8% (n = 22/48;95%CI=31.37-60.83) for embryos classified with TE grade as A, B, and C, respectively (p-value<0.01). Similarly, a decreasing trend was reported in relation to inner cell mass (ICM) quality, when moving from grade A (67,1%, n = 94/140;95%CI=58.23-75.33) to grade C (54.8%, n = 17/31;95%CI=36.03-72.68) (p = 0.03). No clear association was reported for embryo expansion degree. Finally, among laboratory variables (oocyte freezing procedure, fertilization method, incubator type), only time-lapse significantly impacted expected diploid results. Overall, if abnormal PN number is confirmed by time-lapse (n = 42 samples), the accuracy in predicting ploidy abnormalities increased from 29.2% (n = 82/281;95%CI=23.93-34.87), in conventional incubators, to 83.3% (n = 35/42;95%CI=68.64-93.03) (p < 0.01). Consequently, expected diploid rescue rate decreased from 65.5% (n = 184/281;95%CI=59.60-71.03) to 16.7% (n = 7/42;95%CI=6.97-31.36) (p < 0.01). Limitations, reasons for caution Parental DNA analysis should be included to rule-out the residual risk of uniparental disomy in diploid embryos. The multi-center nature of the study didn’t support a uniform PN annotation, especially for centers lacking time-lapse observation. Future studies should focus on the clinical follow-up after the transfer of rescued euploid-diploid embryos. Wider implications of the findings We believe we reported the first evidence of maternal age effect on ploidy results in the largest dataset of abnormally fertilized embryos. We revealed a link between ploidy constitution and blastocyst morphological quality, providing important information for patient counselling. Time-lapse incubators offer a more accurate identification of abnormally fertilized oocytes. Trial registration number n/a

Clinical Review of Juvenile Huntington's Disease.

Juvenile Huntington's disease (JHD) is rare. In the first decade of life speech difficulties, rigidity, and dystonia are common clinical motor symptoms, whereas onset in the second decade motor symptoms may sometimes resemble adult-onset Huntington's disease (AOHD). Cognitive decline is mostly detected by declining school performances. Behavioral symptoms in general do not differ from AOHD but may be confused with autism spectrum disorder or attention deficit hyperactivity disorder and lead to misdiagnosis and/or diagnostic delay. JHD specific features are epilepsy, ataxia, spasticity, pain, itching, and possibly liver steatosis. Disease progression of JHD is faster compared to AOHD and the disease duration is shorter, particularly in case of higher CAG repeat lengths. The diagnosis is based on clinical judgement in combination with a positive family history and/or DNA analysis after careful consideration. Repeat length in JHD is usually > 55 and caused by anticipation, usually via paternal transmission. There are no pharmacological and multidisciplinary guidelines for JHD treatment. Future perspectives for earlier diagnosis are better diagnostic markers such as qualitative MRI and neurofilament light in serum.

Epidemiological exploration of fleas and molecular identification of flea-borne viruses in Egyptian small ruminants

The study aimed to investigate molecularly the presence of flea-borne viruses in infested small ruminants with fleas. It was carried out in Egypt’s Northern West Coast (NWC) and South Sinai Governorate (SSG). Three specific primers were used targeting genes, ORF103 (for Capripoxvirus and Lumpy skin disease virus), NS3 (for Bluetongue virus), and Rdrp (for Coronavirus), followed by gene sequencing and phylogenetic analyses. The results revealed that 78.94% of sheep and 65.63% of goats were infested in the NWC area, whereas 49.76% of sheep and 77.8% of goats were infested in the SSG region. Sheep were preferable hosts for flea infestations (58.9%) to goats (41.1%) in the two studied areas. Sex and age of the animals had no effects on the infestation rate (p > 0.05). The season and site of infestation on animals were significantly different between the two areas (p < 0.05). Ctenocephalides felis predominated in NWC and Ctenocephalides canis in SSG, and males of both flea species were more prevalent than females. Molecular analysis of flea DNA revealed the presence of Capripoxvirus in all tested samples, while other viral infections were absent. Gene sequencing identified three isolates as sheeppox viruses, and one as goatpox virus. The findings suggest that Capripoxvirus is adapted to fleas and may be transmitted to animals through infestation. This underscores the need for ongoing surveillance of other pathogens in different regions of Egypt.

APEAch: Automated Pipeline for End-to-End Analysis of Epigenomic and Transcriptomic Data.

With the advent of next-generation sequencing (NGS), experimental techniques that capture the biological significance of DNA loci or RNA molecules have emerged as fundamental tools for studying the epigenome and transcriptional regulation on a genome-wide scale. The volume of the generated data and the underlying complexity regarding their analysis highlight the need for robust and easy-to-use computational analytic methods that can streamline the process and provide valuable biological insights. Our solution, aPEAch, is an automated pipeline that facilitates the end-to-end analysis of both DNA- and RNA-sequencing assays, including small RNA sequencing, from assessing the quality of the input sample files to answering meaningful biological questions by exploiting the rich information embedded in biological data. Our method is implemented in Python, based on a modular approach that enables users to choose the path and extent of the analysis and the representations of the results. The pipeline can process samples with single or multiple replicates in batches, allowing the ease of use and reproducibility of the analysis across all samples. aPEAch provides a variety of sample metrics such as quality control reports, fragment size distribution plots, and all intermediate output files, enabling the pipeline to be re-executed with different parameters or algorithms, along with the publication-ready visualization of the results. Furthermore, aPEAch seamlessly incorporates advanced unsupervised learning analyses by automating clustering optimization and visualization, thus providing invaluable insight into the underlying biological mechanisms.

Assessing bias in the causal role of HPV in oral cancer: Asystematic review and meta-analysis.

High-risk human papillomaviruses (HPV) are an established cause of oropharyngeal cancer. Their relationship with oral cancer remains unclear with detection ranging from 0% to 100%. HPV DNA detection or evidence of exposure alone is insufficient to conclude causality. This systematic review assesses the extent of bias in studies of HPV detection in cancers of the oral cavity. PubMed, Ovid MEDLINE, EMBASE, and PsycInfo databases were searched for observational studies reporting the effect of HPV in oral cavity specific cancers. All 15 included studies presented HPV DNA detection or serum HPV-antibodies, none included mRNA E6/E7 analysis. Cases with oral cancer had 5.36 times (95% CI 3.29-8.72) higher odds of having HPV detected compared to controls. The odds of HPV detection were higher in cell-based (OR 6.93; 95% CI 0.82-58.55) and tissue samples (OR 5.28; 95% CI 3.41-8.18) than blood-based samples (OR 3.36; 95% CI 1.53-7.40). When cancer site is clearly differentiated between oropharynx and oral cavity, 12 studies showed strong association between HPV and oral cancer, but the available estimates lack internal validity due to inconsistent measurements, high confounding, and lack of gold standard testing. There is not high-quality evidence to conclude a causal relationship of HPV with oral cancer.

Enhancing public health safety: Development and application of a MoS2@CNT-Chit electrochemical DNA biosensor for rapid and accurate detection of S. Typhi

This study introduces an advanced electrochemical biosensor that utilizes MoS2@CNT as an electrode material combined with a specific DNA probe to detect Salmonella Typhi rapidly and accurately. The sensor offers a broad detection range from 1.0 × 10−6 to 1.0 × 10−18 molL−1 and boasts an exceptionally low limit of detection (LOD) of 1.0 × 10−20 molL−1 for the target bacterium. It demonstrates a detection range from 1.0 × 104 to 1.0 × 1011 CFUml−1 in real samples, with a corresponding LOD of 1.0 × 104 CFUml−1. Rigorous testing against base mismatches and various bacterial strains confirms its specificity, ensuring reliable performance. Validated in real samples, the biosensor can accurately identify Salmonella Typhi in water and milk, achieving recoveries ranging from 92.95 % to 99.58 %. The exceptional performance of the biosensor is attributed to the MoS2@CNT electrode material and the specific DNA recognition probe, which enhance electron transfer and reduce steric impedance. These improvements contribute to the sensor's enhanced sensitivity and specificity, making it a significant advancement in public health safety by providing a rapid and accurate tool for detecting Salmonella Typhi in food samples.

History, status and genetic characteristics of native cattle breeds from the Republic of Kazakhstan.

This work provides a comprehensive review of the history, status, and genetic characteristics of cattle breeds in Kazakhstan. The current breeding status is analysed, including information on popular breeds such as Kazakh white-headed, Auliekol, Alatau, Aulieata, and Kalmyk, their production and economic significance. An overview of genetic studies using DNA fingerprinting, microsatellites, and SNPs aimed at identifying unique characteristics, genetic diversity, and genes under selection, as well as markers of economically important and productive traits of Kazakh cattle breeds, is also provided. The study examined the genetic structure of the Kazakh white-headed and Alatau breeds based on whole-genome SNP genotyping. Unique genetic components characterizing Kazakhstan cattle breeds were described, and comparisons were made with genetic data from other breeds. Structural analysis showed that the Kazakh white-headed breed contains genetic components of the Hereford, Kalmyk, and Altai cattle. The Alatau breed has a composite structure, containing components of the Brown Swiss, Braunvieh, Kalmyk, and Holstein breeds. The results not only reveal the genetic diversity and characteristics of cattle breeds in Kazakhstan and the historical development and current state of animal husbandry in the country, but also emphasize the importance of further research to identify adaptive and unique genetic markers affecting economically important traits of local breeds.

Novel buffer for long-term preservation of DNA in biological material at room temperature.

The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8years, human blood stored for 3years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

SNP Array for Small-Shrimp (Genus Acetes) Origin Determination Using Machine Learning.

Accurate origin determination of seafood is crucial for consumer trust and safety. This study was performed to develop a machine learning-based single-nucleotide polymorphism (SNP) analysis technique to determine the origin of Acetes species in salted small-shrimp products. Mitochondrial DNA (COI and 16S rRNA) analysis revealed genetic variations among species and origins. Eight candidate SNPs were identified, six of which were developed into markers for genotyping analysis. Using the developed markers, an SNP array was created and SNP data from salted small-shrimp samples were obtained. Machine learning analysis using a supervised learning algorithm achieved 100% accuracy in classifying the origin of Acetes based on SNP data. This method offers a reliable method for regulatory bodies to combat food fraud and ensure product integrity. The approach can be further improved by expanding the data set to encompass a wider range of species and origins. This study highlights the potential of SNP analysis and machine learning for ensuring seafood authenticity and promoting sustainable practices.

Human Papilloma Virus-Independent/p53abnormal Keratinizing Squamous Cell Carcinoma of the Uterine Cervix Associated With Uterine Prolapse.

Knowledge about the morphologic and molecular characteristics of cervical squamous cell carcinomas (CSCCs) associated with uterine prolapse is very limited. Detailed histopathological and immunohistochemical (p16, p53, and cytokeratin 17), as well as molecular evaluation for human papillomavirus (HPV)-DNA and p53-mutational analyses in 4 consecutive CSCCs associated with uterine prolapse with definition of a hitherto not well-described HPV-independent/p53abnormal precursor lesion (HPV-independent cervical intraepithelial neoplasia [CIN; differentiated CIN]) and molecular tumorigenetic pathway. Cases diagnosed within 7 years with a mean age of 75 (range: 69-83) years and a mean tumor size of 7.3cm (range: 5.2-9.4cm). All patients presented with locally advanced disease, and 1 woman died of the disease within 4, and another within 14 months of follow-up. All CSCCs and their adjacent precursor lesions were negative for p16, with aberrant p53-expression and diffuse and strong staining for cytokeratin 17. Both the CSCCs and their precursors were negative for HPV-DNA but harbored a TP53 mutation. The precursor lesions were characterized by epithelial thickening with superficial keratinization, and the presence of basal and parabasal keratinocytes with mitotic figures beyond the basal layer, thus showing features similar to those seen in differentiated types of vulvar intraepithelial lesions (vulvar intraepithelial neoplasia [VIN] syn. HPV-independent/p53abn VIN), suggesting the terminology of differentiated CIN or HPV-independent/p53abn CIN. An HPV-independent pathogenetic pathway with a p53-alteration was identified for these cases. CSCC associated with uterine prolapse represents HPV-independent tumors harboring a TP53 mutation. For the first time, a precursor lesion of HPV-independent CSCC of the uterine cervix is described with a differentiated VIN-like morphology, and a separate tumorigenic pathway defined.

Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

BackgroundThe massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources.ResultsWe develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb (http://wheat.cau.edu.cn/WheatCNVb/), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties.ConclusionsThe CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.

The advent of forensic DNA databases: It’s time to agree on some international governance principles!

National forensic DNA databases are a valuable investigative tool, that have the potential to increase the efficacy of criminal investigations. Their unfettered expansion in recent years raises unsettling ethical issues that require close attention. DNA database expansion threatens the rights to privacy, non-discrimination, and equality, and can undermine public trust in government. This perspective piece relies on data from an international mapping study of Forensic DNA Databases to document the expansion of these databases, highlight the ethical issues they raise, and propose key recommendations for more responsible use of this infrastructure.

The Efficiency of the Alu Insertion Sequence in Discrimination Among some Individuals

Background: The Alu element is a widely distributed short interspersed nuclear element (SINE) in the human genome and has important applications in forensic science. The current study focused on assessing the effectiveness of Alu insertion polymorphism in forensic DNA profiling to identifying samples of some individuals living in the Babylon Governorate. Materials and methods: DNA was extracted From frozen blood samples (60) individuals were collected from Babylon - Al-Hilla Governorate from 8/8/2022 until 8/9/2022. Results: purified then a PCR technique Alu insertions were A(2q21.1)(111-115bp) 0.75, Alu deletion (0.25), B(8q23.1) (0.375) (0.625) C(13q34) (0.5)(0.5), D(15q23) (0.775) (0.225), E(16q23.3) (0.692) (0.308) and F(19q13.12)(0.616)(0.384) respectively.The alleles with Alu insertions at (2q21.1) were the most prevalent, whereas the Alu insertions at (8q23.1) were the least common. The similarity coefficient among individuals varied from 0.4 to 1, based on the proportion of genetic relatedness between them. Conclusions: Alu elements have efficacy in families’ discrimination it can be used more than one site, set of Alu insertion sequences should be used to accurate results.

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence.

The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.

The transcriptional repressor B cell lymphoma 6 regulates CXCR3 chemokine and human leukocyte antigen II expression in endothelial cells

Interferon gamma (IFN-γ) induces an endothelial proimmunogenic phenotype through the JAK/STAT1 pathway, which can shape the activation of alloreactive leukocytes in transplant rejection. In immune cells, the DNA-binding protein B cell lymphoma 6 (BCL6) controls the transcription of inflammatory genes. This study tested if BCL6 modulates IFN-γ-induced gene expression in endothelial cells. In vitro, BCL6 was IFN-γ-inducible in primary human endothelium, along with CXCR3 chemokines and human leukocyte antigen (HLA). BCL6, HLA II, and CXCL9 were also increased in human cardiac transplants during acute rejection. Knockdown of BCL6 augmented, whereas overexpression and BTB domain inhibitors (BCL6-BTBi) suppressed, HLA II and CXCR3 chemokine expression but not HLA I. Further, BCL6 had a greater effect on HLA-DR and DP but was less involved in regulating HLA-DQ expression. The effect correlated with BCL6 binding motifs in or near affected genes. The BCL6 DNA recognition sequence was highly similar to that of STAT1, and BTBi reduced STAT1’s transcriptional activity in vitro. Our results show for the first time that BCL6 selectively controls IFN-γ-induced endothelial gene expression, advancing our understanding of the endogenous mechanisms regulating donor immunogenicity.

Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies.

Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.

Mitochondrial DNA profiling in combination with autosomal loci as a valuable tool for obtaining statistical significance in forensic cases

Mitochondrial DNA profiling in combination with autosomal loci as a valuable tool for obtaining statistical significance in forensic cases

Integrating wing morphometrics and mitochondrial DNA analysis to assess the filaria vector Mansonia uniformis (Diptera: Culicidae) populations in Thailand.

Mansonia uniformis (Diptera: Culicidae) is recognized as a vector of Brugia malayi and has been reported to transmit Wuchereria bancrofti, both causing lymphatic filariasis in humans. This study employed geometric morphometrics (GM) to investigate wing shape variation and analyzed genetic diversity through cytochrome c oxidase subunit 1 (COI) gene analyses in Ma. uniformis populations across Thailand. Wing GM analyses indicated significant differences in wing shape based on Mahalanobis distances among nearly all population pairs (p < 0.05), with no significant correlation between wing shape and geographic distance (r = 0.210, p > 0.05). Genetic analyses identified 63 haplotypes and 49 polymorphic sites, with the overall population exhibiting a nucleotide diversity of 0.006 (± 0.001) and a haplotype diversity of 0.912 (± 0.017). Deviations from neutrality, as indicated by Tajima's D and Fu's FS tests for the overall Ma. uniformis populations in Thailand, were statistically significant and negative, suggesting population expansion (both p < 0.05). Analysis of molecular variance revealed no significant genetic structure when all populations were categorized based on collection sites and geographic regions. However, significant differences in FST values were observed between some populations. These findings enhance our understanding of the geographical and genetic factors influencing Ma. uniformis populations, which are crucial for developing effective control strategies in Thailand.

Advancements in DNA analysis for distinguishing wild boar and domestic pig: a mini-review on research developments for food authentication studies

Abstract Ensuring food authenticity is integral to quality control and food safety, demanding traceability of food ingredient origins to be prominently featured on labels. Pork, a widely consumed and processed animal protein source, is susceptible to adulteration with wild boar meat, primarily driven by factors such as production costs and profitability. Complicating matters, the quality of wild boar meat obtained through game hunting lacks guarantees for hygienic standards, posing potential harm to consumers. Recent outbreaks of African Swine Fever in pigs and wild boars further emphasize the critical link between food safety and meat authenticity. This study addresses the need for research in distinguishing between pork and wild boar meat to uphold food quality control standards. Establishing the meat origin is not only crucial for quality control but also vital for mapping and tracing meat distribution patterns. The study adopts a DNA-based approach, utilizing biomarkers to distinguish domestic pig and wild boar meat. However, researchers encounter significant challenges due to their shared species (Sus scrofa) and high DNA sequence similarity. The pursuit of robust biomarkers and analytical methods becomes imperative. Exploring both nuclear and mitochondrial DNA, this mini-review outlines the research developments in identifying resilient biomarkers and employing various analytical methods, including conventional PCR, PCR-RFLP, Real-time PCR, microsatellite (STR), and deep sequencing (NGS or GWAS). The paper provides a concise overview of the ongoing efforts to find effective biomarkers and analytical methods based on DNA approaches for distinguishing domestic pigs and wild boars, showcasing their potential applications in food authentication.