Single Nucleotide Polymorphism Variants Research Articles

Genome-Wide Analysis of the Risk Association for the Development of Paranoid Schizophrenia in Russians: Search for Genetic Markers in the 1q43 Chromosomal Region

Schizophrenia is a highly hereditary disorder. Genetic risk is associated with a large number of alleles, including common alleles with little effect that can be found in genome-wide association studies. The aim of this study was to study genetic risk factors for the development of schizophrenia in a genome-wide association analysis (GWAS) in Russians from the Republic of Bashkortostan. The studied sample consisted of 320 patients with paranoid schizophrenia and 402 healthy individuals. GWAS genotyping of DNA samples was carried out on the PsychChip biochip, which included 610,000 single nucleotide polymorphic variants (SNPs).

Insights into genetic diversity and functional significance of the bHLH genes in cotton fiber development

This study investigated the identification and distribution of single nucleotide polymorphisms (SNPs) within basic Helix-Loop-Helix (bHLH) transcription factors (TFs) across diverse cotton (Gossypium hirsutum) accessions, including wild, landrace, and improved varieties. Comprehensive genomic analyses revealed substantial SNP diversity in wild cotton, distinct from that observed in landraces and improved accessions. Comparative analysis showed notable variations in SNP abundance and impact levels across different accessions, with missense SNPs being prevalent. Nucleotide substitution patterns highlighted the dominance of G>A and A>G substitutions. Population genetic analyses unveiled significant genetic diversity within wild accessions and distinct clustering between wild and improved accessions. Temporal expression profiling of bHLH genes during cotton fiber development demonstrated dynamic expression patterns, emphasizing their roles in fiber initiation, elongation, and cellulose biosynthesis. Moreover, association analysis identified SNPs significantly associated within bHLH genes, particularly GhbHLH149, with fiber quality traits, indicating their potential functional significance. Population genetic analyses further revealed evidence of positive selection on GhbHLH149 during cotton improvement. This study provides a comprehensive understanding of SNP diversity, gene expression dynamics, and genetic selection in bHLH genes, offering valuable insights for future cotton breeding efforts aimed at improving fiber quality traits in cotton.

The predictive value of TNF family for pulmonary tuberculosis: a pooled causal effect analysis of multiple datasets

ObjectiveDespite extensive research on the relationship between pulmonary tuberculosis (PTB) and inflammatory factors, more robust causal evidence has yet to emerge. Therefore, this study aims to screen for inflammatory proteins that may contribute to the susceptibility to PTB in different populations and to explain the diversity of inflammatory and immune mechanisms of PTB in different ethnicity.MethodsThe inverse variance weighted (IVW) model of a two-sample Mendelian Randomization (MR) study was employed to conduct causal analysis on data from a genome-wide association study (GWAS). This cohort consisting PTB GWAS datasets from two European and two East Asian populations, as well as 91 human inflammatory proteins collected from 14,824 participants. Colocalization analysis aimed to determine whether the input inflammatory protein and PTB shared the same causal single nucleotide polymorphisms (SNPs) variation within the fixed region, thereby enhancing the robustness of the MR Analysis. Meta-analyses were utilized to evaluate the combined causal effects among different datasets.ResultsIn this study, we observed a significant negative correlation between tumor necrosis factor-beta levels (The alternative we employ is Lymphotoxin-alpha, commonly referred to as LT) (P < 0.05) and tumor necrosis factor receptor superfamily member 9 levels (TNFRSF9) (P < 0.05). These two inflammatory proteins were crucial protective factors against PTB. Additionally, there was a significant positive correlation found between interleukin-20 receptor subunit alpha levels (IL20Ra) (P < 0.05), which may elevate the risk of PTB. Colocalization analysis revealed that there was no overlap in the causal variation between LT and PTB SNPs. A meta-analysis further confirmed the significant combined effect of LT, TNFRSF9, and IL20Ra in East Asian populations (P < 0.05).ConclusionsLevels of specific inflammatory proteins may play a crucial role in triggering an immune response to PTB. Altered levels of LT and TNFRSF9 have the potential to serve as predictive markers for PTB development, necessitating further clinical validation in real-world settings to ascertain the impact of these inflammatory proteins on PTB.

Identification and functional marker development of SbPLSH1 conferring purple leaf sheath in sorghum.

We identified a SbPLSH1gene conferring purple leaf sheath in sorghum (sorghumbicolor(L.) Moench)and developed a functional markerfor it. The purple leaf sheath of sorghum, a trait mostly related to anthocyanin deposition, is a visually distinguishable morphological marker widely used to evaluate the purity of crop hybrids. We aimed to dissect the genetic mechanism for leaf sheath color to mine the genes regulating this trait. In this study, two F2 populations were constructed by crossing a purple leaf sheath inbred line (Gaoliangzhe) with two green leaf sheath inbred lines (BTx623 and Silimei). Based on the results of bulked-segregant analysis sequencing, bulk-segregant RNA sequencing, and map-based cloning, SbPLSH1 (Sobic.006G175700), which encodes a bHLH transcription factor on chromosome 6, was identified as the candidate gene for purple leaf sheath in sorghum. Genetic analysis demonstrated that overexpression of SbPLSH1 in Arabidopsis resulted in anthocyanin deposition and purple petiole, while two single-nucleotide polymorphism (SNP) variants on the exon 6 resulted in loss of function. Further haplotype analysis revealed that there were two missense mutations and one cis-acting element mutation in SbPLSH1, which are closely associated with leaf sheath color in sorghum. Based on the variations, a functional marker (LSC4-2) for marker-assisted selection was developed, which has a broad-spectrum capability of distinguishing leaf sheath color in natural variants. In summary, this study lays a foundation for analyzing the genetic mechanism for sorghum leaf sheath color.

Circulating microRNA profile of long-lived Okinawans identifies novel potential targets for optimizing lifespan and health span.

Nonagenarians and centenarians serve as successful examples of aging and extended longevity, showcasing robust regulation of biological mechanisms and homeostasis. Given that human longevity is a complex field of study that navigates molecular and biological mechanisms influencing aging, we hypothesized that microRNAs, a class of small noncoding RNAs implicated in regulating gene expression at the post-transcriptional level, are differentially regulated in the circulatory system of young, middle-aged, and nonagenarian individuals. We sequenced circulating microRNAs in Okinawan males and females <40, 50-80, and >90 years of age accounting for FOXO3 genetic variations of single nucleotide polymorphism (SNP) rs2802292 (TT - common vs. GT - longevity) and validated the findings through RT-qPCR. We report five microRNAs exclusively upregulated in both male and female nonagenarians with the longevity genotype, play predictive functional roles in TGF-β, FoxO, AMPK, Pi3K-Akt, and MAPK signaling pathways. Our findings suggest that these microRNAs upregulated in nonagenarians may provide novel insight into enhanced lifespan and health span. This discovery warrants further exploration into their roles in human aging and longevity.

Genetic influence on treatment outcomes in patients with pain-related temporomandibular disorders.

Single nucleotide polymorphisms (SNPs) may influence pain susceptibility and impact treatment response in pain-related temporomandibular disorders (TMDp). Explore the role of COMT (rs4646310, rs6269, rs4818, rs4680) and OPRM1 (rs1799971) genotypes in regulating treatment response. Sixty TMDp patients (55 females and 5 males), diagnosed with the Diagnostic Criteria for TMD (DC/TMD), underwent standardised treatment (information and education, home physical therapy, occlusal splint) for 6 months. Treatment outcomes included: pain intensity, pain-free mouth opening, jaw functional limitation, depression, and anxiety. Genotyping for COMT and OPRM1 SNPs was performed using DNA from buccal mucosa swabs and TaqMan assays. Statistical analysis was carried out to compare the changes in treatment outcomes and the influence of genotypes on treatment response. Significantly less pain reduction was observed in minor allele carriers of rs4646310, and rs4680 compared to dominant homozygous (p < .025). Minor allele carriers of rs1799971 and rs4646310 demonstrated worsening in pain-free mouth opening while dominant homozygous exhibited improvement (p < .025). Significantly less anxiety reduction was observed in minor allele carriers of rs4646310 compared to dominant homozygous (p = .003). Of the all variables assessed in the regression model, carrying a minor allele of rs1799971 predicted a poorer treatment response considering pain-free mouth opening while carrying a minor allele of rs4646310 predicted less pain and less anxiety reduction. Our findings indicate that certain SNP variants of the COMT and OPRM1 genes were associated with poorer treatment response and may therefore play a significant role in the classification of TMDp patients. Also, assessment of patient genotype could potentially aid in predicting treatment response.

The Genetic Variants of Long Noncoding RNA MEG3 and Its Association to the Clinical Features of Diabetic Retinopathy

Purpose This study aimed to investigate the potential correlation between the single-nucleotide polymorphism (SNP) of maternally expressed gene 3 (MEG3) and the clinical manifestations of diabetic retinopathy (DR). Methods Five loci of MEG3 SNPs including rs4081134 (G/A), rs10144253 (T/C), rs7158663 (G/A), rs3087918 (T/G) and rs11160608 (A/C) were genotyped by TaqMan allelic discrimination in 457 non-DR patients and 280 DR individuals. Results The distribution frequency of MEG3 SNP rs7158663 GA (AOR: 0.683, 95% CI: 0.478-0.975, p = 0.036) and MEG3 SNP rs7158663 GA + AA (AOR: 0.686, 95% CI: 0.487-0.968, p = 0.032) were significantly lower in the DR group. And the MEG3 SNP rs7158663 GA + AA (AOR: 0.610, 95% CI: 0.377-0.985, p = 0.043) demonstrated a significantly lower distribution frequency in the male DR group. Besides, the DR patients with MEG3 SNP rs7158663 GA + AA genotype showed a significantly lower HbA1c level than the DR patients with MEG3 SNP rs7158663 GG genotype (7.29 ± 1.23 versus 7.74 ± 1.49, p = 0.013). Moreover, in the analysis using data from gene expression data series database, a higher MEG3 level was significantly correlated to a lower miR-182 level in the database (p = 0.0114). Conclusions In this study, the distribution frequency of MEG3 SNP rs7158663 GA + AA genotype was lower in DR, while the DR would develop under lower HbA1c level in DM patients with this MEG3 SNP variant.

Variation in the AA-NAT gene G203A is associated with Awassi and Hamdani sheep fertility

Arylalkylamine-N-acetyl-transferase (AA-NAT) is one of several genes that influence sheep reproduction. Thus, the objective of this study was to investigate whether genetic variability within the AA-NAT gene influenced the reproductive performance of Awassi and Hamdani ewes. A total of 99 twin and 101 single-progeny ewes were analyzed for genomic DNA. Polymerase chain reaction (PCR) was used to produce amplicons of 300, 313, and 287 bp from exons 1, 2, and 3 of the AA-NAT gene. A 300-bp amplicon was genotyped, resulting in two genotypes: GG and GA. Through sequence analysis, a mutation 203 G > A was identified in the GA genotype. The statistical analysis revealed a strong correlation between the single nucleotide polymorphism (SNP) 203 G > A and reproductive performance. Ewes carrying this mutation showed significantly increased litter sizes, twinning rates, lambing rates, and fewer days to lambing compared to those carrying GG. These findings demonstrate that the presence of the 203 G > A SNP variant has a significant positive impact on litter sizes and enhances the fertility of Awassi and Hamdani sheep.

Identifying associations of human surfactant protein A SNPs and allelic variants with retinopathy of prematurity

Retinopathy of prematurity (ROP) is the primary cause of childhood blindness worldwide. Previous studies showed that allelic single nucleotide polymorphic (SNP) variants of the human surfactant protein A genes (SP-A1, SP-A2) are associated with the development of respiratory distress syndrome and bronchopulmonary dysplasia (BPD). In this work, we hypothesized that SP-A SNPs and allelic variants are associated with altered risk of ROP in prematurely born infants. To test this hypothesis, we used a modified PCR-based method to detect variants of the SP-A1 and SP-A2 genes in a cohort of preterm infants. Infants born at &lt;32 weeks’ gestation and/or&lt;1500 grams were enrolled. Scavenged blood samples or cheek swabs were collected and DNA was extracted using the QIAamp DNA Mini Kit. We measured SNPs in SP-A1 and SP-A2 using Taqman probes for allelic discrimination by PCR or PCR/RFLP/sequencing method. Associations of SP-A1 and SP-A2 SNP allele frequencies with ROP and BPD were determined using chi-square and logistic regression analyses. Our results show that, of the total patient cohort (n=59), 42 patients had a BPD diagnosis (23 with ROP and 36 without ROP). DNA analysis of these samples identified associations of SP-A1 and SP-A2 SNPs and variants with ROP. For SP-A1, the following SNP associations were found for ROP using chi-square: rs1059047 (p=0.44), rs1136450 (p=0.63), rs1136451 (p=0.21), rs1059057 (p=0.52). For SP-A2, the following SNPs associations were identified with ROP: rs1059046 (p=0.51), rs17886395 (p=0.050), rs1965707 (p=0.031), rs1965708 (p=0.46). Logistic regression analysis indicated an association of ROP with the SP-A1 6A2 variant (p-value = 0.47, OR (6A2/*)=0.8036, 95%CI [0.2299 - 2.8082], OR (6A2/6A2) = 0.4327, 95%CI [0.1063 - 1.7615]), which conferred protection, as well as an association of ROP with SP-A2 6A2 (p-value = 0.0055) with decreased risk when 1A2 variant is present. We conclude that SP-A1/SP-A2 polymorphisms are associated with the presence of ROP in infants with BPD. The 6A4 SP-A1 and SP-A2 1A2 appear to confer protection in babies against ROP. Further studies will determine the mechanisms of this protective effect. Indiana University, University of Chicago Metcalf Internship Program Grant, The University of Oklahoma Health Sciences Center. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Polymorphism rs117585797 of the ANO2 gene as a genetic marker of a high risk of developing combined proliferative diseases of the uterus in women with endometriosis

Introduction. Endometriosis is a common gynecological disease that has important socio-economic significance for both sick women, their families, and society as a whole. It is often combined with other hyperplastic diseases of the uterus.Aim. To analyze the involvement of GWAS-significant polymorphic loci of sex hormone genes in the development of combined proliferative diseases of the uterus in women with endometriosis. Materials and methods. The sample for the study included 395 women, including 103 patients with isolated endometriosis and 292 patients with endometriosis in combination with uterine fibroids and/or endometrial hyperplasia. All women underwent molecular genetic testing of seven GWAS-significant single-nucleotide polymorphic variants of sex hormone genes (rs34670419, rs11031005, rs11031002, rs148982377, rs112295236, rs1641549, rs117585797). The analysis of associations of polymorphic variants with the risk of developing combined proliferative diseases of the uterus in patients with endometriosis was carried out. To assess the functional effects of SNP associated with the formation of combined proliferative diseases of the uterus in women with endometriosis, the online programs HaploReg and Gtex Portal were used.Results and discussion. Genetic variant A rs117585797 of the ANO2 gene is a risk factor for the development of combined proliferative diseases of the uterus in women with endometriosis (p = 0.05, рperm = 0.05, OR = 4.29). According to the data obtained in silico, the rs117585797 locus localized in the intron of the ANO2 gene affects the affinity of the regulatory DNA motif to the transcription factors Crx and Gsc.Conclusions. Polymorphic locus rs117585797 of the ANO2 gene is associated with a high risk of the formation of combined proliferative diseases of the uterus in patients with endometriosis.

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

GWAS determined genetic loci associated with callus induction in oil palm tissue culture.

GWAS identified six loci at 25kb downstream of WAK2, a crucial gene for cell wall and callus formation, enabling development of a SNP marker for enhanced callus induction potential. Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed, and correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs (P ≤ 0.05) in C1 were identified to develop markers for screening individuals with high potential of callus induction. Among 21 significant SNPs in C1, LD block analysis revealed six SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.

ST2 and IL-33 polymorphisms and the development of childhood asthma: a prospective birth cohort study in Finnish children.

The ST2/IL-33 signaling pathway has an important role in the host inflammatory response. Here we aimed to study the association of ST2 and IL-33 polymorphisms with serum soluble (s) ST2 and IL-33 concentrations in healthy Finnish children and, in addition, their association with childhood asthma. In total, 146 children were followed from birth to the age 7 years for the development of asthma. Single-nucleotide polymorphisms (SNPs) in ST2 and IL-33 were determined, and associations of the SNP variants with serum levels of sST2 and IL-33 at age of 13 months and with recurrent wheezing and childhood asthma at 7 years of age were analyzed. Children with ST2 rs1041973 AC/AA genotypes had significantly lower level of serum sST2 (2453 pg/mL; IQR 2265) than those with CC genotype (5437 pg/mL; IQR 2575; p = < 0.0001). Similar difference was also observed with ST2 rs13408661. No differences were observed between subjects with studied IL-33 SNPs. Children who carried genetic variants of ST2 rs1041973 or rs13408661 seemed to have a higher risk of asthma. In contrast, children who carried genetic variants of IL-33 rs12551268 were less often diagnosed with asthma. Even though these SNPs seemed to associate with asthma, the differences were not statistically significant.

Variación molecular de genes asociados a lipoxigenasas en grano de variedades de soya comercial mexicana

Lipoxygenase enzymes encoded by the Lox1, Lox2 and Lox3 genes play a crucial role in soybean grain, particularly in the development of off-flavors. Understanding molecular variation within Lox genes is essential for the improvement of soybean organoleptic traits. This study investigated the genetic variation in the internal regions of the Lox1, Lox2, and Lox3 genes in mature grain of commercially grown soybean cultivars in Mexico. Genomic DNA from a diverse panel of Mexican soybean cultivars was analyzed using resequencing techniques and in-silico analysis. Single nucleotide polymorphisms (SNP) within the Lox1, Lox2, and Lox3 genes were identified and characterized. The findings indicated that Lox3 gene displayed lower genetic variability compared to Lox1 and Lox2 genes, specifically, was identified a total of 26 SNPs in the Lox1 gene, 11 SNPs in the Lox2 gene, and 5 SNPs in the Lox3 gene among the examined cultivars. A non-synonymous SNP variant of the C/C genotype located in exon 6 of the Lox2 gene was associated with a destabilizing effect on the lipoxygenase 2 enzyme in the Guayparime S-10 and Huasteca 300 cultivars. These findings provide insights into the molecular variation of lipoxygenase-associated genes in Mexican soybean cultivars.

Association of long noncoding RNA H19 rs2839698 C/T with hepatitis B virus infection and hepatocellular carcinoma risk.

The intricate pathogenesis of the hepatitis B virus (HBV) and its progression to hepatocellular carcinoma (HCC) have not yet been fully elucidated. H19 is one of the earliest imprinted long noncoding RNAs (lncRNAs) associated with liver pathobiology. This study investigated the association of H19 single nucleotide polymorphisms (SNPs) rs2839698 C/T and rs217727 C/T with HBV and HBV-related HCC and their correlation with H19 expression level. A total of 230 subjects were enrolled in this study including 100 HBV-infected patients, 30 HBV-related HCC patients, and 100 apparently healthy controls. TaqMan genotyping human assays were utilized to assess allelic discrimination for H19 SNPs. H19 expression was assessed using quantitative real-time polymerase chain reaction (qRT-PCR). Our findings showed that H19 rs2839698 was linked to a higher incidence of HBV infection and HBV-related HCC. Individuals who bear the CT genotype of rs2839698 were more susceptible to HBV infection (OR = 3.05; 95% CI 1.714-5.457; p < 0.001). Those harboring the TT genotype were more prone to develop HCC (OR = 2.625; 95% CI 1.037-6.64; p = 0.038). Our data revealed that rs2839698 could function as a promising predictor of HCC risk. Furthermore, H19 was significantly downregulated in HBV (p < 0.01) and HCC (p < 0.01) patients versus the control group. Significant upregulation of H19 in HCC patients with cirrhosis (p < 0.001) was detected. Altogether, this is considered the first prospective case-control study to address the implication of the genetic variations of H19 SNPs in HBV and HBV-related HCC in Egyptian patients.

Development and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in England and Wales utilising whole genome sequencing data.

Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104. All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.

Enhanced selective discrimination of point-mutated viral RNA through false amplification regulatory direct insertion in rolling circle amplification

Coronaviruses are single-stranded RNA viruses with high mutation rates. Although a diagnostic method for coronaviruses has been developed, variants appear rapidly. Low test accuracy owing to single-point mutations is one of the main factors in the failure to prevent the early spread of coronavirus infection. Although reverse transcription-quantitative polymerase chain reaction can detect coronavirus infection, it cannot exclude the possibility of false positives, and an additional multiplexing kit is needed to discriminate single nucleotide polymorphism (SNP) variants. Therefore, in this study, we introduced a new nucleic acid amplification method to determine whether an infected person has a SNP mutation using a lateral flow assay (LFA) as a point-of-care test. Unlike traditional DNA amplification methods, direct insertion into rolling circle amplification amplifies the target genes without false amplification. After SNP-selective nucleic acid amplification, nuclease enzymes are used to make double-stranded DNA fragments that the LFA can detect, where specific mismatched DNA is found and cleaved to show different signals when a SNP-type is present. Therefore, wild- and SNP-type variants can be selectively detected. In this study, the limit of detection was 400 aM for viral RNA, and we successfully identified a dominant SNP variant selectively. Clinical tests were also conducted.

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration

AbstractWhen populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole‐genome, short‐read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected &gt;35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; &gt;26,000 high‐confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA‐Lys elements. The site frequency spectrum of SVs in protein‐coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein‐coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.

The novel C268A variant of BMP2 is linked to the reproductive performance of Awassi and Hamdani sheep.

Prolificacy-associated genetic markers can be utilized to enhance litter size in the sheep breeding industry. Sheep reproduction is influenced by a multitude of genes, including bone morphogenetic protein 2 (BMP2). This study aimed to explore the potential relationship between variability in the BMP2 gene and reproductive performance in Awassi and Hamdani ewes. The genomic DNA was extracted from 99 single-progeny ewes and 101 twin ewes. Polymerase chain reaction (PCR) was employed to produce an amplicon consisting of four sequence fragments: 277bp, 251bp, 331bp, and 340bp, from exons 1, 2, 3, and 4 of the BMP2 gene, respectively. Three genotypes were identified for amplicons in exon 4 with 340-bp lengths: CC, CA, and AA. Upon analyzing the sequence of the CA genotype 382C > A, a novel mutation was discovered in this genotype. A robust association was identified between the single nucleotide polymorphisms (SNP) 382C > A and reproductive performance through statistical analysis. An important distinction was discovered between ewes carrying SNP 382C > A and those carrying CC in terms of litter sizes, twinning rates, lambing rates, and days to lambing. An analysis of logistic regression revealed a significant association between litter size and the 382C > A SNP. There was a decrease in lamb production among ewes with the CC genotype compared to those with the CA and AA genotypes. These results indicate that the SNP variant 382C > A has a positive influence on the reproductive performance of Awassi and Hamdani sheep. Sheep carrying the 382C > A SNP exhibit increased litter size and overall productivity compared to those without the SNP.

First report on chromosomal abnormalities in Eastern Morocco: Identification of a new case of a de novo partial trisomy 13q using single-nucleotide polymorphism array

BackgroundChromosomal abnormalities are the main cause of birth defects, intellectual disability, and miscarriages. They contribute to significant human morbidity and infant mortality. Here we report for the first time the chromosomal abnormalities encountered in the population of Eastern Morocco. Furthermore, we describe a new case of a de novo partial trisomy 13q combined with a terminal deletion in an 11-day-old girl. MethodsFrom November 2015 to March 2022, 195 patients from the BRO Biobank who were clinically suspected of having chromosomal abnormalities were referred to the cytogenetics laboratory of the Genetics Unit of the Faculty of Medicine and Pharmacy of Oujda for cytogenetic study. Karyotyping analysis was performed on peripheral blood samples using standard R banding techniques. To identify single-nucleotide polymorphism (SNP) and copy number variants (CNVs), Illumina SNP array was used. ResultsAmong 195 studied cases, 32 (16.4 %) had abnormal karyotypes, of which 12 cases had numerical aberrations while 20 cases had structural aberrations. The most common numerical aberrations were Turner syndrome and Down syndrome followed by Edward, Patau, and Klinefelter syndromes. For structural aberrations, translocations were the most common, followed by derivative chromosomes, inversions, deletions, and an addition on chromosome 13 identified in an 11-day-old girl. To further characterize this addition, SNP array was carried out and revealed a 58.8-Mb duplication in region 13q14.3q34 associated with a 1-Mb deletion in region 13q34. Follow-up parental chromosomes analysis showed normal karyotypes for the parents, confirming that this partial trisomy 13q was de novo. Comparison of the phenotype associated with this novel duplication on chromosome 13q with those previously reported confirmed the considerable variability in the phenotype of the patients with partial trisomy 13q. ConclusionThis study provided the first report on chromosomal abnormalities in Eastern Morocco and it enriched the phenotype spectrum of partial trisomy 13q and further confirmed the genotype–phenotype correlations. Furthermore, these findings justify the need to set up microarray comparative genomic hybridization techniques in Morocco for better genetic diagnosis.