Allelic Heterozygosity Research Articles

Association of the OLR1 Gene of the 3’UTR g.8232(A/C) genotypes on milk fatty acid components in Holstein Friesian

Dairy cattle produce milk with a high proportion of saturated fatty acids (SFAs), instead of a low proportion of poly unsaturated fatty acids (PUFA). Oxidized low-density lipoprotein receptor 1 (OLR1) gene plays a key role in reducing oxidized low-density lipoprotein (oxLDL) involved in injury, dysfunction, and inactivation of endothelial cells. Association of the OLR1 gene in the 3’UTR of the g.8232(A/C) genotypes on 21 types of the milk fatty acids of Holstein Friesian (HF) cows were analysed kept at a breeding station in Central Java. Genotyping was analyzed by PCR-RFLP method using Pst1 restriction enzyme. Genotypic data were calculated for allele frequency, genotype frequency, and heterozygosity values. Effects of genotypes on individual fatty acid components were analyzed by General Linier Model. Genotyping resulted in three genotypes of AA, AC and CC with the frequenciest successively 0.275, 0.525, and 0.200; and two alleles for A (0.463) and C (0.538). Genotypes affected medium-chain SFAs for Myristic (C14:0) and long-chain for Palmitic (C16:0) and Stearic (C18:0). The AA genotype generated the lowest levels of myristic and stearic, instead of the highest content of palmitic. Further the AA genotype resulted in the highest level of Oleic (C18:1) of MUFA. Therefore the OLR1 gene of the 3’UTR g.8232 (A>C) SNP is possible considered as a molecular-based selection in reducing SFAs (myristic and stearic) and increasing MUFA (Oleic) in domestic HF cattle.

Low Bottleneck Detection in Long-Lived Species Despite Lost Genetic Diversity: A Case Study of Tuatara and Eastern Massasauga Rattlesnakes.

Population bottlenecks can reduce genetic diversity and may lead to inbreeding depression. However, some studies have provided evidence that long lifespans buffer negative genetic effects of bottlenecks. Others have cautioned that longevity might merely mask the effects of genetic drift, which will still affect long-term population viability. We used microsatellite data from actual populations of tuatara (Sphenodon punctatus) and eastern massasaugas (Sistrurus catenatus) as a starting point for simulated population declines to evaluate the performance of bottleneck tests under a range of scenarios. We quantified losses in genetic diversity for each scenario and assessed the power of commonly used tests (i.e., M-ratio, heterozygosity excess, and mode-shift) to detect known bottlenecks in these moderate- to long-lived species. Declines in genetic diversity were greater in bottlenecks simulated for eastern massasaugas, the shorter-lived species, and mode-shift and heterozygosity excess tests were more sensitive to population declines in this species. Conversely, M-ratio tests were more sensitive to bottlenecks simulated in tuatara. Despite dramatic simulated population declines, heterozygosity excess and mode-shift tests often failed to detect bottlenecks in both species, even when large losses in genetic diversity had occurred (both allelic diversity and heterozygosity). While not eliminating type II error, M-ratio tests generally performed best and were most reliable when a critical value (Mc) of 0.68 was used. However, in tuatara simulations, M-ratio tests had high rates of type I error when Mc was calculated assuming θ = 10. Our results suggest that reliance on these tests could lead to misguided species management decisions.

Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

ContextBlack poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized.AimsHere, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system.MethodsA total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers.Results(1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected.ConclusionOur study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe.Key messageThe genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

Heterozygosity of the Alpha 1-Antitrypsin Pi*Z Allele and Risk of Liver Disease.

The serpin family A member 1 (SERPINA1) Z allele is present in approximately one in 25 individuals of European ancestry. Z allele homozygosity (Pi*ZZ) is the most common cause of alpha 1‐antitrypsin deficiency and is a proven risk factor for cirrhosis. We examined whether heterozygous Z allele (Pi*Z) carriers in United Kingdom (UK) Biobank, a population‐based cohort, are at increased risk of liver disease. We replicated findings in Massachusetts General Brigham Biobank, a hospital‐based cohort. We also examined variants associated with liver disease and assessed for gene–gene and gene–environment interactions. In UK Biobank, we identified 1,493 cases of cirrhosis, 12,603 Z allele heterozygotes, and 129 Z allele homozygotes among 312,671 unrelated white British participants. Heterozygous carriage of the Z allele was associated with cirrhosis compared to noncarriage (odds ratio [OR], 1.53; P = 1.1×10−04); homozygosity of the Z allele also increased the risk of cirrhosis (OR, 11.8; P = 1.8 × 10−09). The OR for cirrhosis of the Z allele was comparable to that of well‐established genetic variants, including patatin‐like phospholipase domain containing 3 (PNPLA3) I148M (OR, 1.48; P = 1.1 × 10−22) and transmembrane 6 superfamily member 2 (TM6SF2) E167K (OR, 1.34; P = 2.6 × 10−06). In heterozygotes compared to noncarriers, the Z allele was associated with higher alanine aminotransferase (ALT; P = = 4.6 × 10−46), aspartate aminotransferase (AST; P = 2.2 × 10−27), alkaline phosphatase (P = 3.3 × 10−43), gamma‐glutamyltransferase (P = 1.2 × 10−05), and total bilirubin (P = 6.4 × 10−06); Z allele homozygotes had even greater elevations in liver biochemistries. Body mass index (BMI) amplified the association of the Z allele for ALT (P interaction = 0.021) and AST (P interaction = 0.0040), suggesting a gene–environment interaction. Finally, we demonstrated genetic interactions between variants in PNPLA3, TM6SF2, and hydroxysteroid 17‐beta dehydrogenase 13 (HSD17B13); there was no evidence of epistasis between the Z allele and these variants. Conclusion: SERPINA1 Z allele heterozygosity is an important risk factor for liver disease; this risk is amplified by increasing BMI.

Translocations and their effect on population genetics in an endangered and cryptic songbird, the Noisy Scrub-bird Atrichornis clamosus

ABSTRACT Best practice for conservation translocations dictates that large founder cohorts be used, in part to ensure that the maximum genetic variation from the source population is captured. Population bottlenecks caused by low founder numbers are understood to typically have a detrimental effect on genetic diversity and promote inbreeding. However, for some species, translocating large numbers of individuals may require an unfeasible allocation of resources or have a harmful effect on the source. The Noisy Scrub-bird (Atrichornis clamosus) is a cryptic and rarely observed passerine that was once believed extinct, and translocations to successfully establish new populations have been instrumental in securing its future. However, due to the inherent difficulties in capturing this elusive bird, these populations have been founded from only 11 to 31 individuals. We used 10 microsatellite markers to compare the genetics of the original source to the two extant translocated populations. Allelic diversity and heterozygosity were generally low but highest in the source population. Although translocations seem not to have conferred significant additional losses, relatedness, inbreeding and mean kinship were highest in the population founded with just 11 individuals. Despite historical evidence to the contrary, we found a bottleneck signature in just one population. The two translocated populations displayed significant differentiation from each other and there was evidence of spatial genetic structure between these populations. Additionally, there was some evidence of cryptic subdivision (Wahlund Effect). In light of these findings, we make recommendations for future management actions to help retain what genetic diversity remains.

Varying genetic imprints of road networks and human density in North American mammal populations.

Road networks and human density are major factors contributing to habitat fragmentation and loss, isolation of wildlife populations, and reduced genetic diversity. Terrestrial mammals are particularly sensitive to road networks and encroachment by human populations. However, there are limited assessments of the impacts of road networks and human density on population‐specific nuclear genetic diversity, and it remains unclear how these impacts are modulated by life‐history traits. Using generalized linear mixed models and microsatellite data from 1444 North American terrestrial mammal populations, we show that taxa with large home range sizes, dense populations, and large body sizes had reduced nuclear genetic diversity with increasing road impacts and human density, but the overall influence of life‐history traits was generally weak. Instead, we observed a high degree of genus‐specific variation in genetic responses to road impacts and human density. Human density negatively affected allelic diversity or heterozygosity more than road networks (13 vs. 5–7 of 25 assessed genera, respectively); increased road networks and human density also positively affected allelic diversity and heterozygosity in 15 and 6–9 genera, respectively. Large‐bodied, human‐averse species were generally more negatively impacted than small, urban‐adapted species. Genus‐specific responses to habitat fragmentation by ongoing road development and human encroachment likely depend on the specific capability to (i) navigate roads as either barriers or movement corridors, and (ii) exploit resource‐rich urban environments. The nonuniform genetic response to roads and human density highlights the need to implement efforts to mitigate the risk of vehicular collisions, while also facilitating gene flow between populations of particularly vulnerable taxa.

How array design creates SNP ascertainment bias.

Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.

Pleiotropic associations of heterozygosity for the SERPINA1 Z allele in the UK Biobank.

Homozygosity for the SERPINA1 Z allele causes α1-antitrypsin deficiency, a rare condition that can cause lung and liver disease. However, the effects of Z allele heterozygosity on nonrespiratory phenotypes, and on lung function in the general population, remain unclear.We conducted a large, population-based study to determine Z allele effects on >2400 phenotypes in the UK Biobank (N=303 353).Z allele heterozygosity was strongly associated with increased height (β=1.02 cm, p=3.91×10−68), and with other nonrespiratory phenotypes including increased risk of gall bladder disease, reduced risk of heart disease and lower blood pressure, reduced risk of osteoarthritis and reduced bone mineral density, increased risk of headache and enlarged prostate, as well as with blood biomarkers of liver function. Heterozygosity was associated with higher height-adjusted forced expiratory volume in 1 s (FEV1) (β=19.36 mL, p=9.21×10−4) and FEV1/forced vital capacity (β=0.0031, p=1.22×10−5) in nonsmokers, whereas in smokers, this protective effect was abolished. Furthermore, we show for the first time that sex modifies the association of the Z allele on lung function.We conclude that Z allele heterozygosity and homozygosity exhibit opposing effects on lung function in the UK population, and that these associations are modified by smoking and sex. In exploratory analyses, heterozygosity for the Z allele also showed pleiotropic associations with nonrespiratory health-related traits and disease risk.

Worldwide variation of the COL14A1 gene is shaped by genetic drift rather than selective pressure.

BackgroundThe aim of this study is to analyze the worldwide distribution of SNP rs4870723 in COL14A1 gene to check if there are significant genetic differences among different populations and to test if the gene is a trait under selection.MethodsGenomic DNA was extracted from 69 unrelated individuals from Sardinia and genotyped for SNP rs4870723. Data were compared with 26 different populations, clustered in 5 super‐populations, from the public 1000 genomes database. Allele frequency and heterozygosity were calculated with Genepop. The Hardy–Weinberg equilibrium and pairwise population differentiation through analysis of molecular variance (AMOVA FST) were determined with Arlequin.ResultsAllele frequencies of COL14A1 rs4870723 were compared in 27 populations clustered in 5 super‐populations. All populations were in the Hardy–Weinberg equilibrium. In almost all populations, allele C was the most frequent allele, reaching the highest values in East Asia. The 27 populations showed an appreciable structure, with significant differences observed between European, African, and Asian populations.ConclusionSignificant differences were observed in the rs4870723 SNP distribution among the populations studied. However, we found no evidence for a selective pressure. Rather, the differentiation among the populations is likely the result of founder effect, genetic drift, and cultural factors, all events known to establish and maintain genetic diversity between populations.

Relationship between Allelic Heterozygosity in BoLA-DRB3 and Proviral Loads in Bovine Leukemia Virus-Infected Cattle.

Simple SummaryBovine leukemia virus (BLV) caused a severe cattle neoplastic disease called enzootic bovine leukosis (EBL). EBL causes significant economic losses in farming by reducing milk production, reproductive performance, and fertility, and through cattle culling or death. The BLV proviral load (PVL) represents the quantity of BLV genome that has integrated into the host’s genome in BLV-infected cells. It has been reported that PVLs differ according to the genetic background of the host, and some studies of BLV-associated host factors have reported on polymorphisms within the bovine major histocompatibility complex (MHC), namely bovine MHC is bovine leukocyte antigen (BoLA-DRB3). However, there is a great diversity in the PVLs associated with carrying various combinations of these alleles, especially for heterozygous alleles. Therefore, this research investigated whether heterogeneity in BoLA-DRB3 allele combinations would affect PVLs during BLV infections in different ages and breeds of cattle in Japan. This is the first report where the association between heterozygous allelic combinations and BLV PVLs phenotypes (HPLs, LPLs) was analyzed. Our findings augment current understanding about the immunological role played by BoLA heterozygosity in BLV-associated PVLs and biocontrol in BLV infections.Enzootic bovine leukosis is a lethal neoplastic disease caused by bovine leukemia virus (BLV), belongs to family Retroviridae. The BLV proviral load (PVL) represents the quantity of BLV genome that has integrated into the host’s genome in BLV-infected cells. Bovine leukocyte antigen (BoLA) class II allelic polymorphisms are associated with PVLs in BLV-infected cattle. We sought to identify relationships between BoLA-DRB3 allelic heterozygosity and BLV PVLs among different cattle breeds. Blood samples from 598 BLV-infected cattle were quantified to determine their PVLs by real-time polymerase chain reaction. The results were confirmed by a BLV-enzyme-linked immunosorbent assay. Restriction fragment length polymorphism-polymerase chain reaction identified 22 BoLA-DRB3 alleles. Multivariate negative binomial regression modeling was used to test for associations between BLV PVLs and BoLA-DRB3 alleles. BoLA-DRB3.2*3, *7, *8, *11, *22, *24, and *28 alleles were significantly associated with low PVLs. BoLA-DRB3.2*10 was significantly associated with high PVLs. Some heterozygous allele combinations were associated with low PVLs (*3/*28, *7/*8, *8/*11, *10/*11, and *11/*16); others were associated with high PVLs (*1/*41, *10/*16, *10/*41, *16/*27, and *22/*27). Interestingly, the BoLA-DRB3.2*11 heterozygous allele was always strongly and independently associated with low PVLs. This is the first reported evidence of an association between heterozygous allelic combinations and BLV PVLs.

Single Marker Association with Mastitis Incidence of Three Microsatellite Loci, BM1258, BM1443 and BM1818, in Egyptian Buffalo

To detect the linkage between single markers of microsatellite type and mastitis incidence in Egyptian buffalo three markers (BM1258, BM1443 and BM1818) and one hundred twenty-three lactating animals were used. The selected animals were tested using Modified White Side Test (MWT) to screen animals for mastitis. Non-denatured polyacrylamide gel was used to determine the sizes of the PCR amplified products using reference animal to verify the allelic sizes obtained. For each marker, the frequencies of alleles and genotypes for both positive and negative animal groups were compared by using the chi-square test and the Fisher's exact test. The odds ratios calculated as an estimate of relative risk of mastitis incidence associated with each microsatellite genotypes. A positive mastitis test reaction (MWT) was revealed in 19.5% of total samples. For BM1258, BM1443, and BM1818, the number of alleles was found to be 4, 3 and 5, respectively. The polymorphism in all three studied loci was high (PIC>0.5). The genetic parameters of these loci, including observed and expected heterozygosity, were estimated using full characterizations of this set of three polymorphic loci. The polymorphic information content, heterozygosity, and number of successful alleles of the studied loci showed that BM1443 had the lowest variability and BM1818 had the highest variability, with 0.597 and 0.757, respectively. The overall effects of the three studied markers on mastitis incidence were significantly (P<0.05) different. The genotypes combination ‘72/79’, ‘74/74’, and ‘79/82’ at BM1258 loci; ‘78/78’ and ‘88/88’ at BM1443 loci, were observed only in the mastitis free animals. On the other hand, BM4505 loci genotypes were found in the positive populations except the combination of genotypes 134/134, 134/140 and 134/144 animals. The information observed in the present study, could be valuable for improving mastitis resistance in Egyptian buffalo breeds through using molecular tools

Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees.

The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of individual lines or accessions within a species. Due to limitations in current sequencing technology, the genotype values for some accessions cannot be clearly called. Additionally, allelic heterozygosity can be very high in some lines, causing genetic and sometimes phenotypic segregation in their descendants. Genetic and phenotypic segregation degrades the original accession’s specificity and makes it difficult to distinguish one accession from another. Therefore, it is vitally important to determine and validate HapMap accessions before one conducts a GWAS analysis. However, to the best of our knowledge, there are no prior methodologies or tools that can readily distinguish or validate multiple accessions in a HapMap population. We devised a bioinformatics approach to distinguish multiple HapMap accessions using only a minimum number of genetic markers. First, we assign each candidate marker with a distinguishing score (DS), which measures its capability in distinguishing accessions. The DS score prioritizes those markers with higher percentages of homozygous genotypes (allele combinations), as they can be stably passed on to offspring. Next, we apply the “set-partitioning” concept to select optimal markers by recursively partitioning accession sets. Subsequently, we build a hierarchical decision tree in which a specific path represents the selected markers and the homogenous genotypes that can be used to distinguish one accession from others in the HapMap population. Based on these algorithms, we developed a web tool named MAD-HiDTree (Multiple Accession Distinguishment-Hierarchical Decision Tree), designed to analyze a user-input genotype matrix and construct a hierarchical decision tree. Using genetic marker data extracted from the Medicago truncatula HapMap population, we successfully constructed hierarchical decision trees by which the original 262 M. truncatula accessions could be efficiently distinguished. PCR experiments verified our proposed method, confirming that MAD-HiDTree can be used for the identification of a specific accession. MAD-HiDTree was developed in C/C++ in Linux. Both the source code and test data are publicly available at https://bioinfo.noble.org/MAD-HiDTree/.

Demographic changes and loss of genetic diversity in two insular populations of bobcats (Lynx rufus)

Among felids worldwide, only 6 of 38 species have stable or increasing populations, and most felid species are threatened by anthropogenic influences, especially habitat loss and fragmentation. We documented changes in genetic diversity in an isolated, reintroduced population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared to another bobcat population on Kiawah Island, South Carolina, USA, that was naturally established and experiences limited immigration from the mainland. The CUIS population declined from 32 reintroduced bobcats in 1989 to 10–24 individuals during 2012–2019, and observed heterozygosity declined from 0.742 to 0.634 (SD = 0.240). Observed heterozygosity of bobcats on Kiawah was 0.699 (SD = 0.153). We estimated that one bobcat immigrated to Kiawah Island every 5.3 years. We compared the predictions of a novel population viability analysis (PVA) to empirical estimates of abundance and genetic diversity on CUIS and used our PVA to identify management actions that are likely to support long-term viability. Mean heterozygosity from the PVA (0.588, SD = 0.065) was within 1 standard deviation of the empirical estimate. The PVA estimated the population would decline following population restoration due to loss of genetic diversity and inbreeding depression. Translocations of one female every four years would stabilize allele heterozygosity similar to the Kiawah Island population, but even translocations of two females every two years would not restore heterozygosity to founder levels. The PVA predicted no management action would result in a one in five probability of extinction within 50 years of reintroduction, but all translocation strategies nearly eliminated extinction risk through 100 years.

Performance and genetic diversity of 23 provenances of northern red oak (Quercus rubra L.) after 25 years of growth in South Korea

Growth traits and genetic diversity of 23 provenances of Quercus rubra introduced from North America were analyzed in a provenance trial established with a randomized block design in Hwaseong, Gyeonggi, South Korea in 1993. Growth variables and survival at age 25 were compared with results from early stages. Height, DBH, volume and stem straightness of Q. rubra was better than those of the domestic oak (Quercus accutissima). Growth of the Dunham Island provenance from New York was the best among the 23 provenances that of the Eagle River provenance from Wisconsin was poorest. Survival rate at age 25 was on average 52%. The longitude of seed origin and growth of provenance were consistently significantly negatively correlated at all ages. Growth of coastal provenances was superior to that of the inland provenances, which were separated by the Appalachian Mountains. Genetic diversity and genetic distance among the provenances were evaluated using microsatellite markers. The allelic frequencies showed high polymorphism in 10 microsatellite loci, and 292 alleles were found. Of 10 loci, two were commonly found in the 23 provenances. The mean allelic diversity and heterozygosity observed among the provenances were similar to those from the native populations of Q. rubra in North America. Nei′s genetic distance among the 23 was estimated and showed that a clear trend between geographic and genetic distances, indicating that some provenances have high genetic diversity with superior growth performance.

Polymorphism of CSN1S1 (g.12164G&gt;A) and CSN2 (g.8913C&gt;A) genes in pure and cross dairy goats

Casein genes directly control milk protein of animals. CSN1S1 (αS1-Casein) and CSN2 (β-Casein) genes influence on milk protein fractions. Genetic polymorphisms of CSN1S1 gene at g.12164G&gt;A locus and CSN2 gene at g.8913C&gt;A locus were identified by PCR-RFLP technique. Animal samples were pure dairy goats providing PE (5 hds.), Saanen (8 hds.) and their crosses providing Sapera (50% Saanen, 50% PE) (51 hds.) and SaanPE (75% Saanen, 25% PE) (3 hds.) from IRIAP dairy goat station. Allele frequency, genotype frequency, heterozygosity value, and Hardy-Weinberg (H-W) equilibrium value were analyzed by Popgen32 program. CSN1S1_g.12164G&gt;A locus resulted in two alleles, i.e. G allele (192 bp, 145 bp, and 101 bp) and A allele (337 bp and 101 bp). The G allele from the highest frequenciest was successively Saanen (0.625), Sapera (0.578), PE (0.400), and SaanPE (0.333). Most dairy goats were heterozygote (Ho&gt;He) and in H-W equilibrium (q2count &lt; q2P0.05). Whereas CSN2_g.8913C&gt;A locus was monomorphic for possesing only C allele (233 bp and 162 bp), without A allele (416 bp). The existent g.12164G&gt;A SNP of the CSN1S1 gene of could be a potencial molecular selection marker of milk protein content in dairy goat.

Molecular Characterization of Giardia duodenalis in Children and Adults Sampled in Algeria.

The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for Giardia. Molecular characterization of Giardia was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (tpi). Of the 119 samples, 80 (67%) were Giardia-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, tpi genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as tpi genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting Giardia in stool samples and that robust amplification and sequencing of the tpi gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on Giardia infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data.

Genetic variability of Nigerian sheep breeds at the insulin-like growth factor-1 (IGF-1) gene locus

The genetic variability of some Nigerian breeds of sheep at the IGF 1 locus was investigate blood samples from 150 sheep (50 each of Yankasa, Balami and Uda sheep) were collected from the Maiduguri abbatoir and analysed at the Biotechnology centre of the University of Maiduguri. A relatively high level of genetic variability was detected in Nigerian sheep; the mean observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.433 and 0.476, respectively. Comparison of expected heterozygosity of alleles between the populations showed that yankasa was the most heterozygous of the sheep populations though the unbiased expected heterozygosity (0.503) for the Yankasa was the same as that of the Balami. All populations were 100% polymorphic at the IGF 1 locus with fixation index ranging from -0.169 to 0.378 and a mean of 0.093, which suggests a general pattern of random mating. Similarly, low mean values for Fis (0.093), F (0.089), Fis (0.089), Fit (0.130) and Fst (0.045) supports the assertion that inbreeding was limited due to outcrossing with relatively high level of gene-flow (Nm = 5.292). The analysis of molecular variance (AMOVA) revealed that only 1% of the total variations observed in the sampled populations is accounted for by the population differences while individual differences accounted for 85%. The UPGMA phylogenetic tree revealed that the Uda and Yankasa populations are closer to each than each is to Balami. Thus, it can be concluded that sufficient genetic variation exist in the studied Nigerian sheep breeds and these populations are unlikely to decline due to inbreeding.&#x0D;

The evolutionary background and functional consequences of the rs2071307 polymorphism in human tropoelastin.

Elastin is a major polymeric protein of the extracellular matrix, providing critical properties of extensibility and elastic recoil. The rs2071307 genomic polymorphism, resulting in the substitution of a serine for a glycine residue in a VPG motif in tropoelastin, has an unusually high minor allele frequency in humans. A consequence of such allelic heterozygosity would be the presence of a heterogeneous elastin polymer in up to 50% of the population, a situation which appears to be unique to Homo sapiens. VPG motifs are extremely common in hydrophobic domains of tropoelastins and are the sites of transient β-turns that are essential for maintaining the conformational flexibility required for its function as an entropic elastomer. Earlier data demonstrated that single amino acid substitutions in tropoelastin can have functional consequences for polymeric elastin, particularly when present in mixed polymers. Here, using NMR and molecular dynamics approaches, we show the rs2071307 polymorphism reduces local propensity for β-turn formation, with a consequent increase in polypeptide hydration and an expansion of the conformational ensemble manifested as an increased hydrodynamic radius, radius of gyration and asphericity. Furthermore, this substitution affects functional properties of polymeric elastin, particularly in heterogeneous polymers mimicking allelic heterozygosity. We discuss whether such effects, together with the unusually high minor allele frequency of the polymorphism, could imply some some evolutionary advantage for the heterozygous state.

Integrating Genetics and Metapopulation Viability Analysis to Inform Translocation Efforts for the Last Northern Leopard Frog Population in Washington State, USA

Population genetic and population viability analyses are powerful instruments that can be used to evaluate the status o populations of conservation concern. However, these two methods are rarely integrated. To better understand the status of the last know Northern Leopard Frog (Lithobates pipiens) population in Washington state, USA, and investigate the potential for translocation efforts we analyzed 96 genetic samples from 2004 and 294 genetic samples from 2014 by using seven microsatellite loci and integrate population genetic data with population viability models. Partitioning of genetic diversity indicated the presence of thre subpopulations in the area, aligning with Washington Department of Fish and Wildlife subunit designation within the watershed. I both years, heterozygosity and average number of alleles per locus were low for all subpopulations (0.20–0.36 and 1.86–2.50, respectively) Point estimates of gene flow out of two of the three subpopulations decreased from 2004 to 2014 based on G″ST (a measure of geneti differentiation) and migration estimates from BayesAss. Summed effective population size for the entire area by using tempora estimates was estimated to be small, with large amounts of uncertainty (sum of 98.4 individuals, 95% confidence interval: 15.6–infinit individuals). Population viability models using genetic estimates of number of adults and migration rates suggest that adults may be th optimal life history stage for successful direct translocation; however, because only metamorphs can be routinely collected, translocatio with head-starting was modeled and active management strategies may be necessary to establish new populations.

Genetic diversity of cucumber (Cucumis sativus) accessions differing in quantitative traits and microsatellite markers

The genetic diversity among 78 cucumber (Cucumis sativus L.) accessions was analyzed using 8 morphological traits and 60 SSR markers under two environmental (open field and protected cultivation) conditions. D2 analysis had grouped the 78 accessions in five major clusters. Cluster I comprised 51 accessions followed by 14, 5, 7 and 1 in cluster II, III, IV, and V respectively. The variation was observed for morphological characters like days to first female flower anthesis (37.53-58.64), days to first fruit harvest (47.28-67.43), fruit length (9.47-26.84 cm), average fruit weight (67.46-417.56 g) and vine length (96.23-170.13 cm). The first four principal components explained 87.72% of the total variation. A total of 171 alleles were amplified with a mean of 2.85 alleles per locus. The polymorphism information content (PIC) varied from 0.05 (UW084478) to 0.59 (UW084186) with a mean value of 0.36. The major allele frequency, gene diversity, and heterozygosity of these SSR markers were 0.36-0.97, 0.05-0.67 and 0.00-0.68, respectively. The dendrogram based on SSR marker analysis classified the 78 genotypes into two major groups those were subdivided into ten subgroups. Collectively, the information obtained will provide a valuable resource for germplasm conservation, genetic analyses and gene discovery in cucumber breeding.