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Results for “Genetic Variation”

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PubMed1992

Genetic variation of simian immunodeficiency viruses in nonhuman primates.

The generation of biologically active proviral DNA clones of simian immunodeficiency virus (SIV) that give rise to infectious virions has allowed the detailed examination of genetic variation in experimentally inoculated monkeys. Studies of nucleotide sequences derived directly from circulating leukocytes of infected monkeys show that the SIV genome undergoes rapid and dramatic variation during the course of infection. The env gene is a major site for variation, and within the Env protein, hypervariable regions analogous to those previously defined for the human immunodeficiency virus type 1 (HIV-1) env gene are apparent. A major exception is the region corresponding to the V3 domain in HIV-1, which has been highly conserved in all SIV studies to date. These data notwithstanding, the role of SIV genetic variation in the pathogenesis of AIDS in monkeys remains unclear. Genetic variation within the env gene does not appear to be sufficient for the development of AIDS since significant variation is observed in both pathogenic and nonpathogenic SIV infections. Furthermore, although it generally is believed that env gene variation might allow HIV and SIV to avoid recognition and elimination by host immune responses, this premise has not been rigorously proven. The use of molecularly cloned SIV in monkey models has provided important quantitative and qualitative information on in vivo sequence variation, and these data, in turn, have laid the groundwork for addressing the undoubtedly complex functional significance of this variation.

Amino Acid Sequence↗

PubMed1997

Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana.

Genetic variation was studied in quantitative traits and molecular markers in six natural Scandinavian populations of Arabidopsis thaliana. Only two of the populations had several molecular marker haplotypes and significant between-family variance components in quantitative traits. There was no genetic variation in the other four populations. The differentiation between the populations was high in both molecular markers and quantitative traits, with FST estimates of above 0.60 in almost all traits. The patterns of variation of the neutral markers and morphological and phenological traits were consistent in all the analyses, as opposed to what has been found in predominantly outcrossing species. The general picture of the level and distribution of genetic variance agrees with the information from other predominantly inbreeding species.

Arabidopsis↗

PubMed1998

Genetic variation and prediction of additive and nonadditive genetic effects for six carcass traits in an Angus-Brahman multibreed herd.

Estimates of covariances and sire expected progeny differences of additive and nonadditive genetic effects for six carcass traits were obtained using records from 486 straightbred and crossbred steers from 121 sires born between 1989 and 1995 in the Angus-Brahman multibreed herd of the University of Florida. Steers were slaughtered at a similar carcass composition end point. Covariances were estimated by REML procedures, using a generalized expectation-maximization algorithm applied to multibreed populations. Straightbred and crossbred estimates of heritabilities and additive genetic correlations were within ranges found in the literature for steers slaughtered on an age- or weight-constant basis for hot carcass weight, longissimus muscle area, and shear force but equal to or less than the lower bound of these ranges for fat-related traits. Maximum values of interactibilities (i.e., ratios of nonadditive variances to phenotypic variances in the F1) and nonadditive genetic correlations were smaller than heritabilities and additive genetic correlations in straightbreds and crossbred groups. Sire additive and total direct genetic predictions for longissimus muscle area, marbling, and shear force tended to decrease with the fraction of Brahman alleles, whereas those for hot carcass weight and fat thickness over the longissimus were higher, and those for kidney fat were lower in straightbreds and F1 than in other crossbred groups. Nonadditive genetic predictions were similar across sire groups of all Angus and Brahman fractions. These results suggest that slaughtering steers on a similar carcass composition basis reduces variability of fat-related traits while retaining variability for non-fat-related traits comparable to slaughtering steers on a similar age or weight basis. Selection for carcass traits within desirable (narrow) ranges and slaughter of steers at similar compositional end point seems to be a good combination to help produce meat products of consistent quality.

Abattoirs↗

PubMed2005

Perspectives on human genetic variation from the HapMap Project.

The completion of the International HapMap Project marks the start of a new phase in human genetics. The aim of the project was to provide a resource that facilitates the design of efficient genome-wide association studies, through characterising patterns of genetic variation and linkage disequilibrium in a sample of 270 individuals across four geographical populations. In total, over one million SNPs have been typed across these genomes, providing an unprecedented view of human genetic diversity. In this review we focus on what the HapMap Project has taught us about the structure of human genetic variation and the fundamental molecular and evolutionary processes that shape it.

Alleles↗

PubMed2006

Genetic variation in the hypothalamic-pituitary-adrenocortical axis regulatory factor, T-box 19, and the angry/hostility personality trait.

Neurotic personality traits are important factors in several psychiatric disorders and suicidal behavior. Here, we have investigated the existence of potential relationships between neurotic personality traits and genetic variation. Non-suicidal parents derived from trios (suicide attempter and both parents) and non-suicidal volunteers, examined by the Neuroticism, Extraversion and Openness (NEO) Personality Inventory - Revised (NEO PI-R), were divided into screening and replication samples. The screening sample (n= 127) was used to select potential relationships between neurotic personality traits and genetic variation among 130 single nucleotide polymorphisms (SNPs). Screening (analysis of variance) with regard to the personality dimension neuroticism indicated potential relationships at three different loci. More detailed analysis of these three SNPs at NEO PI-R facet level indicated four potential relationships. T-test analysis in the replication sample (n= 617) was used to retest the relationships indicated during screening. One of those relationships was confirmed in the replication sample (P= 0.0052; Bonferroni correction), indicating that genetic variation at the human T-box 19 (TBX19) locus is related to the personality trait angry/hostility. Furthermore, using analysis of haplotypes among trios by transmission disequilibrium test and its extension, the family-based association test, overtransmission of a haplotype GAC at the TBX19 locus was associated with increased angry/hostility scores among suicide attempters (P= 0.009; Bonferroni correction). This is to our knowledge the first report on the association of the angry hostility personality trait with genetic variation at the TBX19 locus, an important regulator of the hypothalamic-pituitary-adrenocortical axis.

Adult↗

PubMed1994

Detection of genetic variations in serotype I isolates of infectious bursal disease virus using polymerase chain reaction and restriction endonuclease analysis.

Reverse transcription with polymerase chain reaction (PCR) followed by restriction endonuclease analysis detected genetic variations among serotype I isolates of infectious bursal disease virus (IBDV). Using a set of synthetic primers derived from the large genome segment of APHIS-IBDV, the hypervariable region (AccI-SpeI fragment) located in the VP2 gene was amplified. With all strains, a cDNA fragment of approximately 643 bp was amplified, indicating that there were no apparent deletions or insertions in this region among isolates. Fragments amplified from 9 isolates were digested with 14 restriction enzymes. Restriction fragment profiles generated by restriction enzymes NaeI, StuI, TaqI, and SacI, showed genetic variations among isolates. This study provided a simple and sensitive method for detection of genetic variations among isolates that are closely related serologically and could not be differentiated using current serologic methods.

Animals↗

PubMed2005

Genetic variation and correlation of dietary response in an advanced intercross mouse line produced from two divergent growth lines.

Levels of human obesity have increased over the past 20 years worldwide, primarily due to changes in diet and activity levels. Although environmental changes are clearly responsible for the increasing prevalence of obesity, individuals may show genetic variation in their response to an obesogenic environment. Here, we measure genetic variation in response to a high-fat diet in a mouse model, an F16 Advanced Intercross Line derived from the cross of SM/J and LG/J inbred mouse strains. The experimental population was separated by sex and fed either a high-fat (42% of energy from fat) or low-fat (15% of energy from fat) diet. A number of phenotypic traits related to obesity and diabetes such as growth rate, glucose tolerance traits, organ weights and fat pad weights were collected and analysed in addition to serum levels of insulin, free fatty acids, cholesterol and triglycerides. Most traits are different between the sexes and between dietary treatments and for a few traits, including adult growth, fat pad weights, insulin and glucose tolerance, the dietary effect is stronger in one sex than the other. We find that fat pad weights, liver weight, serum insulin levels and adult growth rates are all phenotypically and genetically correlated with one another in both dietary treatments. Critically, these traits have relatively low genetic correlations across environments (average r =0.38). Dietary responses are also genetically correlated across these traits. We found substantial genetic variation in dietary response and low cross environment genetic correlations for traits aligned with adiposity. Therefore, genetic effects for these traits are different depending on the environment an animal is exposed to.

Animals↗

PubMed1986

Genetic variation of liver lipid content of coturnix quail.

Two experiments were conducted to elucidate the genetic variation in the liver lipid content of coturnix quail. In Experiment 1, the change of the liver lipid content with advancing age was studied. In Experiment 2, the genetic variation of the liver lipid content at 4 weeks of age was analyzed. Liver lipid was extracted with ethanol-ether solution and weighed. Genetic parameters of liver lipid content, body weight, and liver weight were estimated from sib analysis. The means of liver lipid content at 2 and 4 weeks of age were approximately 25% on a dry weight basis in both sexes. After 6 weeks of age, the liver lipid content of the female was higher than that of the male. The liver lipid content of the egg-laying female was slightly higher than that of the nonlaying female. Heritability (h2sire) of liver lipid content from 4-week-old coturnix quail was estimated as h2sire: .62 +/- .73.

Animals↗

PubMed1997

Environmental stress and the expression of genetic variation.

We have started to test the effects of environmental extremes on the expression of genetic variation for traits likely to be under selection in natural populations. We have shown that field heritability may be high for stress response traits in contrast to morphological traits, which tend to show lower levels of heritable variation in nature compared with the laboratory. Selection for increased stress resistance can lead to a number of other evolutionary changes, and these may underlie trade-offs between favourable and stressful environments. Temperature extremes can have a marked influence on the heritability of life history traits. Heritabilities for fecundity can be high when parental flies are reared at low temperatures and under field conditions. The expression of genetic variation for development time is somewhat more complex when temperature extremes are considered. Populations at species margins may be ideal for studying the effects of environmental stress on evolution.

Animals↗

PubMedDate not supplied

Genetic variation at three VNTR loci (D1S80, APOB, and D17S5) in two tribal populations of Andhra Pradesh, India.

This study reports the genetic variation at three variable number of tandem repeat (VNTR) loci (APOB, D17S5 and D1S80) in two tribes (Thoti and Kolam) of Andhra Pradesh, India. Kolams constitute 1% of the total scheduled tribal population of Andhra Pradesh, while Thoti is a numerically small tribe. All three genetic loci were genotyped using the polymerase chain reaction (PCR) technique and were polymorphic in both populations. At the D1S80 locus, both populations showed higher frequencies of allele *31 (9-14%) than other Indian populations. In the APOB system, Thoti showed a very high frequency of allele *37 (54%) and for D17S5 system allele *4 was the most common in Thoti (32%) and allele *2 in Kolam (28%). Both tribes differed statistically significantly from other tribal populations of the region. The level of gene differentiation was low (GST = 0.038) for Indian tribal populations. The allele frequency distribution, heterozygosity and genetic diversity analysis shows that the observed genetic variation is socially and geographically structured.

Alleles↗

PubMed2003

Genetic variation of polygenic characters and the evolution of genetic degeneracy.

The classical model of mutation-selection balance for quantitative characters sums the effects of individual sites to determine overall character value. I develop an alternative version of this classical model in which character value depends on the averaging of the effects of the individual sites. In this new averaging model, the equilibrium patterns of variance in allelic effects and character values change with the number of sites that affect a character in a different way from the classical model of summing effects. Besides changing the patterns of variance, the averaging model favours the addition of loci to the control of character values, perhaps explaining in part the recent observation of widespread genetic degeneracy.

Biological Evolution↗

PubMed2006

Breeding system variation, genetics and evolution in the Turneraceae.

We review the genetics and evolution of breeding systems in the Turneraceae. Distyly occurs in seven of 10 genera and 81% of species. The remaining species are homostylous. Polyploid evolution has been significant in Turnera. Approximately 60% of species are polyploid ranging from diploid through decaploid. No relationship between breeding system and polyploidy is evident. The genetics of distyly involves a one-locus two-allele system (S and s). Evidence from crosses with homostylous species and mutants is consistent with the possibility that a "Primula-type" supergene underlies distyly but does not prove this to be the case. A polygalacturonase, and an alpha-dioxygenase specific to the transmitting tissue of short-styled plants both exhibit morph-limited expression in concert with predictions from an evolutionary model. The function of the proteins in distyly, if any, is unknown. We have begun constructing a fine-scale genetic map of Turnera. Two genetic markers lie within 0.2 cm of the distyly locus. This should provide a starting point for positional cloning of the distyly locus and reveal the genetic architecture and molecular basis of distyly.

Biological Evolution↗

PubMed2003

Normal genetic variation, cognition, and aging.

This article reviews the modulation of cognitive function by normal genetic variation. Although the heritability of "g" is well established, the genes that modulate specific cognitive functions are largely unidentified. Application of the allelic association approach to individual differences in cognition has begun to reveal the effects of single nucleotide polymorphisms on specific and general cognitive functions. This article proposes a framework for relating genotype to cognitive phenotype by considering the effect of genetic variation on the protein product of specific genes within the context of the neural basis of particular cognitive domains. Specificity of effects is considered, from genes controlling part of one receptor type to genes controlling agents of neuronal repair, and evidence is reviewed of cognitive modulation by polymorphisms in dopaminergic and cholinergic receptor genes, dopaminergic enzyme genes, and neurotrophic genes. Although allelic variation in certain genes can be reliably linked to cognition--specifically to components of attention, working memory, and executive function in healthy adults--the specificity, generality, and replicability of the effects are not fully known.

Aging↗

PubMed2005

Genetic variation within exon 2 of the MHC B-LB // gene in Tibetan chicken.

Genetic variation within exon 2 of chicken major histocompatibility complex B-LB // genes was investigated by PCR amplification, cloning and sequencing of a 374 bp fragment of the indigenous Tibetan chicken genomic DNA. Fifteen novel B-LB // alleles were found. Alignment and comparison of 18 allelic sequences from the individuals sampled revealed a total of 62 variable sites (total of 80 mutations) in exon 2, of which 41 were parsimony informative sites. The nucleotide diversity (pi) within the sequence of exon 2 was calculated to be 0.0718. Analysis of nucleotide variation confirmed a lower level of divergence (0.056 +/- 0.008) as estimated by average pairwise distance within the Tibetan chicken population than the five exotic breeds detected. The relative frequencies of synonymous and non-synonymous nucleotide substitutions within the region were 3.25 +/- 0.94% and 15.61 +/- 2.69% , respectively. These results indicated that the genetic variation within exon 2 seemed to have arisen largely by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of beta1 domain coded by exon 2 revealed 11 synonymous mutations and 27 non-synonymous substitutions at the 38 separate sites. Fifty percent (12/24) of the proposed peptide-binding sites were variable within beta1 domain of chicken MHC B-LB // molecules, of which 11 were unique non-synonymous amino acid substitutions. These particular non-synonymous substitutions are considered to be associated with immunological specificity of MHC B-LB // molecule in Tibetan chicken, and they can provide a molecular biological basis for the study of disease resistance in chicken.

Animals↗

PubMed1981

Estimation of genetic variation at the DNA level from restriction endonuclease data.

We consider the estimation of the genetic variation in a natural population when the data are obtained by the use of restriction endonucleases. Under the restriction endonuclease technique, a particular DNA segment is considered and cut wherever a recognition sequence appropriate to the endonuclease occurs. We consider data generated when a random sample of homologous DNA segments is treated in this way with one or a battery of restriction endonucleases. The numbers and sizes of the fragments that result indicate the locations and the frequencies of the recognition sequence (or, with a battery of restriction endonucleases, of each recognition sequence). These frequencies in the sample form the basis for an estimate of the amount of genetic variation in the population.

DNA↗

PubMed2002

Common psychiatric diseases and human genetic variation.

OBJECTIVE: A better understanding of human genetic variation is important in assessing disease epidemiology and phenotypic variation, and may be critical in evaluating genetic aspects of common genetic diseases, such as schizophrenia, bipolar disease and Parkinson's. These diseases are particularly difficult to investigate as there are few peripheral markers, and although a genetic aetiology has long been suspected, robust findings have been hard to establish. METHODS: Variations in alleles at 13 tri-nucleotide gene loci expressed in the brain and implicated in several neurodegenerative diseases, as well as certain other loci, were examined in the Indian population for comparison with other major ethnic groups. RESULTS AND CONCLUSION: In the Indian population, the distribution of alleles at the Machado-Joseph disease locus was similar to the Western European pattern of distribution. Analysis of haplotypes at the locus for Huntington's disease suggested multiple origins, and possible effects of population admixture because of the recent history of the country. At other alleles of neuropsychiatric interest (dopamine receptor, serotonin receptor, serotonin transporter, alcohol dehydrogenase), allele frequencies in the Indian population differed from other populations. Interspecies comparison suggests a gradual expansion in repeat size, with the exception of the CLOCK gene, which displays a contraction of CAG repeat numbers. World-wide differences in disease phenotypes need to be explored, and an appreciation of their genetic basis may provide a window of opportunity for improving our knowledge of the underlying genetic mechanisms.

Journal Article↗

PubMed2003

Genetic variation and the lipid response to dietary intervention: a systematic review.

There is wide interindividual variation in the lipid and lipoprotein responses to dietary change, and the existence of consistent hypo- and hyperresponders supports the hypothesis that responsiveness is related to genetic variation. Many studies have investigated the possibility that the heterogeneity in responsiveness to changes in dietary fat, cholesterol, and fiber intake is explained by variation in genes whose products affect lipoprotein metabolism, eg, apolipoproteins, enzymes, and receptors. A systematic review of the literature was carried out to investigate the effect of genetic variation on the lipid response to dietary intervention. A search strategy for the MEDLINE database retrieved 2540 articles from 1966 to February 2002. This strategy was adapted and performed on the EMBASE database, which retrieved 2473 articles from 1980 to week 9, 2002. Reference lists from relevant journal articles were also checked. This is the first systematic review of the literature, and it summarizes results available from 74 relevant articles. There is evidence to suggest that variation in the genes for apolipoprotein (apo) A-I, apo A-IV, apo B, and apo E contributes to the heterogeneity in the lipid response to dietary intervention. However, the effects of genetic variation are not consistently seen and are sometimes conflicting. Future studies need to have much larger sample sizes based on power calculations and carefully controlled dietary interventions and should investigate the effects of polymorphisms in multiple genes instead of the effects of polymorphisms in single genes.

Apolipoproteins↗

PubMed2005

SNP discovery in associating genetic variation with human disease phenotypes.

With the completion of the human genome project, attention is now rapidly shifting towards the study of individual genetic variation. The most abundant source of genetic variation in the human genome is represented by single nucleotide polymorphisms (SNPs), which can account for heritable inter-individual differences in complex phenotypes. Identification of SNPs that contribute to susceptibility to common diseases will provide highly accurate diagnostic information that will facilitate early diagnosis, prevention, and treatment of human diseases. Over the past several years, the advancement of increasingly high-throughput and cost-effective methods to discover and measure SNPs has begun to open the door towards this endeavor. Genetic association studies are considered to be an effective approach towards the detection of SNPs with moderate effects, as in most common diseases with complex phenotypes. This requires careful study design, analysis and interpretation. In this review, we discuss genetic association studies and address the prospect for candidate gene association studies, comparing the strengths and weaknesses of indirect and direct study designs. Our focus is on the continuous need for SNP discovery methods and the use of currently available prescreening methods for large-scale genetic epidemiological research until more advanced sequencing methods currently under development will become available.

Base Sequence↗