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PubMed1995

Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs.

Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands. The multilocus DNA fingerprinting technique showed very low levels of variation both within and between populations of the harbour seals. For one probe a significant difference in variation between populations was demonstrated. The estimated average heterozygosity, however, diverged more strongly between the two harbour seal populations because of more frequent occurrence of rare alleles in the Scottish population. Low levels of genetic variation seem to be characteristic for the subspecies Phoca vitulina vitulina, but not for all marine mammals in the North Sea, as the grey seal population showed significantly higher variation.

Animals↗
PubMed1974

Genetic variation in a heterogeneous environment. I. Temporal heterogeneity and the absolute dominance model.

The conditions for a stable polymorphism and the equilibrium gene frequency in an infinite population are compared when there is spatial or temporal environmental heterogeneity for the absolute dominance model. For temporal variation the conditions for stability are more restrictive and the equilibrium gene frequency is often at a low gene frequency. In a finite population, temporal environmental heterogeneity for the absolute dominance model was found to be quite ineffective in maintaining genetic variation and is often less effective than no selection at all. For comparison, the maximum maintenance for temporal variation is related to the overdominant model. In general, cyclic environmental variation was found to be more effective at maintaining genetic variation than where the environment varies stochastically. The importance of temporal environmental variation and the maintenance of genetic variation is discussed.

Animals↗
PubMed2000

Genetic variation in ICF syndrome: evidence for genetic heterogeneity.

ICF syndrome is a rare autosomal recessive immunoglobulin deficiency, sometimes combined with defective cellular immunity. Other features that are frequently observed in ICF syndrome patients include facial dysmorphism, developmental delay, and recurrent infections. The most diagnostic feature of ICF syndrome is the branching of chromosomes 1, 9, and 16 due to pericentromeric instability. Positional candidate cloning recently discovered the de novo DNA methyltransferase 3B (DNMT3B) as the responsible gene by identifying seven different mutations in nine ICF patients. DNMT3B specifically methylates repeat sequences adjacent to the centromeres of chromosome 1, 9, and 16. Our panel of 14 ICF patients was subjected to mutation analysis in the DNMT3B gene. Mutations in DNMT3B were discovered in only nine of our 14 ICF patients. Moreover, two ICF patients from consanguineous families who did not show autozygosity (i.e. homozygosity by descent) for the DNMT3B locus did not reveal DNMT3B mutations, suggesting genetic heterogeneity for this disease. Mutation analysis revealed 11 different mutations, including seven novel ones: eight different missense mutations, two different nonsense mutations, and a splice-site mutation leading to the insertion of three aa's. The missense mutations occurred in or near the catalytic domain of DNMT3B protein, indicating a possible interference with the normal functioning of the enzyme. However, none of the ICF patients was homozygous for a nonsense allele, suggesting that absence of this enzyme is not compatible with life. Compound heterozygosity for a missense and a nonsense mutation did not seem to correlate with a more severe phenotype.

Abnormalities, Multiple↗
PubMed2002

Differential expression and genetic variation of hepatic messenger RNAs from genetically lean and fat chickens.

Although excessive adiposity has become a major drawback in meat type chicken production, few of the genes involved in this process have been characterized so far. In order to identify putative genes involved in adiposity, we performed differential display analysis of RNAs extracted from the liver of divergently selected lean and fat chickens. Twenty-six differential products were selected and purified by single strand conformation polymorphism gel electrophoresis before sequencing and Northern blot analyses. An orthologous sequence of a mammalian cytochrome P450 2C subfamily member was proven to be differentially expressed in the liver of lean and fat chickens and could play an important role in the regulation of adiposity. In mammals, these genes are involved in detoxification of xenobiotics and metabolism of some important biological compounds. Four other genes were found differentially expressed to a lower extent. Some unidentified products were shown to be lean or fat specific, with sequence polymorphism and liver specific expression, strongly suggesting that the related gene could be directly involved in adiposity. Our data indicate that differential display can evidence genes with differential expression and with sequence polymorphism, making this strategy more accurate for differential analysis of messenger RNAs.

Adipose Tissue↗
PubMed1987

Use of DNA polymorphisms of the apolipoprotein genes to study the role of genetic variation in the determination of serum lipid levels.

Cloned DNA probes for the apolipoprotein B (apoB) gene and the gene cluster for apoA-I/C-III/A-IV were used to detect restriction fragment length polymorphisms (RFLPs) at these two loci. Samples have been obtained from clinically well individuals, and the RFLP genotypes of each individual have been determined. The data show that at the locus for apoB, genetic variation associated with an RFLP detected by the enzyme XbaI (but not that associated with RFLPs detected by MspI or EcoRI) is involved in determining the normal levels of serum total cholesterol and low density lipoprotein (LDL) cholesterol. In our study, genetic variation associated with the XbaI RFLP accounts for 14% of the total phenotypic variance in cholesterol levels. Information from all three RFLPs can be used in conjunction to give a better definition of the underlying genetic variation. Data from a second study show that genetic variation in the apoA-I/C-III/A-IV gene cluster, associated with the PstI RFLP, is involved in determining the level of apoA-I and, to a lesser extent, the levels of high density lipoprotein (HDL). When genotypes from three RFLPs were used in conjunction as a haplotype, genetic variation in this gene cluster was shown to account for 16% of the phenotypic variance in apoA-I concentration and for 8% of the phenotypic variance in HDL concentration in our sample. These associations suggest that the isolation and sequencing of the apoB and the apoA-I/C-III/A-IV genes from different individuals will give useful information about how changes in the DNA sequence of these genes may lead to alterations in the levels of their respective apolipoproteins, in the level of the lipoproteins with which they are associated and, possibly, in the levels of lipids in the serum.

Apolipoprotein A-I↗
PubMed2005

Detection of low genetic variation in a critically endangered Chinese pine, Pinus squamata, using RAPD and ISSR markers.

With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the percentage of polymorphic loci (P) was 6.45, and the expected heterozygosity (He) was 0.019 at the species level based on RAPD markers. The results of ISSR were consistent with those detected by RAPD but somewhat higher (I = 0.048, Ae = 1.042, P = 12.3, He = 0.029). The genetic variation of the subpopulation on the southwest-facing slope was much higher than that of the subpopulation on the northeast-facing slope, which may be attributed to the more diverse environment on the southwest-facing slope. The genetic differentiation between the two subpopulations was very low. The between-subpopulation variabilities, phiST, calculated from RAPD and ISSR data were 0.011 and 0.024. Because of the lack of fossil records and geological historical data, it was difficult to explain the extremely low genetic diversity of the species. We postulate that this ancient pine might have experienced strong bottlenecks during its long evolutionary history, which caused the loss of genetic variation. Genetic drift and inbreeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity. Human activities such as logging may have accelerated the loss of genetic diversity in P. squamata.

Conservation of Natural Resources↗
PubMed1984

Genetic variation and craniofacial growth in inbred rats.

There has been no experimental study clarifying the contribution of genetic variation to craniofacial growth on a longitudinal basis, although its importance is generally accepted. Utilizing diallel crosses of five strains of inbred rats, the present study concerns an estimation of the contribution genetic variation makes to the longitudinal change of craniofacial size. The overall sizes of craniofacial complex components of F1-offspring rats were investigated postnatally by means of roentgenographic cephalometry, and quantitative genetic analysis was performed by the method of Wearden [1964]. It was revealed that the relative contributions of the genetic and environmental components to total variance in craniofacial size varied with age and that the genetic component of variance significantly increased until the 80th day. On the other hand, the maternal component of variance showed the maximum value during the early periods of postnatal growth (ie, the 10th to 25th day), gradually declining thereafter to a very small amount by the 80th day. The environmental component of variance increased slightly and gradually with age through the experimental period. In conclusion it appeared that genetic variation became more significant during longitudinal growth of the craniofacial complex as the maternal effects diminished.

Age Factors↗
PubMed2006

Torsemide renal clearance and genetic variation in luminal and basolateral organic anion transporters.

AIMS: To investigate the association between torsemide renal clearance and genetic variation in the basolaterally expressed renal organic anion transporters OAT1 and OAT3 and in the luminally situated OAT4. METHODS: We analysed 22 polymorphisms in the OAT coding genes SLC22A6, SLC22A8 and SLC22A11 and their haplotypes and measured torsemide renal clearance in 95 healthy men. In addition, the effect of torsemide on the OAT-mediated transport was studied in vitro. RESULTS: In stably transfected HEK293 cells torsemide (100 microm) inhibited the uptake by human OAT1, OAT3 and OAT4 by 63.1, 58.1 and 68.0%, respectively. Torsemide renal clearance ranged from 6.5 to 43.1 ml min(-1) with a log-normal distribution and a geometric mean of 15.6 ml min(-1) (15.0-16.1 +/- SEM). No clear outlier group was observed. AA carriers of the polymorphism rs11231809 in SLC22A11 had a torsemide renal clearance of 13.3 ml min(-1) (12.7-13.9) compared with 15.1 ml min(-1) (14.5-15.8) in AT and 18.0 ml min(-1) (16.7-19.5) in TT carriers (P = 0.002). The two most frequent haplotypes at SLC22A11 showed an association with torsemide renal clearance. Homozygous carriage of these two haplotypes resulted in renal clearances of 21.2 ml min(-1) (19.0-23.7) and 11.8 ml min(-1) (10.5-13.5), respectively. No association between reanl clearance and genetic variation in SLC22A6 or SLC22A8 was observed. CONCLUSIONS: Genetic variation in the gene encoding the luminally expressed OAT4 rather than in the basolaterally expressed OATs may affect the renal clearance of torsemide.

Adult↗
PubMed2006

A quantitative trait locus analysis of natural genetic variation for Drosophila melanogaster oxidative stress survival.

Little is known about natural genetic variation for survival under oxidative stress conditions or whether genetic variation for oxidative stress survival is associated with that for life-history traits. We have investigated survival in a high-oxygen environment at 2 adult densities using a set of recombinant inbred lines (RILs) isolated from a natural population of Drosophila melanogaster. Female and male oxidative stress survival was highly correlated. Quantitative trait loci (QTLs) for oxidative stress survival were identified on both autosomes. These QTLs were sometimes sex or density specific but were most often not. QTLs were identified that colocalize to the same region of the genome as longevity in other studies using the same set of RILs. We also determined early-age egg production and found QTLs for this trait, but there was no support for an association between oxidative stress survival and egg production.

Age Factors↗
PubMed2004

[Relationship between ATP-binding cassette transporter 1 R219K genetic variation and blood lipids].

OBJECTIVE: To investigate whether ATP-binding cassette transporter 1 (ABCA1) R219K genetic variation is correlated with blood lipids. METHOD: Specimens of peripheral blood were collected from 692 patients with cerebral apoplexy, aged 62 +/- aged 12, and 352 sex- and age-matched persons without cardio-cerebro-vascular disease. Polymerase chain reaction-restricted fragments length polymorphism (PCR-RFLP) was used to determine the ABCA1 genotype: RR type (177 bp), RK type (177 bp, 107 bp, and 70 bp); and KK type (107 bp and 70 bp). The RR and KK type products were sequenced. RESULTS: The level of HDL-C showed an upward trend in the sequence of RR, RK, and KK genotypes with a significant difference between RR genotype (1.3 mmol/L +/- 0.4 mmol/L) and KK genotype (1.4 mmol/L +/- 0.4 mmol/L), especially in the males. The levels of TG tended downward in the sequence of RR, RK, and KK genotypes, however, without a significant difference between any 2 genotypes. Linear regression analysis showed that the HDL-C level was positively correlated with age in the noncarriers of ABCA1R219K genetic variation (RR genotype), and the TC level was negatively correlated with age in the carriers (RK + KK genotype). In the cohort aged </= 70 the HDL-C level was higher in carriers than in noncarriers. CONCLUSION: ABCA1R219K genetic variation results in a beneficial profile of blood lipids, more evident in males. RK + KK genotype is more pronounced in the individuals aged </= 70.

ATP Binding Cassette Transporter 1↗
PubMed1999

[Environmental stress and genetic variation in animal populations].

The impact of environmental stress factors on genetic variation in animal populations is considered. It is tentatively concluded that genetical variability of populations generally increases in stressful environments. The exposure to stressful factors result in an increase of recombination and mutation rates. In quantitative traits, on which the review is focused, stress often leads to an increase in the genetic component of variation. Experiments on Drosophila demonstrated that the effect of stress on genetic variation is stress- and trait-specific. The possible role of stress factors in adaptation and evolution of populations is discussed.

Adaptation, Physiological↗
PubMed2003

Genetic variation of sex allocation in the parasitoid wasp Heterospilus prosopidis.

The genetic variation of sex ratio and sex allocation were examined in a series of half-sib analyses on the sex ratio of braconid parasitoid wasp Heterospilus prosopidis populations collected in Hawaii and Arizona. The mean threshold value and the range of the threshold for change in the sex of offspring in response to resource quality (host size) were determined. Estimates of the narrow-sense heritability (h2) of sex ratio at a specific host size ranged from 0.185 to 0.315, and those of the sex changing point (threshold value) ranged from 0.220 to 0.342. The coefficient of variation (CV(A)) of sex ratio was significantly larger than CV(A) of body weight. We discuss factors that maintained the significant additive genetic variation of sex ratio.

Analysis of Variance↗
PubMed2005

Genetic variation within and among populations of Rhodiola alsia (Crassulaceae) native to the Tibetan Plateau as detected by ISSR markers.

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai-Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai-Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.

DNA Primers↗
PubMed2004

Genetic variation in gorillas.

This review summarizes what is currently known concerning genetic variation in gorillas, on both inter- and intraspecific levels. Compared to the human species, gorillas, along with the other great apes, possess greater genetic variation as a consequence of a demographic history of rather constant population size. Data and hence conclusions from analysis of mitochondrial DNA (mtDNA), the usual means of describing intraspecific patterns of genetic diversity, are limited at this time. An important task for future studies is to determine the degree of confidence with which gorilla mtDNA can be analyzed, in view of the risk that one will inadvertently analyze artifactual rather than genuine sequences. The limited information available from sequences of nuclear genomic segments does not distinguish western from eastern gorillas, and, in comparison with results from the two chimpanzee species, suggests a relatively recent common ancestry for all gorillas. In the near future, the greatest insights are likely to come from studies aimed at genetic characterization of all individual members of social groups. Such studies, addressing topics such as behavior of individuals with kin and non-kin, and the actual success of male reproductive strategies, will provide a link between behavioral and genetic studies of gorillas.

Animals↗
PubMed1987

Genetic variation in paraoxonase activity and sensitivity to diisopropylphosphofluoridate in inbred mice.

The mechanism underlying genetic variation in the acute and chronic responses of mice to diisopropylphosphofluoridate (DFP) are unknown. We investigated whether variation in metabolism of organophosphates by A-esterase, as exemplified by the enzyme paraoxonase, was correlated to the degree of sensitivity to DFP in four inbred mouse strains. LD50s and plasma paraoxonase were measured in each strain. We observed genetic variation in both of these measures, but there was no significant correlation between the two measures. We conclude that plasma paraoxonase activity does not underlie genetic variation in sensitivity to the lethal effects of DFP in mice since it does not determine the degree of sensitivity or resistance to DFP.

Animals↗
PubMed1999

Genetic variation maintained in multilocus models of additive quantitative traits under stabilizing selection.

Stabilizing selection for an intermediate optimum is generally considered to deplete genetic variation in quantitative traits. However, conflicting results from various types of models have been obtained. While classical analyses assuming a large number of independent additive loci with individually small effects indicated that no genetic variation is preserved under stabilizing selection, several analyses of two-locus models showed the contrary. We perform a complete analysis of a generalization of Wright's two-locus quadratic-optimum model and investigate numerically the ability of quadratic stabilizing selection to maintain genetic variation in additive quantitative traits controlled by up to five loci. A statistical approach is employed by choosing randomly 4000 parameter sets (allelic effects, recombination rates, and strength of selection) for a given number of loci. For each parameter set we iterate the recursion equations that describe the dynamics of gamete frequencies starting from 20 randomly chosen initial conditions until an equilibrium is reached, record the quantities of interest, and calculate their corresponding mean values. As the number of loci increases from two to five, the fraction of the genome expected to be polymorphic declines surprisingly rapidly, and the loci that are polymorphic increasingly are those with small effects on the trait. As a result, the genetic variance expected to be maintained under stabilizing selection decreases very rapidly with increased number of loci. The equilibrium structure expected under stabilizing selection on an additive trait differs markedly from that expected under selection with no constraints on genotypic fitness values. The expected genetic variance, the expected polymorphic fraction of the genome, as well as other quantities of interest, are only weakly dependent on the selection intensity and the level of recombination.

Alleles↗
PubMed1982

Genetic variation in human apolipoprotein E.

Genetic variation in human apoprotein E was studied using the technique of isoelectric focusing applied to delipidated very low density lipoprotein from 426 Christchurch blood donors and 7 patients with type III hyperlipoproteinemia. Six phenotypes were distinguishable by the relative proportions of the apoprotein E isomers. In the blood donors, observed frequencies for these were: E3/3 = 51.4%; E4/3 = 25.0%; E4/4 = 1.0%; E3/2 - 20.0%; E4/2 = 1.2%; and E2/2 = 1.4%. All seven patients with type III hyperlipoproteinemia exhibited phenotype E2/2. Family studies of apoprotein E variants support a mode of inheritance controlled by three alleles acting at one gene locus. On this basis, the alleles occurred in the blood donor population with frequencies of 0.72 for the epsilon 3 allele, 0.12 for the epsilon 2 allele, and 0.16 for the epsilon 4 allele. The epsilon 2 allele influenced plasma cholesterol. The mean plasma cholesterol in subjects heterozygous for the epsilon 2 allele was 5.32 mmol/l, very significantly less (P less than 0.01) than the mean of 5.84 mmol/l in an age- and sex-matched group of subjects without this allele in their genotype. The mean plasma cholesterol value of 4.92 mmol/l for the five individuals homozygous for the epsilon 2 allele was also significantly less (P less than 0.05) than for age- and sex-matched subjects without the epsilon allele, whose mean was 5.80 mmol/l.

Alleles↗