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PubMed2004

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

Africa, Western↗

PubMed2003

Challenges and complexities in estimating both the functional impact and the disease risk associated with the extensive genetic variation in human DNA repair genes.

Individual risk and the population incidence of disease result from the interaction of genetic susceptibility and exposure. DNA repair is an example of a cellular process where genetic variation in families with extreme predisposition is documented to be associated with high disease likelihood, including syndromes of premature aging and cancer. Although the identification and characterization of new genes or variants in cancer families continues to be important, the focus of this paper is the current status of efforts to define the impact of polymorphic amino acid substitutions in DNA repair genes on individual and population cancer risk. There is increasing evidence that mild reductions in DNA repair capacity, assumed to be the consequence of common genetic variation, affect cancer predisposition. The extensive variation being found in the coding regions of DNA repair genes and the large number of genes in each of the major repair pathways results in complex genotypes with potential to impact cancer risk in the general population. The implications of this complexity for molecular epidemiology studies, as well as concepts that may make these challenges more manageable, are discussed. The concepts include both experimental and computational approaches that could be employed to develop predictors of disease susceptibility based on DNA repair genotype, focusing initially on studies to assess functional impact on individual proteins and pathways and then on molecular epidemiology studies to assess exposure-dependent health risk. In closing, we raise some of the non-technical challenges to the utilization of the full richness of the genetic variation to reduce disease occurrence and ultimately improve health care.

Amino Acid Substitution↗

PubMed1997

Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene.

The purpose of this study was to detect genetic variation in the porcine H-FABP gene, a candidate gene for meat quality traits in pigs. Lambda phages containing the porcine H-FABP gene were isolated by plaque hybridization with human H-FABP cDNA. The coding and flanking intronic sequences of the porcine H-FABP gene were determined as well as 1.6 kb of the 5' upstream region. The various potential regulatory sequences in this region are in accordance with the function and expression of the protein in muscle and mammary tissue. Furthermore, comparison with the homolog region of the mouse identified a highly conserved 13-bp element (CTTCCT [A/C] TTTCGG) that may be involved in regulation of expression. The porcine H-FABP gene was localized on Chromosome (Chr) 6 by porcine sequence-specific PCR on DNA from a pig/rodent cell hybrid panel. In addition, part of the H-FABP gene was screened for genetic variation by PCR-RFLP analysis. Three PCR-RFLPs were detected, one in the upstream region (HinfI) and two in the second intron (HaeIII and MspI). In most pig breeds the corresponding alleles have a variable distribution, possibly a consequence of selective breeding. This genetic variation will enable us to investigate the role of the H-FABP locus in porcine production and meat quality traits.

Amino Acid Sequence↗

PubMed1988

Competitive interactions in Drosophila melanogaster: genetic variation for interference through media conditioning.

Interference, which is one of two aspects of the process of competition which take place in genetically heterogeneous mixtures has been studied in the Texas population of Drosophila melanogaster. Both survival and mean adult weight were investigated in the population itself (which displays high levels of aggression and little response) and in LA, a genotype derived from the population (which displays low aggression and high levels of response) in both homotypically and heterotypically conditioned media. The results presented here show that the competitive effects of conditioning depend not only on the concentration of the conditioned medium but also on the genotype of the larvae which conditioned the medium and that of the flies which respond to such media. It was also concluded that medium conditioning is one of a range of biological parameters involved in the determination of the aggression and response components of the competitive interaction among Drosophila larvae. Thus the competitive fitness of a genotype of D. melanogaster is related not only to genetic variation for aggression and response but also to genetic variation in the ability to condition media and the sensitivity to such media.

Animals↗

PubMed1999

Genetic variation in rates of nondisjunction: association of two naturally occurring polymorphisms in the chromokinesin nod with increased rates of nondisjunction in Drosophila melanogaster.

Genetic variation in nondisjunction frequency among X chromosomes from two Drosophila melanogaster natural populations is examined in a sensitized assay. A high level of genetic variation is observed (a range of 0.006-0.241). Two naturally occurring variants at the nod locus, a chromokinesin required for proper achiasmate chromosome segregation, are significantly associated with an increased frequency of nondisjunction. Both of these polymorphisms are found at intermediate frequency in widely distributed natural populations. To account for these observations, we propose a general model incorporating unique opportunities for meiotic drive during female meiosis. The oötid competition model can account for both high mean rates of female-specific nondisjunction in Drosophila and humans as well as the standing genetic variation in this critical fitness character in natural populations.

Animals↗

PubMed1999

Genetic variation and correlations between genotype and locomotor physiology in outbred laboratory house mice (Mus domesticus).

Laboratory strains of house mice (Mus domesticus) are increasingly used as model organisms in evolutionary physiology, so information on levels of genetic variation is important. For example, are levels of genetic variation comparable to those found in populations of wild house mice? We studied allozymes to estimate genetic variation in outbred Hsd:ICR mice, which have been used in several studies with evolutionary emphasis. The physiological significance of allozyme variation remains obscure. Several workers have reported relationships between multi-locus heterozygosity and metabolic traits, but endotherms have not been studied. Therefore, we also measured mice for basal metabolic rate (BMR), maximal oxygen consumption during forced treadmill exercise (VO2max), and 12 other traits related to locomotor physiology, before genotyping them for 10 allozyme loci. Four of these loci were polymorphic, all were in Hardy-Weinberg equilibrium, and inbreeding coefficients were not significantly different from zero. Average heterozygosities were 11%, similar to values reported for wild populations of house mice. Fourteen percent of the associations between single-locus genotype and physiological traits were statistically significant. Multi-locus heterozygosity was not significantly related to VO2max, but was positively correlated with BMR, a result opposite to the negative correlation between standard metabolic rate and heterozygosity reported in many ectotherms. Therefore, the proposed mechanisms for the effect of multi-locus heterozygosity on metabolic rate in ectotherms may not apply to endotherms.

Animals↗

PubMed2001

Identifying main evolutionary mechanisms shaping genetic variation of Leuciscus cephalus L. 1758 (Cyprinidae) in western Greece: discordance between methods.

Numerous methods can be used in intraspecific phylogeographic studies to infer the evolutionary mechanisms that shaped observed genetic variation in populations. However, these methods are scarcely used jointly, and the evolutionary outcomes they could propose are not fully compared. In this study, using a chub (Leuciscus cephalus; Cyprinidae) mitochondrial DNA data set (13 populations in Western Greece, 14 haplotypes), we compare three distinct 'historical' methods that could possibly infer relative importance of basic evolutionary mechanisms (isolation vs migration) shaping genetic variation: the nested clade analysis, the psi-test and the 'mismatch distributions'. Taking together, interpretations of these analyses allow to draw a picture of the evolutionary history of chub in Western Greece based on isolation and genetic drift for higher clades. However, results issued each method can differ for low differentiated clades. We discuss such differences and suggest that methods should be used jointly in phylogeographic studies for a better evaluation of the evolutionary mechanisms that shaped genetic variation.

Animals↗

PubMed2004

Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms.

Cicer reticulatum, C. echinospermum, C. bijugum, C. judaicum, C. pinnatifidum, C. cuneatum and C. yamashitae are wild annual Cicer species and potential donors of valuable traits to improve chickpea (C. arietinum). As part of a large project to characterize and evaluate wild annual Cicer collections held in the world gene banks, AFLP markers were used to study genetic variation in these species. The main aim of this study was to characterize geographical patterns of genetic variation in wild annual Cicer germplasm. Phylogenetic analysis of 146 wild annual Cicer accessions (including two accessions in the perennial C. anatolicum and six cultivars of chickpea) revealed four distinct groups corresponding well to primary, secondary and tertiary gene pools of chickpea. Some possible misidentified or mislabelled accessions were identified, and ILWC 242 is proposed as a hybrid between C. reticulatum and C. echinospermum. The extent of genetic diversity varied considerably and was unbalanced between species with greatest genetic diversity found in C. judaicum. For the first time geographic patterns of genetic variation in C. reticulatum, C. echinospermum, C. bijugum, C. judaicum and C. pinnatifidum were established using AFLP markers. Based on the current collections the maximum genetic diversity of C. reticulatum, C. echinospermum, C. bijugum and C. pinnatifidum was found in southeastern Turkey, while Palestine was the centre of maximum genetic variation for C. judaicum. This information provides a solid basis for the design of future collections and in situ conservation programs for wild annual Cicer.

Cicer↗

PubMed2003

Genetic variation in organisms with sexual and asexual reproduction.

The genetic variation in a partially asexual organism is investigated by two models suited for different time scales. Only selectively neutral variation is considered. Model 1 shows, by the use of a coalescence argument, that three sexually derived individuals per generation are sufficient to give a population the same pattern of allelic variation as found in fully sexually reproducing organisms. With less than one sexual event every third generation, the characteristic pattern expected for asexual organisms appear, with strong allelic divergence between the gene copies in individuals. At intermediary levels of sexuality, a complex situation reigns. The pair-wise allelic divergence under partial sexuality exceeds, however, always the corresponding value under full sexuality. These results apply to large populations with stable reproductive systems. In a more general framework, Model 2 shows that a small number of sexual individuals per generation is sufficient to make an apparently asexual population highly genotypically variable. The time scale in terms of generations needed to produce this effect is given by the population size and the inverse of the rate of sexuality.

Gene Frequency↗

PubMed2006

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.

Abstract Ecotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large-scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000-bp region examined. Overall nucleotide diversity, measured as (Total), was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.

Canada↗

PubMed2005

Soft sweeps: molecular population genetics of adaptation from standing genetic variation.

A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.

Adaptation, Physiological↗

PubMed2000

Behaviour plasticity without learning: phenotypic and genetic variation of naïve Daphnia in an ecological trade-off.

The swimming behaviour of adult Daphnia largely governs their depth, which has a direct effect on both individual foraging success and predation avoidance. We treated individual swimming behaviour as a threshold character and used directional changes in average clonal depth within experimental tubes as a test for character plasticity. We compared the swimming behaviours of two cohabiting, phenotypically similar Daphnia (Daphnia galeata and Daphnia galeata-Daphnia rosea hybrid) to determine (1) whether there is inherited variation (H(2)) for different traits (responses to hunger and predator cues); (2) whether changes in genetic parameters (norm of reaction and character state) across four environments could be simulated by combinations of the presence or absence of a predator cue and high or low hunger levels; and (3) whether these Daphnia would respond to directional selection, particularly in a trade-off environment (high hunger and predator cue treatments). Responses of both D. galeata and the D. galeata-rosea hybrid to hunger and a predator cue and the trade-off environment were plastic. Daphnia galeata expressed significant genetic variation within (H(2)) and between environments (heritability of plasticity). Both the character state and norm of reaction estimates of heritable variation in the hybrid were close to zero. Genetic correlations were positive and stable across six environmental pairs in Daphnia galeata. Most hybrid genetic correlations were not significant. The phenotypic distributions of both D. galeata and the hybrid were bimodal in the trade-off environment. The D. galeata distribution was partly due to between-clone variation and the hybrid distribution was almost entirely due to within-clone variation. Genetic variation expressed by D. galeata in the trade-off environment appears to depend on both clone by environment interactions and stable inherited differences. These results indicate that while plastic phenotypic responses cause a similar opportunity for selection in D. galeata and the hybrid, their responses to selection would be different in the trade-off and in related environments. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMed2004

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred.

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign F(IS) estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

Animals↗

PubMed1985

Genetic variation in body size, composition, temperature, and feed intake in mature chickens.

Genetic variation for more than 40 traits was assessed in 26 stocks of mature chickens reared together and fed ad libitum from hatching to slaughter at 507 days of age. There was greater genetic variation among males than among females. The intraclass correlation, t, was high (greater than .75) for measures of size and weight and moderate (.20 to .60) for most other traits (P less than .05) including a measure of lean distribution (.37). Three main categories of stocks were studied, viz. outbred Leghorns, medium-sized stocks, and contemporary heavy meat chickens. Differences in lean distribution were not associated with category, but differences of 40 to 50 g/kg lean in the breast of some stocks may be caused by a single gene. Lean:bone ratios were similar in medium and heavy stocks but were greater (P less than .05) in heavy meat-types compared with outbred Leghorns. Bone density was higher (P less than .01) in females compared with males and in outbred Leghorns compared with heavier stocks (P less than .01). Heavy meat-type males were leaner (P less than .01) and had proportionately less fat in the abdominal cavity than outbred Leghorns. Carcass fatness was similar among stocks of females, but abdominal fat was lower in Leghorns selected for high egg production compared with unselected Leghorns (P less than .05) and heavy stocks (P less than .001). One resistant and two Marek's disease-susceptible stocks were replicated in a specific pathogen-free (SPF) environment. Spleen weight was larger (P less than .001) in the conventional environment. Females were relatively smaller (P less than .05) than males in the conventional environment. Body temperature (t = .25, P less than .05) and feed intake were assessed in males. Heavy meat birds had a lower (P less than .01) body temperature than outbred Leghorns and medium-sized stocks. Differences among stocks for feed intake (t = .77) were significant (P less than .05); however, they were greatly reduced when feed intake was expressed as g/kg liveweight (LW) (t = .49) or g/kg LW.75 (t = .25). Outbred Leghorns ate less in absolute terms but significantly more (P less than .01) as a proportion of LW or LW.75 than the medium and heavy lines.

Animals↗

PubMed2005

[Association between genetic variations in methylenetetrahydrofolate reductase and risk of colorectal cancer in a Chinese population].

OBJECTIVE: To investigate the association between genetic variations in methylenetetrahydrofolate reductase (MTHFR) and the risk of colorectal cancer in a Chinese population. METHODS: One hundred and ninety-eight cases of colorectal cancer and 420 controls were genotyped for detecting MTHFR C677T and A1298C polymorphisms by PCR-RFLP methods. The adjusted odds ratios (OR) and 95% confidence intervals (CI) were calculated by using unconditional logistic regression model. RESULTS: The frequency of the MTHFR C677T allele found among cases was significantly more frequent than that among controls (51.3% to 44.4%, P = 0.02). As compared with the 677CC genotype, the 677TT genotypes had a 67% (95% CI, 1.05 - 2.66) increased risk of colorectal cancers. However, there appeared no any correlations between the genetic variations of MTHFR and the cancer metastasis. CONCLUSION: These findings demonstrated that the genetic variation of MTHFR C677T should be a genetic susceptibility factor for colorectal cancer in a Chinese population.

Asian People↗

PubMed1989

Genetic variation in an inbred plant: variation in tissue cultures of soybean [Glycine max (L.) Merrill].

Although soybean [Glycine max (L.) Merrill] grows as an inbreeding, generally homozygous, plant, the germplasm of the species contains large amounts of genetic variation. Analysis of soybean DNA has indicated that variation of RFLP (restriction fragment length polymorphism) markers within the species usually entails only two alleles at any one locus and that mixtures of such dimorphic loci account for virtually all of the restriction fragment variation seen in soybean (G. max), and in its ancestors, G. soja and G. gracilis. We report here that tissue cultures prepared from root tissue of individual soybean plants develop RFLP allelic differences at various loci. However, these newly generated alleles are almost always the same as ones previously found and characterized in other varieties of cultivated soybean (cultivars). This repeated generation of particular alleles suggests that much of the genetic variation seen in soybean could be the consequence of specific, relatively frequently employed, recombinational events. Such a mechanism would allow inbred cultivars to generate genetic variation (in the form of alternative alleles) in a controlled manner, perhaps in response to stress.

DNA Probes↗

PubMed2001

Genetic variation in coagulation and fibrinolytic proteins and their relation with acute myocardial infarction: a systematic review.

BACKGROUND: It is pathophysiologically conceivable that genetic variations in coagulation and fibrinolytic proteins are associated with the risk of myocardial infarction. Methods and Results- We performed a literature search to identify published case-control studies correlating the factor V Leiden or prothrombin G20210A mutations or fibrinogen G-455A or plasminogen activator inhibitor-1 (PAI-1) 4G/5G polymorphisms with the risk of myocardial infarction. Studies were included only if they used solid diagnostic criteria and complied with published methodological criteria. A common OR with corresponding 95% CI was calculated for the risk of myocardial infarction in a fixed-effect model according to Mantel-Haenszel. The factor V Leiden and prothrombin G20201A mutations did not significantly correlate with myocardial infarction (OR 1.26, 95% CI 0.94 to 1.67, P=0.12 and OR 0.89, 95% CI 0.59 to 1.35, P=0.6, respectively). Inclusion of the studies that investigated young patients (<55 years) made the association significant for factor V Leiden (OR 1.29, 95% CI 1.03 to 1.61, P=0.02). Homozygosity for the fibrinogen -455A allele was significantly associated with a decreased risk of myocardial infarction (OR 0.66, 95% CI 0.44 to 0.99, P=0.04), whereas the PAI-1 4G4G genotype was significantly associated with increased risk (OR 1.20, 95% CI 1.04 to 1.39, P=0.04). CONCLUSIONS: Associations between these genetic variations and myocardial infarction were weak or absent. In the absence of clinical implications, our results indicate that screening of patients with myocardial infarction for these genetic variations is not warranted.

Humans↗

PubMed2006

A model-based approach to capture genetic variation for future association studies.

Genome-wide association studies are still constrained by the cost of genotyping. For this reason, the selection of a reduced set of markers or tags able to capture a significant proportion of the genetic variation is an important aspect of these studies. Most tagging SNP selection methods have been successful in capturing the genetic variation of the data from which the tags have been chosen. However, when these tags are used in an independent data set, a significant proportion of the remaining SNPs (non-tags) are not captured and, in most cases, there is no information on which SNPs are captured. We propose to use a probabilistic model to predict the non-tags based on a set of tags, as a way to capture genetic variation. An important advantage of this method is that it directly predicts the genotype of the non-tags with which we can test for association with the phenotype and which could help to elucidate the location of genes responsible for increasing disease susceptibility. Additionally, this method provides an estimate of the probabilities with which the predictions are made, which reflects the confidence of the probabilistic model. We also propose new methods to select the tagging SNPs. We empirically show by using HapMap data that our approach is able to capture significantly more genetic variation than methods based solely on a pairwise LD measure.

Algorithms↗