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Results for “Genetic Variation”

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PubMed2002

Genetic variation in three species of Hordeum, and the selection of accessions for the Barley Core Collection.

Starch gel electrophoresis of isozymes was used to investigate the level and distribution of genetic variation in accessions of three wild, diploid Hordeum species. Allelic variation was assessed for seven isozyme loci and used in the statistical analysis of 18 accessions of Hordeum brachyantherum subsp. californicum, 29 accessions of H. murinum subsp. glaucum and 11 accessions of H. pusillum. A major purpose with this study was to evaluate the selection of accessions for the international Barley Core Collection, complementing existing passport data. Allelic variation was found in all three species. The variation was mainly between accessions, as most accessions were fixed for certain alleles. Since all three species are self-pollinated, this was anticipated. The fact that the accessions have undergone one or several regeneration cycles from a rather limited number of individuals, after being collected, likely also have reduced the variation. The accessions were clustered by subjecting the genetic distances between them to UPGMA statistical treatment. The clusters in the dendrograms displayed for H. brachyantherum subsp. californicum and H. pusillum distinct patterns related to the geographical origin of the accessions. The accessions of H. murinum subsp. glaucum were less variable than the other two, and did not reveal such a clear pattern. By comparing the already made, geographically based, selection of accessions with the results from this study, it was evident that the selection had worked fairly well for H. brachyantherum subsp. californicum, but less so for the other two species.

Aconitate Hydratase↗

PubMed2004

Genetic variation in clinical varicella-zoster virus isolates collected in Ireland between 2002 and 2003.

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP, and including two other epitope regions e1 and c1, was sequenced. No new single nucleotide polymorphisms (SNPs) were detected, indicating stability of these epitopes in clinical isolates of VZV. However, when four informative polymorphic markers consisting of defined regions from genes 1, 21, 50, and 54 were sequenced 14 variable nucleotide positions were identified. Phylogenetic analysis showed the presence of three highly supported clades A, B, and C circulating in the Irish population. Approximately one third (6/16; 37.5%) of the Irish VZV isolates in this study belonged to genotype C, 4/16 (25%) to genotype A, and 4/16 (25%) to genotype B. A smaller number 2/16 (12.5%) belonged to genotype J1. This indicates remarkable heterogeneity in the Irish population given the small sample size. No evidence was found to suggest any of the 16 isolates was a recombinant. These findings have implications for the model of geographic isolation of VZV clades to certain regions as the circulating Irish VZV population appears to comprise approximately equal numbers of each of the main genotypes. This data is inconsistent with a model of strict geographical separation of VZV genotypes and suggests that VZV diversity is more pronounced in certain areas than had been thought previously.

Adult↗

PubMedDate not supplied

Genetic variation in the widespread lichenicolous fungus Marchandiomyces corallinus.

The lichenicolous basidiomycete Marchandiomyces corallinus is widely distributed in North America and Europe, where it commonly is found on a variety of lichens. Theoretically either of these characteristics, a wide geographic range or generalized host ecology, could provide opportunities for genetic differentiation within this species. To determine how genetic variation is partitioned in M. corallinus, 12 fungal isolates were obtained from locations in North America and Europe; at two locations, in Washington County, Maine, and on the Isle of Mull in Scotland, fungi also were isolated from different lichen hosts. Vegetative mycelial compatibility tests were used to determine compatibility groupings from among the isolates; in addition, several PCR amplification products (RAPD, nuITS rDNA) were obtained for each isolate. A number of distinct compatibility groups were recognizable based on geography, not host ecology. In addition compatible isolates always were restricted to either North America or Europe. However RAPD markers indicated that compatible isolates are not always genetically identical. The presence of sequence heterozygosity at specific positions indicated that the isolates are heterokaryotic and a number of distinct haplotypes could be identified based on ITS variation at three separate locations. This type of genetic variation in these fungi suggests that sexual recombination is possible and that genetic differentiation has taken place recently as a result of geographic isolation, not host switching.

Basidiomycota↗

PubMed2001

Genetic variation in the 5-HT5A receptor gene in patients with bipolar disorder and major depression.

In the present study, genetic variation of the 5-HT5A receptor was analyzed in patients affected by affective disorders and healthy controls. The sample consisted of 181 patients with major depression, 88 patients with bipolar affective disorder (BP) and 157 unrelated controls (C), all of Spanish origin. Two polymorphisms (-19G/C and 12A/T) in the 5-HT5A receptor gene were analyzed by polymerase chain reaction amplification and subsequent enzyme digestion. No genotype, allele or haplotype differences were found when we compared patients and controls. When clinical variables were considered as possible tools for detecting genetic heterogeneity, no differences were found. Our results suggest that the polymorphisms analyzed in the 5-HT5A receptor gene do not play a major role in the pathogenesis of affective disorders.

Adult↗

PubMed1998

Meta-analysis of studies on genetic variation in 5-HT2A receptors and clozapine response.

Serotonin (5-HT) neurotransmitter receptors are targeted by atypical antipsychotic drugs. We hypothesized that genetic variation in these receptors may affect clinical response to the drugs targeting them. This hypothesis has been tested by several studies in which the correlation between polymorphic variants in the 5-HT2A receptor gene and clinical response to the atypical antipsychotic clozapine was investigated. The results of these studies either found association between 5-HT2A genetic variants and clozapine response or found differences in the same direction which did not reach statistical significance. Meta-analysis of these studies including 373 patients who responded to the treatment and 360 non-responders showed association between two 5-HT2A polymorphisms, 102-T/C and His452Tyr, and clozapine response. Statistical analysis of extreme responders showed a clearer association of the 102-T/C with clozapine response. These results reinforce the hypothesis and strengthen the candidacy of these receptors as important therapeutic targets.

Alleles↗

PubMed1999

Genetic variation in Beauveria bassiana populations associated with the darkling beetle, Alphitobius diaperinus.

A study was conducted to assess genetic variation within and among populations of Beauveria bassiana (Deuteromycotina: Hyphomycetes) associated with the darkling beetle, Alphitobius diaperinus (Coleoptera: Tenebrionidae), using RAPD markers. A hierarchical collection of samples (strains from the same insect specimen, from insects from the same location, and from insects from different locations) was obtained from infected beetles from North Carolina (NC) and West Virginia (WV), USA. Ten primers resolved 81 strains into 80 distinct multiband phenotypes reflecting the substantial amount of variation that was present. Variation present within populations was evident not only in the separation of each strain as a distinct multiband phenotype but also in the separation of strains within a population into separate clusters. Among populations, a group sharing more than 89% similarity was observed among all the strains from Martin Co. and Greene Co., NC and 61% of the strains collected from WV. Some genetic differentiation was present among the other populations but the separation was not distinct with a few strains from some populations showing greater affinity to strains from other collection sites.

Animals↗

PubMed1988

Genetic variation of Venezuelan equine encephalitis virus strains of the ID variety in Colombia.

To determine the degree of genetic variation within one serologic group of Venezuelan equine encephalitis virus and the relatedness of viruses with different epidemiologic backgrounds isolated within the same country, virion RNA from 16 isolates belonging to subtype I were compared by RNase T1 oligonucleotide fingerprinting. RNA fingerprints of 12 enzootic isolates showed a large degree of heterogeneity, even though they were serologically indistinguishable. A reference enzootic strain from Colombia showed more genetic relatedness to three epizootic strains isolated in the same country, than to its own serogroup prototype strain isolated in Panama. Thus, genetic relatedness within Venezuelan equine encephalitis strains in Colombia seems to be a function of geography rather than epidemiology.

Animals↗

PubMed2005

Comprehensive evaluation of common genetic variation within LRRK2 reveals evidence for association with sporadic Parkinson's disease.

Parkinson's disease (PD) is a complex neurodegenerative disorder whose aetiologies are largely unknown. To date, mutations in six genes have been found causal for some rare familial forms of the disease and common variation within at least three of these is associated with the more common sporadic forms of PD. LRRK2 is the most recently identified familial PD gene, although its role in sporadic disease is unknown. In this study, we have performed the first comprehensive evaluation of common genetic variation within LRRK2 and investigated its contribution to risk of sporadic PD. We first characterized the linkage disequilibrium within LRRK2 using a panel of densely spaced SNPs across the gene. We then identified a subset of tagging-SNPs (tSNP) that capture the majority of common variation within LRRK2. Both single tSNP and tSNP haplotype analyses, using a large epidemiologically matched sporadic case-control series comprising 932 individuals, yielded significant evidence for disease association. We identified a haplotype that dramatically increases disease risk when present in two copies (OR=5.5, 95%CI=2.1-14.0, P=0.0001). Thus, we provide the first evidence that common genetic variation within LRRK2 contributes to the risk of sporadic PD in the Chinese population.

Adult↗

PubMed2004

In silico study of transcriptome genetic variation in outbred populations.

Dissecting the genetic architecture of regulatory elements on a genome-wide basis is now technically feasible. The potential medical and genetical implications of this kind of experiment being very large, it is paramount to assess the reliability and repeatability of the results. This is especially relevant in outbred populations, such as humans, where the genetic architecture is necessarily more complex than in crosses between inbred lines. Here we simulated a chromosome-wide SNP association study using real human microarray data. Our model predicted, as observed, a highly significant clustering of quantitative trait loci (QTL) for gene expression. Importantly, the estimates of QTL positions were often unstable, and a decrease in the number of individuals of 16% resulted in a loss of power of approximately 30% and a large shift in the position estimate in approximately 30-40% of the remaining significant QTL. We also found that the analysis of two repeated measures of the same mRNA can also result in two QTL that are located far apart. The intrinsic difficulties of analyzing outbred populations should not be underestimated. We anticipate that (many) conflicting results may be collected in the future if whole-genome association studies for mRNA levels are carried out in outbred populations.

Alleles↗

PubMed2006

Association of genetic variation within UBL5 with phenotypes of metabolic syndrome.

The BEACON gene was initially identified using the differential display polymerase chain reaction on hypothalamic mRNA samples collected from lean and obese Psammomys obesus, a polygenic animal model of obesity. Hypothalamic BEACON gene expression was positively correlated with percentage of body fat, and intracerebroventricular infusion of the Beacon protein resulted in a dose-dependent increase in food intake and body weight. The human homolog of BEACON, UBL5, is located on chromosome 19p in a region previously linked to quantitative traits related to obesity. Our previous studies showed a statistically significant association between UBL5 sequence variation and several obesity- and diabetes-related quantitative physiological measures in Asian Indian and Micronesian cohorts. Here we undertake a replication study in a Mexican American cohort where the original linkage signal was first detected. We exhaustively resequenced the complete gene plus the putative promoter region for genetic variation in 55 individuals and identified five single nucleotide polymorphisms (SNPs), one of which was novel. These SNPs were genotyped in a Mexican American cohort of 900 individuals from 40 families. Using a quantitative trait linkage disequilibrium test, we found significant associations between UBL5 genetic variants and waist-to-hip ratio (p = 0.027), and the circulating concentrations of insulin (p = 0.018) and total cholesterol (p = 0.023) in fasted individuals. These data are consistent with our earlier published studies and further support a functional role for the UBL5 gene in influencing physiological traits that underpin the development of metabolic syndrome.

Adult↗

PubMed2006

Genetic variation within Taenia multiceps in Sardinia, Western Mediterranean (Italy).

Investigations were undertaken on Taenia multiceps to determine if genetic variation was present within the parasites of Sardinia (Italy). Forty samples were obtained from various locations of Sardinia and deoxyribonucleic acid (DNA) was extracted. Polymerase chain reaction (PCR) was performed on NADH dehydrogenase I (ND1) and cytochrome c subunit 1 (CO1) mitochondrial genes and amplicons were then sequenced and aligned with Bioedit software. Pairwise comparison between the ND1 sequences of the T. multiceps isolates showed differences ranging from 1.27 to 2.54% using an isolate obtained from Wales as an outgroup, while COI sequences showed within the samples coming from Sardinia a lesser degree of variability, ranging from 0.22 to 0.67%. Considering the two genes, it was possible to define at least three specific genetic variants in Sardinian samples, which we have termed Tm1, Tm2, and Tm3. This is the first description of genetic variability in T. multiceps. Further investigations will be required to understand to what extent the genetic variability described in this paper would be reflected also in phenotypic differences.

Animals↗

PubMed1998

Genetic variation and phylogenetic analysis of open reading frames 3 and 4 of various equine arteritis virus isolates.

The genetic variation in equine arteritis virus (EAV) nonstructural (NS) protein-encoding open reading frames (ORF) 3 and 4 genes was investigated. Nucleotide and deduced amino acid sequences from seven different EAV isolates (one European, one American and five Canadian isolates) and the Arvac vaccine strain were compared with those of the Bucyrus reference strain. ORF 3 nucleotide and amino acid sequence identities amongst these isolates (including the Arvac vaccine strain) and the Bucyrus reference strain ranged from 85.6 to 98.8%, and 85.3 to 98.2%, respectively, whereas ORF 4 nucleotide and amino acid sequence identities ranged from 90.4 to 98.3%, and 90.8 to 97.4%, respectively. Phylogenetic tree analysis based on the ORF 3 nucleotide sequences showed that the European Vienna isolate could be classified into a genetically divergent group from all other isolates and the Arvac vaccine strain. In contrast, a phylogenetic relationship among all EAV isolates and the Arvac vaccine strain based on the ORF 4 nucleotide sequences was observed.

Animals↗

PubMed2006

Genetic variation and relationships among eight Indian riverine buffalo breeds.

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.

Animals↗

PubMed1984

Genetic variation in restriction patterns among mouse amylase gene complexes.

The expression of pancreatic amylase in the mouse exhibits pronounced genetic variation. Congenic lines with various amylase complexes on a common C3H/As background have different numbers and forms of isoenzymes. The relative ratio of these isoenzymes may vary, as does the overall production of pancreatic amylase, which in some lines is three- to fourfold higher than in others. DNA from a number of lines was digested with endonucleases and hybridized to an amylase cDNA probe. The restriction patterns from inbred stocks and the corresponding congenic lines are identical, demonstrating that the majority of (if not all) amylase-like DNA sequences is found within the amylase complex. Congenic lines with specific amylase expression, for instance, in enzyme production, show different restriction patterns, whereas three lines with the same amylase phenotype have a uniform pattern. Most of the variation in amylase expression is represented among congenic lines derived from Danish mice. A comparison of such lines with others of remote geographic origin reveals that the restriction patterns of the "Danish" lines have by far the highest degree of resemblance. This observation seems to exclude major rearrangements within the amylase complex as the cause of the differences in enzyme expression, which instead are likely to be due to variation in regulatory elements associated with the active structural amylase genes in the complex.

Amylases↗

PubMed2000

Postsealing genetic variation and population structure of two species of fur seal (Arctocephalus gazella and A. tropicalis).

Commercial sealing in the 18th and 19th centuries had a major impact on the Antarctic and subantarctic fur seal populations (Arctocephalus gazella and A. tropicalis) in the Southern Ocean. The intensive and unrestricted nature of the industry ensured substantial reductions in population sizes and resulted in both species becoming locally extinct at some sites. However, both species are continuing to recover, through the recolonization of islands across their former range and increasing population size. This study investigated the extent and pattern of genetic variation in each species to examine the hypothesis that higher levels of historic sealing in A. gazella have resulted in a greater loss of genetic variability and population structure compared with A. tropicalis. A 316-bp section of the mitochondrial control region was sequenced and revealed nucleotide diversities of 3.2% and 4.8% for A. gazella and A. tropicalis, respectively. There was no geographical distribution of lineages observed within either species, although the respective PhiST values of 0.074 and 0.19 were significantly greater than zero. These data indicate low levels of population structure in A. gazella and relatively high levels in A. tropicalis. Additional samples screened with restriction endonucleases were incorporated, and the distribution of restriction fragment length polymorphism (RFLP) and sequence haplotypes were examined to identify the main source populations of newly recolonized islands. For A. tropicalis, the data suggest that Macquarie Island and Iles Crozet were probably recolonized by females from Marion Island, and to a lesser extent Ile Amsterdam. Although there was less population structure within A. gazella, there were two geographical regions identified: a western region containing the populations of South Georgia and Bouvetoya, which were the probable sources for populations at Marion, the South Shetland and Heard Islands; and an eastern region containing the panmictic populations of Iles Kerguelen and Macquarie Island. The latter region may be a result of a pronounced founder effect, or represent a remnant population that survived sealing at Iles Kerguelen.

Animals↗

PubMed1996

Mobility of Australian flying-foxes, Pteropus spp. (Megachiroptera): evidence from genetic variation.

Black (Pteropus alecto) and grey-headed (Pteropus poliocephalus) flying-foxes inhabit large ranges in coastal north and eastern Australia. P. poliocephalus is endemic to region and is classified as vulnerable. The bats are known to migrate in response to flowering and fruiting of their food plants, but direct observation of movement patterns is difficult. Protein electrophoresis was used to investigate genetic subdivision among populations. High gene flow was inferred for both species with an estimated exchange of 15 (P. alecto) and 28 (P. poliocephalus) individuals between populations per generation. Wright's FST, an index of among population genetic variation, was low, 0.023 (P. alecto), 0.014 (P. poliocephalus), reflecting the homogenising action of movements across the species' ranges. An FST value of 0.028 has been reported for a third Australian species, the little red flying-fox, P. scapulatus. The FST values for Australian flying-foxes are closer to those found for birds than the typically higher values for mammals and we conclude that these flying-foxes are essentially panmictic and for management purposes should be treated as migratory species.

Alleles↗

PubMed2001

Assessment of the ratio of pollen to seed flow in a cline for genetic variation in a quantitative trait.

A dispersal-selection cline model is analysed to evaluate the role of the ratio of pollen to seed flow (r) in spatial genetic variation, with a focus on clines in additive and dominant variances of major genes affecting a quantitative trait, assuming one locus with two alleles, no genetic drift and no mutation. It is shown that under weak selection, steady-state departures from the value at Hardy-Weinberg equilibrium (HWE) for genotype frequency (D) and additive variance (DeltaVa) generally display a small value on one side of the selection boundary point, a high value around the point, and a moderate value on the other side of the boundary point. A large value of r can enhance formation of this pattern. However, this is not the case for clines in the average effect of a gene substitution (Deltaalpha) or in dominance variance (DeltaVd), where large values of r can eradicate the clines. Direct use of their values at HWE to approximate the real case is acceptable. There is an expected turning point that divides clines of either additive variance or dominance variance into two subclines, each with a shorter width than that of allele frequency. Integration of these properties can help to indicate the existence of major genes affecting a quantitative trait.

Gene Frequency↗

PubMed2006

[Population genetic variation and structure analysis on five populations of mirror carp Cyprinus carpio L. using microsatellites].

In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations.

Alleles↗