Number Of Alleles Research Articles

Genetic evaluation of the breeding strategy effectiveness for horses of the New Altai breed

The purpose of the study was to study the dynamics of the main selected traits in horses of the New Altai breed and the genetic characteristics of the breed. In this paper, the indicators of the main measurements of the body and live weight of horses, depending on gender and region of birth, are analyzed. The main genetic and population parameters of the breed were calculated based on microsatellite DNA loci: the total number of alleles at 17 loci (Na), the average number of alleles per locus (Nv), the level of polymorphism (Ae), observed (Ho) and expected (He) heterozygosity, coefficients of intrapopulation inbreeding (Fis), genetic similarity (RXY) and genetic distances (DXY). It has been established that the horses of the New Altai breed are characterized by a relatively high level of polymorphism and genetic diversity, both in the breed as a whole and in the context of breeding regions. The high genetic similarity of the New Altai breed with the Russian Heavy Draft and Altai breeds has been revealed. The study of the genetic structure of the breed, the levels of its intra- and inter-population diversity in combination with classical zootechnical assessment methods showed the consistency of the chosen cultivation strategy of the New Altai breed.

Morphological and molecular diversity of eggplant accessions (Solanum melongena L) using Simple Sequence Repeats (SSR) markers

The evaluation of various desirable characteristics in eggplant genotypes has facilitated the efficient process of selecting and improving their traits. Morphological parameters have proven to be valuable in assessing the similarities or differences among different accessions, while molecular data have been used to support the conclusions drawn from the morphological analysis. This study was conducted to evaluate the performance of 42 eggplant genotypes collected from Malaysia, China, and Thailand. Data for growth, yield, and related traits were collected and subjected to analysis of variance (ANOVA) using SAS 9.4. The field trial experiment was designed as a completely randomized block design with three replications. Analysis of variance (ANOVA) showed that the traits under study were highly significant (p ≤ 0.01). MV18 (5.97 kg) and TV17 (5.59 kg) were observed to have high yields per plant. The SSR markers used exhibited moderate average values for the number of alleles (2.53). The major allele frequency displayed a high average value (0.53) and a moderate average number of effective alleles (2.31). Additionally, the observed Shannon's information index, expected heterozygosity, and PIC were high (0.84, 0.54, and 0.45, respectively). 42 accessions were grouped into five major clusters based on similarities using the unweighted pair-group method with arithmetic averages based on similarity matrices UPGMA Dendrogram and the EIGEN module. The findings of this study indicate that the use of simple sequence repeat (SSR) markers can effectively estimate genetic diversity and analyze phylogenetic relationships. Moreover, these markers can assist eggplant breeders in selecting desirable quantitative traits within their breeding program.

Population genetic structure of tropical bed bug (Hemiptera: Cimicidae) populations and their breeding pattern in Iraq.

A study was conducted to investigate the population genetic structure and breeding pattern of 140 tropical bed bugs, Cimex hemipterus (F.) (Hemiptera: Cimicidae), collected from 14 infested sites in major cities in Iraq. The samples were genotyped using a set of 7 polymorphic microsatellite markers. High genetic variety was seen among populations, with an average of 2-9 alleles per locus. The number of alleles across 7 microsatellite loci was between 6 and 18. There was a notable disparity in the alleles per loci when comparing the overall population to those within it. The overall population exhibited an average observed heterozygosity of 0.175 and an average expected heterozygosity of 0.730. Among the population, the average observed heterozygosity was 0.173, while the average expected heterozygosity was 0.673. Analysis of molecular variance (AMOVA) revealed that 93% of the genetic variability was within the populations, and 7% was among them. The genetic differentiation coefficient (FST = 0.045), indicates a low degree of genetic differentiation and a high degree of inbreeding (FIS = 0.761), as indicated by notably significant positive inbreeding coefficients. Admixed individuals were revealed using STRUCTURE and neighbor-joining phylogenetic trees, demonstrating moderate gene flow between populations and a lack of genetic structure in the regional groups. Thus, both active dispersion and human-mediated dispersion possess the potential to influence the low population genetic structure of tropical bed bug C. hemipterus populations in Iraq, which can have implications toward tropical bed bug and management strategies.

Analysis of the genetic variability of camel populations in Kazakhstan using ISSR-PCR markers

In this study, we analyzed the genetic characteristics of camel populations of Kazakhstan using ISSR-PCR markers. As a result, fragments of the following sizes were identified using the (AG)9C primer: 200, 320, 370, 430, 580, and 700 bp. Based on the (GA)9C primer, the length of the amplicons was 300, 350, and 430 bp. An analysis of the genetic differences of camels in the populations was carried out using ISSR-PCR markers. As a result, the number of allelic indices of polymorphic loci of the (AG)9С primer and related polymorphic loci in the population of the Shymkent population was equal to 77.78%, the allelic index of polymorphic loci of camels in the Taraz population - 33.3%, Kyzylorda and Atyrau populations - 44,44%. In camels selected for the study, the number of observed alleles (Na) averaged 1.27, the effective number of alleles (Ne) was equal to 1.37, the genetic diversity (h) according to Nei was equal to 0.21 and the Shannon index (I) was equal to 0.30. The average allelic score for polymorphic loci was 50.0% across four populations. Based on our results, the two markers used in the work were informative in assessing the genetic diversity of camel populations.

Impact of genetic background as a risk factor for atherosclerotic cardiovascular disease: A protocol for a nationwide genetic case-control (CV-GENES) study in Brazil.

Atherosclerotic Cardiovascular Disease (ASCVD) represents the leading cause of death worldwide, and individual screening should be based on behavioral, metabolic, and genetic profile derived from data collected in large population-based studies. Due to the polygenic nature of ASCVD, we aimed to assess the association of genomics with ASCVD risk and its impact on the occurrence of acute myocardial infarction, stroke, or peripheral artery thrombotic-ischemic events at population level. CardioVascular Genes (CV-GENES) is a nationwide, multicenter, 1:1 case-control study of 3,734 patients in Brazil. Inclusion criterion for cases is the first occurrence of one of the ASCVD events. Individuals without known ASCVD will be eligible as controls. A core lab will perform the genetic analyses through low-pass whole genome sequencing and whole exome sequencing. In order to estimate the independent association between genetic polymorphisms and ASCVD, a polygenic risk score (PRS) will be built through a hybrid approach including effect size of each Single Nucleotide Polymorphism (SNP), number of effect alleles observed, sample ploidy, total number of SNPs included in the PRS, and number of non-missing SNPs in the sample. In addition, the presence of pathogenic or likely pathogenic variants will be screened in 8 genes (ABCG5, ABCG8, APOB, APOE, LDLR, LDLRAP1, LIPA, PCSK9) associated with atherosclerosis. Multiple logistic regression will be applied to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI), and population attributable risks will be calculated. Clinical trial registration: This study is registered in clinicaltrials.gov (NCT05515653).

Genetic diversity and fine-scale genetic structure of the conifer Podocarpus lambertii in a forest-grassland mosaic from Southern Brazil

Abstract Podocarpus lambertii (Podocarpaceae) is an endangered conifer, endemic to Brazil and occurring in continuous forest and forest-grassland landscapes from the Araucaria Forest. Aiming to support conservation efforts for P. lambertii populations and gain insights into the preservation of forest-grassland mosaics in southern Brazil, we assessed the spatial pattern, genetic diversity, and fine-scale genetic structure (FSGS) within a population situated in a forest-grassland mosaic. The study was conducted in a 9-ha plot in forest-grassland mosaic. All P. lambertii individuals with height ≥ 0.1 m were sampled and the population was stratified into four demographic categories (Seedling, Juvenile, Immature, and Reproductive). For each of these categories, we used 13 allozyme markers to evaluate the spatial pattern, genetic diversity and FSGS. All individuals occurred inside the forest-patches, presenting an aggregated pattern of distribution. Low genetic diversity was recorded for all categories and for the population ( H ⌢ E = 0.046 {\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\frown$}}\over H} _E} = \,0.046 ), as well as a high number of rare alleles (20). Positive and significant FSGS was estimated only for the Juveniles ( θ ⌢ x y = 0.012 {\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\frown$}}\over \theta } _{xy}} = \,0.012 ) up to maximum distance of 7.1 m, and the minimum viable area for the long-term conservation of Reproductive genetic diversity was approximately 68 ha. The set of our findings suggests that conservation actions need to enhance connectivity among forest-patches to prevent the loss of rare alleles due to genetic drift. Additionally, we highlight the significance of preserving forest-patches as repositories of species diversity and as crucial connectors between populations.

Sex-Specific Susceptibility Loci Associated With Coronary Artery Aneurysms in Patients With Kawasaki Disease.

Kawasaki disease (KD) is an acute vasculitis that primarily affects children under age 5 years. Approximately 20-25% of untreated children with KD and 3-5% of those treated with intravenous immunoglobulin therapy develop coronary artery aneurysms (CAAs). The prevalence of CAAs is much higher in male than in female patients with KD, but the underlying factors contributing to susceptibility to CAAs in patients with KD remain unclear. This study aimed to identify sex-specific susceptibility loci associated with CAAs in KD patients. A sex-stratified genome-wide association study (GWAS) was performed using previously obtained GWAS data from 296 KD patients and a new replication study in an independent set of 976 KD patients by comparing KD patients without CAA (controls) and KD patients with aneurysms (internal diameter ≥5 mm) (cases). Six male-specific susceptibility loci, PDE1C, NOS3, DLG2, CPNE8, FUNDC1, and GABRQ (odds ratios [ORs], 2.25-9.98; p=0.00204-1.96×10-6), and 2 female-specific susceptibility loci, SMAD3 (OR, 4.59; p=0.00016) and IL1RAPL1 (OR, 4.35; p=0.00026), were significantly associated with CAAs in patients with KD. In addition, the numbers of CAA risk alleles additively contributed to the development of CAAs in patients with KD. A sex-stratified GWAS identified 6 male-specific (PDE1C, NOS3, DLG2, CPNE8, FUNDC1, and GABRQ) and 2 female-specific (SMAD3 and IL1RAPL1) CAA susceptibility loci in patients with KD.

Genetic variability of the endangered fish lake minnow (Eupallasella percnurus) in populations newly established by translocation and those existing long term in Poland.

The lake minnow Eupallasella percnurus is a small leuciscid fish. In Poland, this species has been in a continuous decline since the mid-20th century and is presently considered as a extremely endangered. According to Polish law, E. percnurus is a strictly protected species that requires active conservation measures. In Poland, one the most common and effective measure of active protection E. percnurus is initiation of new populations. For this purpose, in 2004-2012, juvenile individuals originating from aquaculture conditions were translocated to group of isolated water bodies not inhabited by this species. The juveniles were offspring of parental fish belonging to the same local population, which is extinct at present. Five of those attempts were successful. The aim of the present study was to assess the genetic variation in a group new populations and compare genetic variation indicators with 13 old populations that had existed for decades. The polymorphism of 13 microsatellite markers was investigated, significance of differences in the genetic variation indicators between the groups were tested using a one-way analysis of variance (ANOVA). The mean values of all summary statistics under study, i.e. observed heterozygosity, expected heterozygosity and the total number of alleles, were higher in the group of new populations compared to almost all old ones. A similar dependence was found for Garza-Williamson M values, where the mean for the group of new populations was higher than in almost all old populations. Our results indicate that all recently established E. percnurus populations have not yet experienced any extensive founder effects or bottlenecks. They have preserved a large part of the genetic variability typical of their maternal population, which might also have been relatively high. This feature of new populations, may give them a relatively high ability to adapt to changing environments in the future.

Sickle Cell Gene Frequency Analysis in Visapur, District Chandrapur: A Case Study of Single Village from Central India

Sickle cell anemia burden is generally studied by calculating how many sickle cell carriers are found in specific diagnostic camps based on combination of screening test and confirmatory tests i.e. sickle cell carrier prevalence method. Where as actual total numbers of alleles can be estimated by combining data of how many carriers and homozygous patients are found in the confirmatory testing camps, which is a gene frequency calculation method. Aim of this study is to compare prevalence and gene frequency calculations for one village data, for study conducted in year 2005 at Visapur village, Chandrapur district, Central India. Sampling was done in village school followed by screening and confirmatory testing at field work laboratory at Ballarpur city which included solubility test, hemoglobin estimation, hemoglobin electrophoresis using cellulose acetate membrane method followed by pedigree analysis after parent studies. This is a sickle cell anaemia study of single village data point. Out of total population of the village, 6.68% population were randomly studied. Total registrations done for 755 individuals and out of that total 628 individuals were tested (N = 628, 293 were females and 335 were males) for solubility tests followed by haemoglobin electrophoresis. For socioeconomically disadvantages groups, it was noted that out of 628 individuals, tribals were 111 and non-tribals, 517. Out of total tested, N=628, SCD homozygous status were found in 7 cases (Hb S+S electrophoresis pattern). In 87 cases sickle cell carrier status (Hb A+S electrophoresis pattern) were observed and in remaining 534 individuals, non-sickle cell status observed i.e. Hb A+A electrophoresis pattern. Based on this sickle cell prevalence observed for total tribal and non-tribal is 13.85% After classifying tribal Vs non-tribal population, 7 homozygous patients were found in non-tribal communities, 5 in Schedule caste, 1 in OBC and 1 in open category, there is no SCD patient found in tribal community. Out of 50 sickle cell carriers, 7 were found from tribal community and remaining all 80 belongs to non-tribal community. Out of which, 49 are from scheduled cast and 31 from OBC community. After studying sickle cell prevalence and gene frequency pattern, it is found that gene frequency gives more accurate status of sickle cell anaemia even in small population size, i.e. independent study of single village, as compared to estimation sickle cell anemia using sickle cell carrier prevalence method.

Molecular Diversity Analysis of Some Selected Brri Developed Rice Varieties Using Ssr Markers

Molecular characterization of 26 modern rice varieties of Bangladesh was performed using 52 simple sequence repeat markers (SSRs) to estimate the genetic diversity and to reveal genetic relationships among rice cultivars. A total of 156 alleles were detected where the number of alleles per locus generated by each marker varied from 2 to 7, with an average of 3. The band size for a given microsatellite locus ranged from 79 to 278 bp. The polymorphism information content (PIC) for the SSR loci ranged from 0.08 to 0.79, with an average of 0.35. RM566 was the best marker for identification and variability assessment of varieties as revealed by PIC values. A UPGMA dendrogram generated using the NTSYS-pc revealed four clusters with a similarity coefficient of 0.55, whereas phylogenetic cluster analysis of the SSR data based on Nei-genetic distance divided the varieties into three groups. Two- and three-dimensional graphical views of principal coordinate analysis showed the spatial distribution of the varieties and revealed that BRRI dhan56, BRRI dhan51, BRRI dhan52, BRRI dhan61, BRRI dhan62 and BRRI dhan66 were found far away from the centroid of the cluster. The findings of this study are helpful for varietal identification, background selection during backcross breeding and for selecting the suitable genetically diverse parents for crossing programs. SAARC J. Agric., 21(2): 1-14 (2023)

Genetic diversity in cassava based on agronomical, physiological and est-microsatellite markers under moisture stress conditions

Genetic diversity of 23 cassava accessions was studied using agro-physiological and EST-Microsatellite markers. Based on agronomical and physiological parameters the genotypes were classified into 6 clusters. Cluster-2 had highly 10 genotypes while the clusters-5 and 6 had single accession. The high yielding and highly drought tolerant genotype 8S501 stood alone in cluster-5. It had high cluster mean values for majority of the traits. The genotypes present in cluster-4 & 5 and cluster-1 & 2 were divergent and hybridization between these two groups may result in superior genotypes for drought tolerance. The EST-Microsatellites obtained from drought transcriptome of cassava showed that the mean number of alleles per locus was 1.81 with an average size of 217.7 basepairs (bp). The locus, MeESSR47 (Thylakoid membrane phosphoprotein 14 kDa, chloroplast precursor, putative), had more heterozygosity (0.387) and Shannon’s Index (0.575) among all the loci. These results cumulatively showed the low polymorphism in the EST regions of cassava DNA. The dendrogram showed 4 clusters based on EST Microsatellite diversity. The microsatellite based cluster classification of genotypes did not follow the diversity based on agronomical traits under moisture stress condition. A weak correlation revealed by Mantel test also indicated that there was no relation between agronomical and molecular diversity.

Optimisation of a DNA extraction protocol from fingerprints for the analysis of nuclear STR and mitochondrial DNA genetic profiles

Abstract Most of the cells found in fingerprints belong to the cornified barrier of the epidermis (stratum corneum), lack nuclei and cytoplasmic organelles, and are filled with keratin. Nuclear and mitochondrial DNA is degraded and embedded in the keratin mesh, a very resistant protein that is difficult to remove during DNA extraction. In this work, we studied the possible negative effect of keratin on PCR reactions and the influence of keratinase and proteinase K on the extraction of DNA from fingerprints. The role of glycogen in the DNA yield during the precipitation step and the importance of washing the obtained DNA with 70% ethanol were also studied. DNA was extracted from 96 fingerprints corresponding to recent prints and stored for 1, 5, and 18 months from 6 individuals. No differences were observed in the concentration of extracted DNA or in the number of nuclear STR alleles in the genetic profiles of fingerprints stored during different times. However, sex differences were observed in both the concentration of DNA obtained and the number of nuclear STR alleles detected, being lower in females than in males. In 80% of the fingerprints genetic profiles were obtained with at least half of the STR nuclear markers and, in 50% of the fingerprints genetic profiles were obtained with more than 90% of the markers, which would allow an unambiguous identification of the donor. In all fingerprints where mtDNA was analysed, complete sequencing of the HV1 and HV2 regions was possible, which increases the accuracy of the results obtained. The optimised protocol allowed obtaining a complete STR nuclear genetic profile of a 20-year-old palmprint. Key Points

Correlation of 20 Single-Nucleotide Polymorphisms with Weight and Wool Traits in Alpine Merino Sheep.

SNPs associated with important traits of fine-wool sheep that were previously obtained through genome-wide association analysis screening were verified and analyzed. A total of 20 SNPs related to birth weight, bundle strength, cleaning rate, and fiber diameter were screened using whole-genome resequencing, and the SNPshot assay was used to detect and analyze polymorphisms. This study found that, among the 20 SNPs associated with important traits in Alpine Merino sheep, 8 were monomorphic and 12 were polymorphic, of which 6 showed moderate polymorphisms and 6 showed low polymorphisms. The heterozygosity of the 12 polymorphic loci ranged from 0.10 to 0.49, the effective number of alleles ranged from 1.11 to 1.98, and the polymorphic information content ranged from 0.09 to 0.37. The chi-square test showed that only RHPN2:g.42678119T>G and RALYL:g.90030866A>G were in Hardy-Weinberg disequilibrium (p < 0.05); the other loci were in equilibrium (p > 0.05). These SNPs associated with important traits in Alpine Merino sheep provide a theoretical basis for genomic selection and molecular design breeding.

Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (Vigna radiata L. Wilczek): Cross-Species Transferability and Population Genetic Studies in Vigna Species

The genus Vigna is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different Vigna species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Utilizing allelic data, the 25 Vigna accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of Vigna accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the Vigna genus.

Effects of Recurrent Selection on Population Structure and Allele Frequencies in the M3S Maize Population

The effects of four cycles of recurrent selection on the allele frequencies of simple sequence repeat (SSR) markers and population structure were examined in the Maksimir 3 Synthetic (M3S) maize population (Zea mays L.). Genotyping of 32 plants from each selection cycle at 38 SSR loci revealed that the mean number of alleles per locus and the mean expected heterozygosity were preserved across selection cycles, indicating the maintenance of sufficient genetic variability in the population required for future genetic gain. The Waples test of selective neutrality revealed that genetic drift was the main force in changing allele frequencies in the population. The proportion of selectively non-neutral loci in single cycles of selection varied between 16% and 37%. Some non-neutral loci shared the same genomic locations with previously published QTLs controlling important agronomic traits. An analysis of molecular variance revealed that 5.6% of the genetic variation occurred among and 94.4% within cycle populations. Between 5% and 29% of loci were found to be in a significant Hardy–Weinberg (HW) disequilibrium, with the majority showing an excess of homozygosity. The excess of homozygosity at several loci was highly consistent across cycle populations, suggesting positive assortative mating as a possible cause of the observed HW disequilibrium. Linkage disequilibrium (LD) tests revealed that the M3S population was essentially in linkage equilibrium. The proportion of pairs of loci in significant LD varied from 0.1% to 1.8% across selection cycles, probably due to the effects of genetic drift and epistatic selection.

Genetic diversity, Population Structure and their Association with Body Weight in Egyptian Chicken Strains

A Genetic characteristics and population structure within and among Egyptian indigenous chicken strains are important for identifying some genetic resources. The present study aimed to use microsatellite markers to determine similarity and genetic distance among different genotypes and their association with growth and production traits in Egyptian indigenous chicken strains. The current study included 800 chickens and 100 genomic DNA samples obtained from four Egyptian local chicken strains of four different areas (Dokki-4, Mandarah, Anshas, and Al-Salam) in Egypt. Their genetic characteristics, population structure, phylogenetic relationships, and their association with body weight were analyzed using seven microsatellite markers. The performance of 200 chicks from each strain was assessed in terms of individual body weight and growth rate. Al-Salam strain had a significantly higher body weight than the other strains up to 12 weeks of age among the four lines of Egyptian local chickens. Additionally, male chickens across all strains indicated significantly higher body weight than females from 2 weeks of age until the end of the experiment. The study revealed a total of 68 alleles from the 7 loci across 4 chicken strains, with an average of 9.71. The average of observed heterozygosity, expected heterozygosity, and polymorphism information content were 0.799, 0.358, and 0.707, respectively. The Mandarah strain had the highest observed allele number of 5.37; however, the lowest observed allele number was 3.12 for the Dokki strain. Analysis of population structure revealed that the four chicken strains should be divided into three clusters based on the highest log-likelihood values (ΔK value, 56.3). The results showed a degree of heterozygosity in the Mandara strain with 66.7% individual memberships, indicating a level of admixture. On the other hand, the Al-Salam strain indicated a high genetic diversity with 99% individual membership. The current study provides valuable insights for future genetic polymorphism studies, the advancement of breeding programs, and strategies for the conservation of the Egyptian local chicken strains.

HLA-B*46:01:01:01 and HLA-DRB1*09:01:02:01 are associated with anti-rHuEPO-induced pure red cell aplasia

Treatment of anemia in patients with chronic kidney disease (CKD) with recombinant human erythropoietin (rHuEPO) can be disrupted by a severe complication, anti-rHuEPO-induced pure red cell aplasia (PRCA). Specific HLA genotypes may have played a role in the high incidence of PRCA in Thai patients (1.7/1,000 patient years vs. 0.03/10,000 patient years in Caucasians). We conducted a case–control study in 157 CKD patients with anti-rHuEPO-induced PRCA and 56 controls. The HLA typing was determined by sequencing using a highly accurate multiplex single-molecule, real-time, long-read sequencing platform. Four analytical models were deployed: Model 1 (additive: accounts for the number of alleles), Model 2 (dominant: accounts for only the presence or absence of alleles), Model 3 (adjusted additive with rHuEPO types) and Model 4 (adjusted dominant with rHuEPO types). HLA-B*46:01:01:01 and DRB1*09:01:02:01 were found to be independent risk markers for anti-rHuEPO-induced PRCA in all models [OR (95%CI), p-values for B*46:01:01:01: 4.58 (1.55–13.51), 0.006; 4.63 (1.56–13.75), 0.006; 5.72 (1.67–19.67), 0.006; and 5.81 (1.68–20.09), 0.005; for DRB1*09:01:02:01: 3.99 (1.28–12.49), 0.017, 4.50 (1.32–15.40), 0.016, 3.42 (1.09–10.74), 0.035, and 3.75 (1.08–13.07), 0.038, in Models 1–4, respectively. HLA-B*46:01:01:01 and DRB1*09:01:02:01 are susceptible alleles for anti-rHuEPO-induced PRCA. These findings support the role of HLA genotyping in helping to monitor patients receiving rHuEPO treatment.

The Potential of Complementary Sex-Determiner Gene Allelic Diversity for Studying the Number of Patrilines within Honeybee Colonies

Polyandry, a fundamental aspect of honeybee biology, influences genetic diversity within bee colonies. The Csd gene, responsible for sex determination, exhibits a high intraspecific polymorphism, making it a promising candidate for studying patrilines. This study investigates the potential of the complementary sex-determiner gene (Csd) as a marker for genetic studies of honeybee colonies, comparing its efficacy with standard microsatellite markers. A worker bee brood from five colonies was genotyped using both Csd and microsatellite markers. The results showed that Csd alleles offer higher variability than microsatellite markers, providing a superior resolution in genotyping. The number of distinct Csd alleles in each colony surpassed microsatellite markers, demonstrating the potential of Csd for detailed genetic analyses. Despite challenges in Csd amplification efficiency, a two-step nested PCR protocol proved effective. Interestingly, Csd genotyping alone identified more patrilines than the set of five microsatellite markers, emphasizing its efficacy. Combining Csd and microsatellite genotyping enhances the resolution of genetic studies in honeybee colonies, offering valuable insights into genetic diversity, reproductive success, and social dynamics. The Csd gene emerges as a promising tool for advancing genetic studies in honeybee populations.

Genetic Relationships of Indigenous King Coconut (Cocos nucifera L.) Populations as Determined by SSR Markers

King Coconut (KC) is an indigenous and highly valuable germplasm resource in Sri Lanka. Yet, KC populations' genetic diversity, relationships, and conservation strategies are not fully understood. Indigenous old KC populations have been dispersed across a few ancient villages in Sri Lanka. Five geographically dispersed locations were selected in Sri Lanka, and 20 KC individuals from each location were collected for the current study. Six randomly selected samples from every geographical location, together with the standard two Sri Lanka Red Dwarf and two Sri Lanka Tall varieties were initially genotyped using 21 SSR markers for polymorphism. Based on the results, ten polymorphic SSR markers were selected and used for genotyping. Power Marker, STRUCTURE, and GenAlex software were used for the SSR genetic analysis. Results revealed 0.62 mean Gene Diversity (Hs), 4.2 mean allele number, and 0.55 polymorphic information content (PIC). Clear differentiation of populations was observed with the STRUCTURE and UPGMA dendrogram. Single branching in the UPGMA dendrogram for Anuradhapura and Marandawila KC populations revealed high genetic uniformity over multi-branched Kadugannawa and Colambageara populations. According to AMOVA, 64% of the genetic variation has been partitioned among populations, indicating moderate population differentiation. Detail analysis, including a higher number of KC populations and systematic molecular analysis using more SSRs/SNPs needed in the future before implementing conservation and utilization strategies.

Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections.

Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. Borrelia burgdorferi, a bacterium that causes Lyme disease, is typically transmitted among wildlife by Ixodes ticks. Despite the existence of many alleles of B. burgdorferi's sensu stricto outer surface protein C (ospC) gene, most human infections are caused by a small number of ospC alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with ospC. To characterize the wildlife host association of B. burgdorferi's ospC alleles, we used metagenomics to sequence ospC alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (Peromyscus spp.) and only one HIA was detected at a site where mice were rarely captured. ospC allele U was exclusively found in chipmunks (Tamias striatus), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.