Wild Genotype Research Articles

Development of a technique for analyzing the lengths of restriction fragments to assess the mefloquine resistance of plasmodium falciparum based on the identification of single-nucleotide polymorphisms (A958146T, A961013G, G961625T) of the PFMDR1 gene

ABSTRACT. A method for identifying single nucleotide polymorphisms of the PfMDR1 gene (A958146T, A961013G, G961625T) based on the analysis of the lengths of restriction fragments using polymerase chain reaction technology with specific primers is presented. To identify the polymorphism A958146T (amino acid substitution N86Y), it was proposed to amplify a fragment of parasitic deoxyribonucleic acid with a length of 417 bp, including the 86th codon of the PfMDR1 gene, followed by treatment of the amplicon with ApoI endonuclease, the restriction site of which includes the sequence of the analyzed mutation. With the Plasmodium falciparum genotype unchanged, the isolated deoxyribonucleic acid site is divided into two fragments of size 239 and 179 bp. In the case of an altered genotype containing a single nucleotide missense mutation A T, the original fragment 417 bp will be preserved. When designing the system to detect the amino acid substitution N1042D caused by the A961013G mutation, a pair of specific primers were selected that limit the 404 bp-long section of parasitic deoxyribonucleic acid. For restriction analysis, the most optimal was the use of AseI endonuclease, which in the case of an unchanged Plasmodium falciparum genotype divides the initial amplicon into 4 fragments (132, 116, 99 and 25 bp), and in the presence of A G mutation into 3 (248, 99, 25 bp). It was found that a fragment of the PfMDR1 gene, including the G961625T mutation leading to the amino acid substitution D1246Y, contains 1 site corresponding to the restriction site of endonuclease BglII. Therefore, in the case of the wild genotype of Plasmodium falciparum, the initial fragment of deoxyribonucleic acid is cut into 2 short sections (300 and 269 bp). With the D1246 mutation, the replacement of the nucleotide G T leads to the disappearance of the restriction site, so only one source fragment (509 bp) will be recorded on the electrophoregram. Based on the analysis of the data obtained, criteria for evaluating the drug resistance of Plasmodium falciparum have been developed. The decrease in sensitivity to mefloquine and its derivatives of pathogens of tropical malaria can be evidenced by positive results obtained using the developed methods for detecting haplotypes A T (N86Y (band 417 bp)), A G (N1042D (bands 248, 99 and 25 bp)), G T (D1246Y (509 bp)). The developed methods can be used to analyze the spread of drug-resistant tropical malaria.

Genetic Analysis of the Cultivars of Ping’ou Hybrid Hazelnut (C. heterophylla Fisch. × C. avellana L.) in China Based on SSR Markers

Ping’ou hybrid hazelnut is one of the most profitable tree nuts in China, but economically important cultivars must first be genetically validated to meet industrial demand. Traditional approaches used for cultivar identification are mainly trait-based and unreliable. Previous approaches at the DNA level, focusing on the identification of species or/and varieties that originated in China, were not used widely in hybrid hazelnut because there was no proper standard sample. In this research, a multiplexed fingerprinting test was conducted to allow for hazelnut cultivar identification using SSR markers derived from European hazelnut. Twenty-seven SSR markers were used to fingerprint 57 genetically unique Ping’ou hybrid hazelnut and related wild species. All markers showed a high level of polymorphism, as indicated by mean values for observed heterozygosity (Ho = 0.84), expected heterozygosity (He = 0.80), and polymorphism information content (PIC = 0.78). A total of 301 alleles were detected, and the number of effective alleles varied from 6 for KG817 and GB818 to 18 for B654, with an average of 11.2 alleles per locus. Moreover, the Shannon’s information index (I) ranged from 1.293 for BR215 to 2.385 for B654, with an average of 1.908. The neighbor-joining tree, principal coordinate analysis, and Bayesian analysis revealed clear separation between hybrid cultivars and wild forms (Cluster/group I), as well as the differentiation within hybrid genotypes (Clusters/groups II and III). Additionally, the NJ dendrogram demonstrated a further split within Clusters/group III (III a and III b). Altogether, with the comparable SSR information of the European hazelnut cultivar ‘Barcelona’, the newly developed marker sets can assist in the germplasm identification of hazelnut cultivars and reproductive materials. Importantly, these combined SSR loci can be applied to characterize the genetic relationships and population structures among wild genotypes and hybrid cultivars, which will then provide information to guide hazelnut breeding based on their genetic background.

Different Functional and Taxonomic Composition of the Microbiome in the Rhizosphere of Two Purslane Genotypes

Soil microbial communities have an important role in plant establishment and health. Particularly, the role of the soil microbiome in agriculture is of current interest. The study of microbial communities associated with purslane could open questions about the rational exploitation of the microbiota for sustainable agricultural purposes. In this study, the composition of the fungal and bacterial communities and the bacterial metabolic functions, associated with the rhizospheres of two purslane genotypes (one commercially available and one collected from the wild in Spain) were evaluated. The results showed a clear effect of purslane genotype on fungal and bacterial community composition and functional profiles. The bacterial community of the commercial purslane rhizosphere was characterized by more numerous metabolic pathways, mainly pathways related to Terpenoids and Polyketides, Carbohydrate, Lipid, and Amino Acid metabolism. By contrast, the rhizosphere bacterial community of the Spanish (wild) genotype was characterized by the enrichment of functions related to cellular processes such as cell motility and transport. We hypothesize that these differences could be due to differential effects of root exudate composition on the microbial functional community composition. This finding points out the need to consider differences in the functional characteristics of plant genotypes when selecting the beneficial microorganisms to be used as biofertilizers aiming to maximize plant growth and resistance to environmental stressors.

Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus.

The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or have been proposed as untapped sources of variability in breeding programs (e.g., Asparagus acutifolius L.). In the present work, we applied reduced-representation sequencing to examine a panel of 378 diverse asparagus genotypes, including commercial hybrids, interspecific lines, wild relatives of garden asparagus, and doubled haploids currently used in breeding programs, which enabled the identification of more than 200K single-nucleotide polymorphisms (SNPs). These SNPs were used to assess the extent of linkage disequilibrium in the diploid gene pool of asparagus and combined with preliminary phenotypic information to conduct genome-wide association studies for sex and traits tied to spear quality and production. Moreover, using the same phenotypic and genotypic information, we fitted and cross-validated genome-enabled prediction models for the same set of traits. Overall, our analyses demonstrated that, unlike the diversity detected in wild species related to garden asparagus and in interspecific crosses, cultivated and wild genotypes of A. officinalis L. show a narrow genetic basis, which is a contributing factor hampering the genetic improvement of this crop. Estimating the extent of linkage disequilibrium and providing the first example of genome-wide association study and genome-enabled prediction in this species, we concluded that the asparagus panel examined in the present study can lay the foundation for determination of the genetic bases of agronomically important traits and for the implementation of predictive breeding tools to sustain breeding.

A review of the current state of knowledge on Pseudoxytenanthera ritchiei- a lesser known bamboo species with high utilization potential from Peninsular India

Pseudoxytenanthera ritchiei (Munro) H. B. Naithani is a unique bamboo species with fully solid culms. This bamboo species is endemic to the Peninsular India and has a scattered distribution in the forest ecosystems of Kerala. In Kerala, the species was abundantly found in Nilambur and Mannarkad forests and had high demand in the market. However, unsustainable harvesting over a significant period resulted in resource depletion from these forests (Kumar et al., 2009). Though P. ritchiei shares many characteristics which make Pseudoxytenanthera stocksii a commercially important bamboo species, the former is not listed as a priority species by the National Bamboo Mission while the latter is included in the list. Moreover, the potential of P. ritchiei remains untapped in Kerala, primarily due to a lack of information on its distribution and availability, and secondly due to a lack of supply of sufficient quantity for commercial use. These are clumping bamboo and do not require much space, making them suitable for home gardens and as a border crop in fields. Hence, we argue that there is a good justification for this species to be given preference and large-scale cultivation to be encouraged outside forest areas after having developed appropriate methods for quality stock production. Steps must also be taken to ensure the conservation of the species in its natural habitat to prevent the loss of the wild and diverse genotypes which at present lack sufficient documentation. This review features information gleaned from available literature on this less-studied species, and its potential for utilization. The currently available information relating to distribution, propagation, floral morphology, flowering history, eco-system services etc. is also highlighted.

Relationship of GHRL Gene Polymorphism with Milk Production and Components in Holstein Cows

The current study was conducted in private station located in the middle of Iraq by using 100 samples of blood to determine the effect of GHRL gene polymorphism on milk traits in Holstein cows. Results showed two alleles with co-dominance and three genotypes was detected in the site -97, the allele frequency was 0.72 and 0.28 for G and A allele respectively. Results showed a significant effect of SNP on lactation period length (P<0.01). The cows with mutant genotype (AA) were the longest lactation period (241 day) while the cows with wild genotype were the shortest lactation period. Total milk yield affected significantly (P<0.01) by allele type, the highest quantity of milk yield was in cows with mutant genotype namely, 3366.77 Kg. High significant differences in daily milk yield were reported in cows according the alleles type, AA cows genotypes achieved 13.97 Kg /day compared with the cows with GG genotype which achieved 8.82 kg/day. Milk components such as lactose and protein were affected significantly (P<0.01) by GHRL gene SNP, the highest rate of lactose and protein were noticed in cows with wild genotype namely, 5.45 and 3.60% respectively. Milk fat differed significantly (P<0.05) in cows depending on its genotype, the highest rate was recorded in cows with wild genotype (GG) namely 3.90%.

Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers.

Przewalski horses are considered the last living population of wild horses, however, they are secondarily feral offspring of herds domesticated ~ 5000 years ago by the Botai culture. After Przewalski horses were almost extinct at the beginning of the twentieth century, their population is about 2500 individuals worldwide, with one of the largest breeding centers in Askania-Nova Biosphere Reserve (Ukraine). The research aimed to establish the maternal variation of Przewalski horses population maintained in Askania-Nova Reserve based on mitochondrial DNA hypervariable 1 and hypervariable 2 regions profiling, as well as, analysis of Y chromosome single nucleotide polymorphism unique for Przewalski horses, and coat color markers: MC1R and TBX3. The mtDNA hypervariable regions analysis in 23 Przewalski horses allowed assigning them to three distinctly different haplotypes, showing the greatest similarity to the Equus caballus reference, the Equus przewalskii reference, and to extinct species-Haringtonhippus. The Y chromosome analysis using fluorescently labelled assays differentiated horses in terms of polymorphism (g731821T>C) characteristic of Equus przewalskii. All male individuals presented genotype C characteristics for Przewalski horses. The polymorphisms within the coat color genes indicated only native, wild genotypes. The Y chromosome and coat color analysis denied admixtures of the tested horses with other Equidae.

Non-synonymous SNPs variants of PRKCG and its association with oncogenes predispose to hepatocellular carcinoma

BackgroundPRKCG encodes PKC γ, which is categorized under the classical protein kinase C family. No studies have specifically established the relationship between PRKCG nsSNPs with structural and functional variations in PKC γ in the context of hepatocellular carcinoma (HCC). The present study aims to uncover this link through in-silico and experimental studies. MethodsThe 3D structure of PKC γ was predicted. Molecular Dynamic (MD) Simulations were run and estimates were made for interactions, stability, conservation and post-translational alterations between wild and mutant structures. The association of PRKCG levels with HCC survival rate was determined. Genotyping analyses were conducted to investigate the deleterious PRKCG nsSNP association with HCC. mRNA expression of PKC γ, HIF-1 alpha, AKT, SOCS3 and VEGF in the blood of controls and HCC patients was analyzed and a genetic cascade was constructed depicting these interactions.ResultsThe expression level of studied oncogenes was compared to tumour suppressor genes. Through Alphafold, the 3D structure of PKC γ was explored. Fifteen SNPs were narrowed down for in-silico analyses that were identified in exons 5, 10 and 18 and the regulatory and kinase domain of PKC γ. Root mean square deviation and fluctuation along with the radius of gyration unveiled potential changes between the wild and mutated variant structures. Mutant genotype AA (homozygous) corresponding to nsSNP, rs386134171 had more frequency in patients with OR (2.446), RR (1.564) and P-values (< 0.0029) that highlights its significant association with HCC compared to controls in which the wild genotype GG was found more prevalent.ConclusionnsSNP rs386134171 can be a genetic marker for HCC diagnosis and therapeutic studies. This study has laid down a road map for future studies to be conducted on HCC.

#6128 IMPACT OF MANNOSE-BINDING LECTIN DEFICIENCY ON GRAFT SURVIVAL IN TRANSPLANT RECIPIENTS WITH IGAN

Abstract Background and Aims The progression of IgA nephropathy (IgAN) has been associated with Mannose -Binding Lectin levels (both excess or deficiency). The MBL deficiency, is associated with the rs5030737, the rs1800450 and the rs1800451, who represent the “O” allele. Since lectin pathway deregulation may impact on IgA progression on native kidney we hypothesized that the presence of the “O” allele and therefore MBL deficiency, could influence also the graft survival in recipients with a biopsy-proven diagnosis of IgAN on native kidneys. Therefore we investigated the role of MBL “O” allele in kidney transplant recipients with IgAN. Method We enrolled 32 kidney transplant recipients with biopsy-proven IgAN on the native kidney. The region in MBL encompassing the SNPs rs5030737, rs1800450 and rs1800451were amplified using PCR and analyzed by Sanger sequencing.Clinical data at baseline and during the follow-up were collected from patients’ records. An eGFR &amp;lt;60mL/min/1.73m2 (MDRD equation) was considered as main outcome at univariate and multivariate analyses. Results The 38% of patients carry the“O” allele and 62% of patients the “A” allele which is associated with the wild genotype. No difference between the two groups as for demographic features, donor and transplant-related variables has been found. Interestingly we found that patients with the “O” allele had a worse graft outcome (P = 0.01) during a mean follow-up of 151 months (Figure 1). The “O” allele was an independent predictor for the graft survival in a Cox survival analysis model adjusted for donor's and recipient's age, acute rejection, and disease recurrence (HR 0.046; 95% I.C. 0.005-0.423; P = 0.01). Moreover we found a link between the genetic background and the MBL serum level (Figure 2). Conclusion Our study suggest a potential role of the MBL deficiency in the long term graft dysfunction in kidney transplant recipient with IgAN.

Development and validation of a novel nomogram to predict the impact of the polymorphism of the ICAM-1 gene on the prognosis of ischemic cardiomyopathy.

The current study investigated the association between polymorphisms of the ICAM-1 gene and prognosis of Ischemic cardiomyopathy (ICM), and developed a prognostic nomogram for ICM on the basis of ICAM-1 gene variants. The current study included totally 252 patients with ICM. In addition, PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) was used to genotype SNPs in the ICAM-1 gene in the patients. Later, the nomogram model was built by combining clinical data and ICAM-1 gene variants. This study used the least absolute shrinkage and selection operator (LASSO) regression model to optimize feature selection into an ICM prognostic model. Furthermore, multivariate Cox-regression was applied to build the prognostic model, which included clinical and gene features chosen by the LASSO regression model. Following that, the receiver operating characteristic (ROC) curve, C-index, calibration plot analyses and decision curve analysis (DCA) were carried out to evaluate the discrimination ability, consistency, and clinical utility of the prognostic model, and the bootstrap method was adopted for internal validation. predicting factors rs112872667, treating by PCI or CABG, ventricular arrhythmia, left ventricular end-diastolic diameter (LVDD), use of β-blockers, systolic blood pressure (SBP), heart rate (HR), and serum sodium were incorporated into the prognostic nomogram. The constructed nomogram performed well in discrimination ability, as observed by the time-dependent C-index. Furthermore, as shown by calibration curves, our nomogram's predicted probabilities were highly consistent with measured values. With threshold probabilities, DCA suggested that our nomogram could be useful in the clinic. mutation of rs112872667 have critical predictive value on the prognosis of ICM, ICM patients with the mutant genotype (CT or TT) have higher survival probability than those with the wild genotype (CC). Mutation of rs112872667 in ICAM-1 gene have critical predictive value on the prognosis of ICM, ICM patients with the mutant genotype (CT or TT) have higher survival probability than those with the wild genotype (CC).

Comparative analysis of the open reading frames protein genes of genotype 4 Hepatitis E virus in swine and wild boar

The goal of this study was to determine the molecular diversity of the open reading frames (ORFs) ORF1, ORF2, ORF3 protein genes from full-length genomes of genotype 4 hepatitis E virus (HEV) from pigs and wild boars at protein and gene level. Statistical technique Shannon entropy was used for mutational analysis of ORF1–ORF3 protein genes to identify amino acid substitutions in the HEV 4 sequences isolated from pigs and wild boars that were most susceptible to mutations. Gene selective pressure for genes was estimated using Tajima’s neutrality test. The ORF regions of 11 swine and 11 wild boar genotype 4 HEV isolates with complete genomes from the GenBank database were analyzed comparatively. The total number of polymorphic sites was determined. Nonsynonymous (amino acid changing) and synonymous (amino acid preserving) substitutions were identified in ORF1, ORF2, ORF3 in swine and wild boar HEV 4 isolates. No evidence of recombination was found for ORFs in 11 swine HEV 4 isolates, ORF2, ORF3 in 8 wild boar HEV 4 isolates. However, a recombination fragment with a length of 430 nucleotides was detected in the ORF1 gene of 3 wild boar HEV 4 isolates. Positive D Tajima factors were determined for ORF1, ORF2, ORF3 genes of swine HEV 4 and ORF1, ORF2 genes of wild boar HEV 4. While a negative value of D Tajima’s factor was determined for ORF3 gene of wild boar HEV 4. Molecular characteristics showing principal distinctions between the open-reading frames of swine and wild boar genotype 4 hepatitis E virus were obtained. Wild boar ORF1 is characterized by lower nucleotide diversity π value (0.144) and higher number of segregated sites S value (1,688) comparing with higher π value (0.159) and lower S value (1,602) of swine ORF1. Positive values of D Tajima’s factor for ORF1, ORF2 ORF3 genes of swine HEV 4 and ORF1, ORF2 genes of wild boar HEV 4 show on positive selection of these genes. Negative value of D Tajima’s factor for ORF3 gene of wild boar HEV 4 indicates onto purifying selection decreasing variability in ORF3 gene of wild boar HEV 4. The largest number of amino acid variation sites (19.2%) was found for wild boar HEV 4 ORF3 followed by swine HEV 4 ORF3 (15.7%) comparing with other swine and wild boars HEV 4 ORFs

Interleukins (IL-23 and IL-27) serum levels: Relationships with gene polymorphisms and disease patterns in multiple sclerosis patients under treatment with interferon and glatiramer acetate

Backgroundinterleukin 23 (IL-23) is an important factor involved in the survival and proliferation of T helper 17 cells (Th17), known for their implication in multiple sclerosis (MS). By contrast, IL-27 regulates and modulates the function of T lymphocytes, in particular as a suppressor of Th17 differentiation. The aims of the study were i) to test the association of cytokines with the clinical and genetic characteristics in each of the multiple sclerosis groups (CIS - clinically isolated syndrome, RRMS - relapsing-remitting MS and SPMS – Secondary progressive MS) and ii) to evaluate the association between serum levels of IL-23 and IL-27 with T4730C (IL-27), A964G (IL-27) and R381Q (IL-23) gene polymorphisms in RRMS patients. MethodsBlood samples were obtained from 82 patients diagnosed with MS under treatment with glatiramer acetate (GA), interferon beta (IFN) 1 A and 1 B. IL-23 and IL-27 serum concentrations were measured by enzyme-linked immunosorbant assay (ELISA). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used in order to determine the genotypes for R381Q (IL-23) polymorphisms, T4730C (IL-27) and A964G (IL-27). ResultsPatients with SPMS, RRMS and CIS respectively differed significantly regarding age distribution (p = 0.003) but the studied MS groups were similar regarding age at disease onset (p = 0.528) and treatment type (p = 0.479). A significant increase of mean serum IL-27 was noticed in cases with early onset (age at disease onset <28 years) of RRMS (mean difference: 4.2 pg/ml, 95% CI: 0.8–5.3 pg/ml), compared to cases with later onset of RRMS (age at disease onset ≥28 years). RRMS patients with wild GG genotype of R381Q (IL-23) showed a significant increase of mean serum IL-23 than patients with variant AG genotype (mean difference: 115.1 pg/ml, 95% CI: 8.6–221.6 pg/ml). A trend for a higher increase in means of serum IL-23 (p = 0.086) was observed in RRMS patients carriers of AA genotype of A964G (IL-27) polymorphism in comparison with patients with AG or GG genotypes. We found no significant monotonic correlation of IL-27, IL-23 serum levels with age at disease onset (years) and duration of disease (p > 0.05) in the CIS and SPMS group respectively but a significant correlation between IL-23 and the duration of disease-modifying treatment was noticed only in the SPMS group. ConclusionsThe results of the current study suggest an association between IL-23 levels and the R381Q gene polymorphism and also a relationship between IL-27 serum levels and early age at disease onset in RRMS patients.

Integrin alpha-4 gene polymorphism in relation to natalizumab response in multiple sclerosis patients

Objectives: The aim of this study was to assess the possible the association between +3061 (G&gt;A, rs1143676) missense mutation in exon 24 of the integrin α-4 subunit (ITGA-4) gene and the response to natalizumab in a sample of Iraqi multiple sclerosis patients. Methods: A sample of 59 patients with multiple sclerosis (16 males and 43 females; mean age of 32 years; age range of 15 to 52 years) receiving natalizumab for at least 12 consecutive months were involved in the study between March and August/ 2022. The sample was categorized into two groups according to their response to natalizumab treatment (responders and non-responders). Polymerase chain reaction and Sanger’s sequencing for the extracted deoxyribonucleic acid was performed to identify the polymorphism at ITGA-4 gene promoter region. Results: The 3061 AA and AG genotypes were present in both groups (responders and non-responders to natalizumab treatment) with the lack of the wild form GG genotype. The AG genotype was significantly present in the non-responders’ group and appeared to have a significant impact on the responsiveness to natalizumab by increasing the propensity of being non-responder with a positive correlation (Phi-coefficient of 0.294) on the contrary of AA genotype. Conclusion: The +3061 (G.A) missense mutation is related to the response to natalizumab in multiple sclerosis patients with the AG genotype, thereby increasing the likelihood of non-response significantly.

The Relationship Between The Polymorphism of Beta A (Βa) Sheet of Inhibin Gene and Semen Characteristics in Holstein Bulls

This study aimed to test a linkage between Inhibin beta A (INHβA) polymorphism and semen quality in Holstein bulls in Iraqi Artificial Insemination Center. The experiment trial was carried out on (12 n) pure Holstein breed bulls. The study period started from January 2022 until February 2022. The Ejaculates were collected and its characteristics were evaluated immediately, additionally, 10 ml of blood were collected from each bull (12 samples) for genomic DNA extraction to determine the single nucleotide polymorphisms (SNPs) and compared with semen quality. The findings showed the presence of four variants at Exon 2; C (903) T, C (916)Y, G (917)K, and G (966) R in Exon 2 when compared with Gene sequence ID: XM_024990466.1. Two out of four Exon 2 SNPs were non-sense mutations(C (903) T and G (966) R), while the remains were missense which made the change in Arginine &gt; phenylalanine at position (306). Regarding the volume of ejaculates, the results recorded that non-significant difference was shown in whole alleles of the loci, except in one locus (G (966) R), the bulls that had a wild allele (A) recorded maximum collected volume (p &lt; 0.001). In addition, the bulls that represented wild genotypes showed a significant increase in sperm concentration and both mass and individual motility than mutant genotypes in all loci. Moreover, The results of the dead sperm percentage showed a non-significant correlation between the genotypes of all loci except in C (903) T, which demonstrated the superiority of the wild allele over the mutant. Lastly, the results prevailed that the mutant genotype related to the bad semen quality for the bulls, while, the wild genotypes showed good semen parameters, these results may be due to the effect of SNPs on the expression of INHA or the increase in its activity.

Genetic diversity and origin of captive lion (Panthera leo) in South Africa: an assessment and comparison to wild populations

South Africa has a large captive lion (Panthera leo) sector, but detailed knowledge on the origin of individuals and any potential genetic value to conservation targets is lacking. In 2021, the South African government committed to closing the sector and have since appointed a Ministerial Lion Task Team (2022) to initiate this process. Some have suggested that captive lions could be integrated into wild populations as part of the process but information on the genetic origins and diversity of captive lions is critical if this is to be explored further. Both the Biodiversity Management Plan for lions in South Africa (2015) and a High-Level Ministerial report for the South African government (2021) have called for more information on the genetic composition of captive lions. To determine the probable origin of captive lions in South Africa we summarised existing survey responses from captive facilities (collected 2017–2018) and CITES permit data (issued 1991–2019). Survey data suggest that most lions were sourced from within the South African captive sector. However, many CITES permits were also issued for the import of lions from across Africa and beyond, indicating possible mixed origins within the sector. To evaluate genetic relationships between captive and wild lions in South Africa we standardised existing microsatellite marker data from three laboratories and analysed genotypes of captive lions from 31 properties. A comparison of captive and wild lion genotypes revealed that the genetic composition of captive lions is currently comparable to existing wild South African lions. Captive lions cluster with similar probabilities to three of four regional reference populations of wild lions included in the study and no major signatures of inbreeding were identified. However, captive lions are highly genetically interconnected across properties and represent a smaller effective population size compared to Kruger National Park, the largest population of wild lions in South Africa, suggesting some risk of future inbreeding. There were also signatures of genetic drift which should be investigated further as it will likely compromise any potential conservation genetic value of captive lions in the future. The findings of this study should be considered when planning the fate of individuals within South Africa’s captive lion sector and within the broader context of African lion conservation.

IL-4Rα (rs1801275) A>G polymorphism in Egyptian immune thrombocytopenia (ITP) patients: a single center experience

IntroductionChronic immune thrombocytopenia (cITP) is characterized by dysregulation of the immune response. Until recently, the role of Th2-related cytokine gene polymorphisms was unclear. Interleukin 4 (IL-4) exerts its functions by binding to three types of IL-4 receptor (IL-4R) complexes. We aimed to explore the potential association between the gene polymorphism of IL-4Rα and cITP. MethodsWe investigated the clinical impact of the IL-4Rα (rs1801275) A>G single nucleotide polymorphism (SNP) using the polymerase chain reaction (PCR) followed by the restriction fragment length polymorphism (RFLP) method in 82 cITP patients and 60 healthy controls (HCs). ResultsThe IL-4Rα (rs1801275) A>G polymorphism analysis showed the mutant GG genotype was significantly higher in control females (p = 0.033). The wild AA genotype had a higher bleeding score (p = 0.02) in the adulthood onset group. Furthermore, the wild AA genotype in the cITP childhood onset group was significantly associated with the disease severity, as well as the response to treatment (p = 0.040). ConclusionThe mutant G allele is protective against the susceptibility to cITP in the Egyptian females. The IL-4Rα (rs1801275) A>G polymorphism may affect the clinical severity of cITP and treatment response in the Egyptian population.

Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits.

Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

Superior salt tolerance in wild soybean (G. soja) is associated with better ion ‘exclusion’ ability from leaves and mesophyll cells than cultivated soybean genotypes (G. max)

Soybean (Glycine max) is a salt-sensitive crop. However, wild soybean (Glycine soja) is a potential source of germplasm to improve salt tolerance in G. max. This study evaluated the response of cultivated soybean (G. max cv. Bunya and Lee) and wild soybean (G. soja) to ionic components of salt stress to test the hypothesis that wild and cultivated soybean genotypes differ in leaf tissue tolerance to Na+ and/or Cl–. The soybean genotypes were subjected to NaCl, Na+ salts, and Cl– salts at 50, 75 and 100 mM, and a non-saline control to analyse the effect of salts/ions on growth, tissue ion concentrations and photosynthesis. Cryo-SEM X-ray microanalysis was used to evaluate cellular [Na], [Cl] and [K] in various cell types within leaflets. NaCl and Na+ salts reduced shoot and root dry mass more than Cl– salts in the three genotypes. Soja maintained higher photosynthetic rates (84 % of control) than Lee (70 % of control) and Bunya (60 % of control) in the 75 mM treatments. Soja had lower [Na+] in leaves and mesophyll cells than Lee and Bunya. G. soja had greater tolerance to salinity than G. max due to better ‘ion exclusion’ from leaves and photosynthetically active mesophyll cells.

Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar.

The diversity of domestic pig breeds and their hybridization increases the variety of phenotypes expressed in hybrids. The aim of this study was to quantify the differences of cranial morphologies between local Lithuanian Indigenous Wattle pigs and theirhybrids with wild boar. A total of sixteen craniometric measurements were performed on the lateral, ventral and dorsal sides of 71 skulls of Lithuanian Indigenous Wattle pigs and their hybrids, including 1/4 wild boar (WB), 1/2 wild boar and 3/4 wild boar genotypes. The weight of the skull was affected by the genotype, live weight and sex of the animal. The size of the skull, particularly related to skull length parameters, increased consistently with the increase of the wild boar proportion in the hybrids. However, the Sus scrofa genotype did not affect the skull height. Clear discrimination was possible between the local Lithuanian breed pigs and their hybrids with different proportions of wild boar and between individual groups of hybrids. The most correct classification was determined on the basis of the overall and length parameters of the crania. This could contribute to better management and utilization of hybrids.

Association of Methylenetetrahydrofolate Reductase Gene Polymorphism in Mothers With Adverse Clinical Outcomes in Neonates.

The presence of polymorphic methylenetetrahydrofolate reductase(MTHFR) in mothers poses a risk for numerous detrimental outcomes in neonates. The present study investigated the association of maternal MTHFR A1298C and C677T single nucleotide polymorphisms (SNPs) with the clinical outcomes in their neonates. The cross-sectional study included 60 mothers and their neonates. Blood samples from mothers were analyzed for MTHFR A1298C and C677T SNP genotyping by real-time polymerase chain reaction. Clinical details of mothers and neonates were documented. Study groups were stratified based on wild, heterozygous, and mutant genotypes for the respective polymorphisms observed in mothers. Multinomial regression was applied for the association, followed by gene model formulation to estimate the impact of the genetic variants on the outcomes. The frequency percentages of mutant CC1298 and TT677 genotypes were 25% and 8.06%, respectively, and the mutant allele frequencies (MAF) were 42.5% and 22.5%. Percentages of adverse outcomes such as intrauterine growth restriction, sepsis, anomalies, and mortality were higher in neonates born to mothers with homozygous mutant genotypes. Maternal C677T MTHFR SNPs revealed a significant association with neonatal anomalies (p = 0.001). The multiplicative risk model depicted OR (95% CI) for CT vs. CC+TT as 3.0 (95% CI: 0.66-13.7), and for TT vs. CT+CC was 15 (95% CI: 2.01-112.12). The C677T SNP in mothers predicted a dominant model for neonatal death (OR (95% CI): 5.84 (0.57-60.03), p = 0.15), whereas the A1298C reported recessive model for 1298CC mothers (OR (95% CI): 11 (1.05-115.5), p = 0.02). Both the genotypes assumed a recessive model for adverse neonatal outcomes: OR (95%CI) for CC vs. AA+ACwas 3.2 (0.79-12.9, p = 0.1), and for TT vs. CC+CT was 5.48 (0.57-175.7, p = 0.2). The risk for sepsis in neonates was nearly six times higher in those born from mothers with homozygous CC1298 and TT677 than in the wild and heterozygous variants. Mothers with C677T and A1298C SNPs are highly susceptible to adverse outcomes in their neonates. Hence, screening the SNPs during the antenatal period can purposefully serve as a better predictive marker, following which proper clinical management could be planned.