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PubMed2000

Genetic variation within and among patches of the clonal species, Vaccinium stamineum L.

Once thought to be dominated by a few genets, clonal plant populations can contain high levels of genetic diversity. Sexual reproduction and vegetative growth strategy affect the amount and distribution of genetic diversity within clonal plant populations. We determined the scale of genetic diversity in a population of Vaccinium stamineum, a clonal shrub that forms discrete patches. Using the random amplified polymorphic DNA (RAPD) technique, we surveyed the genetic diversity of V. stamineum within and among patches from a 1-ha site. We found 67 unique RAPD profiles among the 99 sampled individuals from 22 patches. In two patches, all the sampled individuals had the same RAPD profile. In seven patches, every individual sampled had a different RAPD profile. The remaining patches showed mixed RAPD profiles which suggested both clonal and sexual reproduction. Each unique RAPD profile was restricted to one patch (with one exception), which suggests that clonal growth occurs at the patch scale. High levels of genetic variation within some patches may be explained by somatic mutation; however, seedling recruitment is a more likely explanation.

DNA, Plant↗

PubMed1987

Genetic variation in cytochrome P-450-dependent demethylation in Drosophila melanogaster.

The genetic variation in the basal capacity to N-demethylate aminopyrine, d-benzphetamine and ethylmorphine was studied in microsomes from adult Drosophila of 9 different strains. Ethylmorphine and d-benzphetamine N-demethylase activity varied about fourfold between the strains, with the highest capacity for both reactions in the Aflatoxin B1-sensitive Florida 9 and the lowest in the insecticide-resistant Hikone R. The two activities were closely correlated with each other but not with aminopyrine demethylation or any previously studied cytochrome P-450-dependent reaction, indicating a common determination by a separate cytochrome P-450 form(s). Aminopyrine N-demethylase activity was more than fourfold higher in the DDT-resistant Oregon R than in Berlin K. A genetic analysis of aminopyrine N-demethylation revealed that the high activity in the Oregon R(R) strain was inherited as an apparently semidominant second chromosome trait. The similar mode of inheritance as well as the close correlation between aminopyrine demethylase and the previously analysed biphenyl 4-hydroxylase activity suggests that these activities are under the same genetic control.

Aminopyrine↗

PubMed1986

Genetic variation for superoxide dismutase level in Drosophila melanogaster.

We have studied genetic variation for levels of activity of the enzyme superoxide dismutase (SOD) in Drosophila melanogaster. We have constructed 34 lines homozygous for a given second and a given third chromosome derived from eight original lines; all lines were homozygous for the "fast" (F) allele of Sod. The variation in the relative levels of SOD CRM ranges from 1 to 1.6. The second chromosomes modify the SOD level, even though the structural Sod locus is in the third chromosome, and the specific effect of a given second chromosome depends on the particular third chromosome with which it is combined. This indicates that the variation in SOD content is controlled by polygenic modifiers present in the second (and in the third) chromosome. In addition to these trans-acting modifiers, we have isolated a cis-acting element (SodCA1) that reduces SOD CRM levels to 3.5% of a typical F/F homozygote. SodCA1 is either a mutation in a regulatory site closely linked to the structural locus or a change in the coding sequence affecting the rate of degradation of the enzyme.

Alleles↗

PubMed2006

Evolutionary aspects of diet, the omega-6/omega-3 ratio and genetic variation: nutritional implications for chronic diseases.

Anthropological and epidemiological studies and studies at the molecular level indicate that human beings evolved on a diet with a ratio of omega-6 to omega-3 essential fatty acids (EFA) of approximately 1 whereas in Western diets the ratio is 15/1 to 16.7/1. A high omega-6/omega-3 ratio, as is found in today's Western diets, promotes the pathogenesis of many diseases, including cardiovascular disease, cancer, osteoporosis, and inflammatory and autoimmune diseases, whereas increased levels of omega-3 polyunsaturated fatty acids (PUFA) (a lower omega-6/omega-3 ratio), exert suppressive effects. Increased dietary intake of linoleic acid (LA) leads to oxidation of low-density lipoprotein (LDL), platelet aggregation, and interferes with the incorporation of EFA in cell membrane phospholipids. Both omega-6 and omega-3 fatty acids influence gene expression. Omega-3 fatty acids have anti-inflammatory effects, suppress interleukin 1beta (IL-1beta), tumor necrosis factor-alpha (TNFalpha) and interleukin-6 (IL-6), whereas omega-6 fatty acids do not. Because inflammation is at the base of many chronic diseases, dietary intake of omega-3 fatty acids plays an important role in the manifestation of disease, particularly in persons with genetic variation, as for example in individuals with genetic variants at the 5-lipoxygenase (5-LO). Carotid intima media thickness (IMT) taken as a marker of the atherosclerotic burden is significantly increased, by 80%, in the variant group compared to carriers with the common allele, suggesting increased 5-LO promoter activity associated with the (variant) allele. Dietary arachidonic acid (AA) and LA increase the risk for cardiovascular disease in those with the variants, whereas dietary intake of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) decrease the risk. A lower ratio of omega-6/omega-3 fatty acids is needed for the prevention and management of chronic diseases. Because of genetic variation, the optimal omega-6/omega-3 fatty acid ratio would vary with the disease under consideration.

Biological Evolution↗

PubMed1996

Detection of genetic variation in Ustilago maydis strains by probes derived from telomeric sequences.

Genetic variation using probes derived from telomeric sequences was analysed among several Ustilago maydis strains in an attempt to identify discriminative fingerprint patterns. Three groups of wild isolates from different geographical areas and one group of standard laboratory strains were examined. Analysis of the endmost restriction fragments (EFs) and of the endmost-associated restriction fragments (EAFs) of the chromosomes revealed group differences. Most of the EFs in two groups of strains showed a similar length whereas in the other two groups they were distributed in classes of different lengths. Furthermore, analysis of the EAFs permitted possible fingerprint patterns to be predicted for each group of strains based on the occurrence of amplified bands as well as the presence or absence of distinct bands which were shown to be present in terminal as well as in interstitial sites of the chromosome. The approach evaluated in this work yielded highly polymorphic fingerprint patterns and could be used to distinguish groups of fungal isolates; this approach may also be effective for other fungal systems.

DNA Fingerprinting↗

PubMed2003

Genetic variation within and among fragmented populations of lesser prairie-chickens (Tympanuchus pallidicinctus).

As a result of recurrent droughts and anthropogenic factors, the range of the lesser prairie-chicken (Tympanuchus pallidicinctus) has contracted by 92% and the population has been reduced by approximately 97% in the past century, resulting in the smallest population size and most restricted geographical distribution of any North American grouse. We examined genetic variation through DNA sequence analysis of 478 base pairs of the mitochondrial genome and by assaying allelic variation at five microsatellite loci from lesser prairie-chickens collected on 20 leks in western Oklahoma and east-central New Mexico. Traditional population genetic analyses indicate that lesser prairie-chickens maintain high levels of genetic variation at both nuclear and mitochondrial loci. Although some genetic structuring among lesser prairie-chicken leks was detected within Oklahoma and New Mexico for both nuclear and mitochondrial loci, high levels of differentiation were detected between Oklahoma and New Mexico populations. Nested-clade analysis of mitochondrial haplotypes revealed that both historic and contemporary processes have influenced patterns of haplotype distributions and that historic processes have most likely led to the level of differentiation found between the Oklahoma and New Mexico populations.

Alleles↗

PubMed1979

Evolution of human influenza A viruses in nature: recombination contributes to genetic variation of H1N1 strains.

In June of 1977, a new influenza A pandemic was started by strains of the H1N1 serotype. Oligonucleotide fingerprint analysis of the RNA from viruses isolated during the early stage of this pandemic demonstrated that genetic variation among these 1977 strains could be attributed to sequential mutation [Young, J.F., Desselberger, U. & Palese, P. (1979) Cell, 18, 73-83]. Examination of more recent strains revealed that the H1N1 variants that were isolated in the winter of 1978-1979 differed considerably from the H1N1 viruses isolated the previous year. Oligonucleotide and peptide map analysis of the new prototype strain (A/Cal/10/78) suggested that it arose by recombination. It appears that only the HA, NA, M, and NS genes of this virus are derived from the earlier H1N1 viruses and that the P1, P2, P3, and NP genes most likely originate from an H3N2 parent. These data suggest that genetic variation in influenza virus strains of the same serotype is not restricted to mutation alone, but can also involve recombination (reassortment).

Antigens, Viral↗

PubMed2003

Bone density in sheep: genetic variation and quantitative trait loci localisation.

Bone density (BD) is an important factor in osteoporotic fracture risk in humans. However, BD is a complex trait confounded by environmental influences and polygenic inheritance. Sheep provide a potentially useful model for studying differences in BD, as they provide a means of circumventing complex environmental factors and are a similar weight to humans. The aims of this study were to establish whether there is genetic variation in BD in sheep and then to localise quantitative trait loci (QTLs) associated with this variation. We also aimed to evaluate the relationship between fat and muscle body components and BD in sheep. Results showed that there was significant (P < 0.01) genetic variation among Coopworth sheep sires for BD. This genetic difference was correlated (P < 0.01) with body weight and muscle mass. A number of QTLs exceeding the suggestive threshold were identified (nine in total). Of these, two (chromosomes 1, P < 0.05; chromosome 24, P < 0.01) were significant using genome-wide permutation significance thresholds (2000 iterations). The position of the QTL on chromosome 24 coincided with a number of other body composition QTLs, indicating possible pleiotropic effects or the presence of multiple genes affecting body composition at that site. This study shows that sheep are potentially a useful model for studying the genetics of BD.

Animals↗

PubMed2007

Germ-line genetic variation of TP53 in osteosarcoma.

BACKGROUND: Osteosarcoma (OS) has been well described in individuals with germ-line TP53 mutations (Li-Fraumeni Syndrome) but typically occurs sporadically in adolescents and young adults. Single nucleotide polymorphisms (SNPs), the most common germ-line genetic variation, have been associated with risk for other types of cancer. We hypothesized that genetic variation in TP53 could be associated with OS risk based on its critical role in cell growth and effect of somatic mutations in OS tumors. PROCEDURE: Twelve common SNPs in TP53 were genotyped in a case-control study of sporadic OS. These SNPs spanned the TP53 locus and captured common haplotypes. Genotype data were analyzed using contingency tables for additive, dominant, and recessive genetic models. PHASEv2.1 and HaploStats were used to evaluate haplotypes. RESULTS: The recessive model suggested an increased risk of OS when two copies of TP53-34 C>G variant (IVS2+38, rs1642785) were present, P = 0.041, odds ratio (OR) 6.70 (95% confidence interval [CI] 1.06-41.6). The TP53-01 variant C>G (Pro72Arg, rs1042522) may also be associated with increased risk for OS, P = 0.028, OR 7.5 (95% CI 1.20-46.3). Common TP53 haplotypes as well as the remaining 10 SNPs were not associated with risk for OS. CONCLUSIONS: These data do not indicate a strong link between variation in TP53 and OS risk, although they provide preliminary evidence of an increased risk of OS associated with variants at IVS2+38 and Pro72Arg. The findings warrant replication in further studies.

Adolescent↗

PubMed1982

Genetic variation in natural populations: problem of electrophoretically cryptic alleles.

Electrophoretic studies have shown that the average frequency of heterozygous loci per individual is about 12% in Drosophila and other invertebrates and about 6% in vertebrates. It is estimated that only about two-thirds of all amino acid substitutions change net electric charge; hence, a large fraction of all genetic variation may be undetected by electrophoresis. Peptide mapping of 11 independent alleles coding for alcohol dehydrogenase in Drosophila melanogaster has uncovered one cryptic variant; thus, the frequency of electrophoretically cryptic variation is apparently low, about 9% in this sample. Nevertheless, with a simple model it is shown that this degree of cryptic variation, if it is typical of other loci, would substantially change our current estimates of genetic variation: the average heterozygosity would increase from about 12% to about 25% for invertebrates and from about 6% to 21% for vertebrates. A variety of techniques--including sequential electrophoresis and heat or urea denaturation--have been used by various investigators to detect electrophoretically cryptic variation. These techniques appear to be less effective than peptide mapping for detecting cryptic variation, but, like peptide mapping, they suggest that standard electrophoresis may detect most of the protein variation present in natural populations. The charge-state model of protein variation proposes that the "alleles" detected by electrophoresis are extremely diverse classes consisting of many electrophoretically cryptic alleles. The alcohol dehydrogenase peptide-mapping results are inconsistent with the charge-state model.

Alleles↗

PubMed2003

Genetic variation in the psychomotor stimulant properties of cocaine in Mus musculus.

RATIONALE: The psychomotor stimulant properties of drugs are argued to be a key feature of abuse liability. Several studies, primarily using inbred strains of mice, have demonstrated genetic variation in the psychomotor stimulant properties of cocaine. As of yet, however, no gene(s) has been identified which influences this phenotype. OBJECTIVES: The purpose of the present study was to examine a number of inbred strains of mice, including several closely related substrains, for cocaine-induced locomotor activation. Such substrain differences would suggest the possibility of a major gene effect. These data will also help to further characterize the range of genetic variation in response to cocaine. METHODS: Mice from 11 inbred strains were initially injected with saline and activity monitored for 30 min; mice were then removed from the activity monitor, injected with saline or one of six doses of cocaine, and activity was monitored for an additional 30 min. RESULTS: Compared to several other closely related C57BL substrains, we found the C57BL/10SnJ substrain to be significantly less activated following cocaine administration. In contrast, the C57BR/cdJ and C57L/J substrains showed extremely high levels of cocaine-induced locomotor activation. CONCLUSIONS: The genetic similarity between C57BL/10SnJ and the other closely related C57BL substrains suggests the possibility that the aberrant behavioral response to cocaine observed in B10SnJ mice may be due to a major gene effect. Similarly, the differences found in the C57BR/cdJ and C57L/J substrains may also be influenced by a major gene. The strains examined in this study will be useful tools for identification of relevant quantitative trait loci.

Animals↗

PubMed2004

Redistribution of gene frequency and changes of genetic variation following a bottleneck in population size.

Although the distribution of frequencies of genes influencing quantitative traits is important to our understanding of their genetic basis and their evolution, direct information from laboratory experiments is very limited. In theory, different models of selection and mutation generate different predictions of frequency distributions. When a large population at mutation-selection balance passes through a rapid bottleneck in size, the frequency distribution of genes is dramatically altered, causing changes in observable quantities such as the mean and variance of quantitative traits. We investigate the gene frequency distribution of a population at mutation-selection balance under a joint-effect model of real stabilizing and pleiotropic selection and its redistribution and thus changes of the genetic properties of metric and fitness traits after the population passes a rapid bottleneck and expands in size. If all genes that affect the trait are neutral with respect to fitness, the additive genetic variance (VA) is always reduced by a bottleneck in population size, regardless of their degree of dominance. For genes that have been under selection, VA increases following a bottleneck if they are (partially) recessive, while the dominance variance increases substantially for any degree of dominance. With typical estimates of mutation parameters, the joint-effect model can explain data from laboratory experiments on the effect of bottlenecking on fitness and morphological traits, providing further support for it as a plausible mechanism for maintenance of quantitative genetic variation.

Gene Frequency↗

PubMed2004

Genetic variation in cancer predisposition: mutational decay of a robust genetic control network.

A computational model of cancer progression is used to study how mutations in genes that control tumor initiation and progression accumulate in populations. The model assumes that cancer occurs only after a cell lineage has progressed through a series of stages. The greater the number of stages, the more strongly the individual is protected against cancer. It is shown that an extra stage initially improves the survival of individuals by decreasing mortality from cancer. However, the additional buffering by an extra stage reduces the impact of any single hereditary mutation and therefore allows the accumulation of more nonlethal mutations in the population. Extra stages thereby lead to the evolution of partially decreased cancer mortality and significantly increased genetic predisposition to disease in the population as a whole. In general, the model illustrates how all robust control networks allow the accumulation of deleterious mutations. An increase in the number of buffering components leads to significant mutational decay in the protection provided by each buffering component and increased genetic predisposition to disease. An extra buffering component's net contribution to survival and reproduction is often small.

Aging↗

PubMed1991

Residual feed consumption in laying hens. 2. Genetic variation and correlations.

The study described here deals with the quantification of the genetic variation of "residual feed consumption" (RFC) of hens of a White Leghorn population during a 44-wk laying period (20 to 64 wk of age) in 11 time segments of 4 wk each, fed either a commercial or a low-energy diet (11.7 and 10.0 MJ ME/kg, respectively, where 1 MJ = .239 Mcal). The RFC is defined operationally as the difference between the observed feed consumption of a laying hen and its consumption as predicted from a model with metabolic body weight, egg mass production, and body weight gain as independent variables. The RFC was found to be highly heritable in all periods. The heritability of RFC accumulated over the whole laying period (RFC-T) was estimated as .42 to .62. For each time segment between 32 and 56 wk of age, genetic correlations between RFC and RFC-T were estimated to be larger than .91. The genetic sources causing variation in RFC during the first part of lay seem to differ from those causing variation later on, and to be of less importance during the rest of the laying period. It was concluded that RFC shows a considerable systematic and permanent additive genetic variance, and that RFC measurements for selection can be limited to one to three time segments between 32 and 56 wk. Furthermore, less environmental variance and therefore higher heritabilities and genetic correlations seemed to exist for birds fed the low energy diet in comparison with those fed the commercial diet. No clear differences could be found between genetic and phenotypic correlation estimates of RFC with feed consumption, metabolic body weight, egg mass production, and body weight gain.

Animals↗

PubMed1987

Genetic relationships and additive genetic variation of productive and reproductive traits in Guernsey dairy cattle.

Data were first lactation production and reproduction records initiated from 1958 to 1981 in two experiment station Guernsey herds. Heritability estimates using paternal half sib groups were .24 +/- .12 for milk yield, .27 +/- .12 for fat yield, and .77 +/- .15 for fat percentage. Heritability estimates for reproductive traits ranged from .01 to .04 for number of services, service period, conception rate, and days open, but were higher for days in milk at first breeding (.12) and age at first calving (.13). Except for age at first calving, coefficients of additive genetic variation were larger for reproductive traits than for productive traits. Genetic correlations between measures of production and reproduction were moderate to large and antagonistic, except that the relationship between production and age at first calving was favorable. Breeding value estimates for milk yield and reproduction were negatively correlated for sires with above average breeding values for milk yield. Huge phenotypic variances for reproductive traits masked substantial additive genetic variation for these traits. When all things are considered it seems unwise to ignore reproductive performance in selection programs for dairy cattle.

Animals↗

PubMed1985

Further studies of genetic variation in Schistosoma mansoni.

Genetic studies on the human blood fluke Schistosoma mansoni were undertaken using starch gel electrophoresis to detect new gene loci and allelic variation. The number of enzyme staining systems useful with S. mansoni was increased from 14 to 34. It was found that unmated female worms stained as well as male worms. Three new polymorphic loci, fructose biphosphatase (FBP), gly-leu dipeptide peptidase (PEP-4), and glyceraldehyde-3-phosphate dehydrogenase (G3PDH) were detected. This brings the known number of polymorphic loci to 10 for this species. One locus (FBP) was found to be polymorphic in the PR-1 strain of S. mansoni. This strain was previously reported to be invariant.

Animals↗

PubMed2002

Effect of white pine blister rust (Cronartium ribicola) and rust-resistance breeding on genetic variation in western white pine (Pinus monticola).

Western white pine (Pinus monticola) is an economically and ecologically important species from western North America that has declined over the past several decades mainly due to the introduction of blister rust (Cronartium ribicola) and reduced opportunities for regeneration. Amplified fragment length polymorphism (AFLP) was used to assess the genetic variation in northern Idaho populations of western white pine (including rust-resistant breeding stock) in relation to blister rust. A total of 176 individuals from four populations was analyzed using 163 AFLP loci. Within populations, an average 31.3% of the loci were polymorphic (P), and expected heterozygosity (H(e)) was 0.123. Genetic differentiation values (G(st)) showed that 9.4% of detected genetic variation was explained by differences among populations. The comparison between the rust-resistant breeding stock and a corresponding sample derived from multiple natural populations produced similar values of P (35% vs. 34.4%) and H(e) (0.134 vs. 0.131). No apparent signs of a genetic bottleneck caused by rust-resistance breeding were found. However, a comparison of two natural populations from local geographic areas showed that the population with low pressure from blister rust had higher polymorphism and heterozygosity than the population that had experienced high mortality due to blister rust: P (30.7% vs. 25.1%) and H(e) (0.125 vs. 0.100), respectively. In addition, the population from low blister-rust pressure had twice as many unique alleles as the blister rust-selected population. The genetic distance and Dice's similarity coefficients among the four populations indicated that the local population that survived high blister-rust pressure was genetically similar to the rust-resistant breeding stock.

Crosses, Genetic↗

PubMed1986

Examples of the effect of genetic variation on competing species.

An ordinary differential equation model for two competing populations with genetic variation in one population is presented. The degree of frequency dependence needed to produce various configurations of stable equilibria is discussed. For example, if the fitnesses are frequency independent then there may exist stable polymorphism although the genetically varying population becomes extinct in each fixation plane. Stable polymorphism where the genetically invariant population becomes extinct in each fixation plane requires frequency dependence in the fitness of the genetically invariant population.

Alleles↗