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Results for “programmed genetic variation”

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PubMed2006

High ponderal index at birth predicts high estradiol levels in adult women.

Inter-individual variation in levels of sex hormones results from differences in genetic, developmental, and environmental factors. We tested a hypothesis that programming of the fetal neuroendocrine axis may predispose some women to produce higher levels of steroid hormones during their menstrual cycles as adults. One hundred forty-five regularly menstruating 24- to 36- year-old women collected daily saliva samples for one menstrual cycle. Data on women's birth weights and birth lengths were obtained from medical records. A positive relationship was observed between ponderal index at birth (an indicator of nutritional status, calculated as birth weight/(birth length)(3)) and levels of estradiol (E2) in menstrual cycles, after controlling for potential confounding factors. Mean E2 was 16.4 pmol/l in the low ponderal index tertile, 17.3 pmol/l in the moderate ponderal index tertile, and 19.6 pmol/l in the high ponderal index tertile (the high ponderal index group had significantly higher E2 than both low and moderate ponderal index groups, P=0.0001). This study shows a positive association between ponderal index recorded for women at birth and levels of E2 measured during their menstrual cycles as adults. This suggests that conditions during fetal life influence adult production of reproductive hormones and may contribute to inter-individual variation in reproductive function. In addition, because large size at birth is one of the factors linked with an increased risk of breast cancer, our findings provide a physiological link for the observed positive relationship between indicators of energetic conditions during fetal growth and breast cancer in women.

Adult↗
PubMedDate not supplied

Macroevolution simulated with autonomously replicating computer programs.

The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. The evolutionary outcome of selection acting on novel variation arising over long periods is therefore difficult to predict. The classical problem of this kind is whether 'replaying the tape of life' would invariably lead to the familiar organisms of the modern biota. Here we study the long-term behaviour of populations of autonomously replicating computer programs and find that the same type, introduced into the same simple environment, evolves on any given occasion along a unique trajectory towards one of many well-adapted end points.

Adaptation, Biological↗
PubMed1997

Genetic epidemiology of seropositivity for Trypanosoma cruzi infection in rural Goias, Brazil.

Chagas' disease is a zoonotic disease found throughout Latin America. Despite control programs in many of the affected countries, infection with Trypanosoma cruzi continues to be a major public health concern. In Brazil alone, approximately 53 million people live in endemic areas. Research with humans and with animal models indicates that there is variation in susceptibility to infection with T. cruzi. The reasons for this variation are not known although several studies have implicated genetic factors. An indirect immunofluorescence assay was used to assess seropositivity for T. cruzi infection in 716 adults from the municipality of Posse, Goias, Brazil. Detailed genealogic information was gathered at the time of sampling, which allowed assignment of 525 individuals to 146 pedigrees containing between two and 103 individuals; the remaining 191 unrelated individuals were retained as independents in the analysis. Using a maximum likelihood variance decomposition approach, we performed quantitative genetic analyses to determine if genetic factors could partially account for the observed pattern of seropositivity. The maximum likelihood estimate of the heritability of T. cruzi infection was 0.56 +/- 0.27 (mean +/- SE), indicating that genetic factors account for more than half of the observed variation in infection status. An additional 23% of the variation (c2 = 0.23 +/- 0.09) is attributable to the effects of shared environment, as assessed by common household. The results indicate that genetic factors play an important role in determining epidemiologic patterns of T. cruzi infection. Further characterization of these genetic factors may suggest new biologic areas to be targeted by prevention and intervention programs.

Adolescent↗
PubMed2004

GDPC: connecting researchers with multiple integrated data sources.

UNLABELLED: The goal of this project is to simplify access to genomic diversity and phenotype data, thereby encouraging reuse of this data. The Genomic Diversity and Phenotype Connection (GDPC) accomplishes this by retrieving data from one or more data sources and by allowing researchers to analyze integrated data in a standard format. GDPC is written in JAVA and provides (1) data sources available as web services that transfer XML formatted data via the SOAP protocol; (2) a JAVA API for programmatic access to data sources; and (3) a front-end application that allows users to manage data sources, retrieve data based on filters, sort/group data based on property values and save/open the data as XML files. AVAILABILITY: The source code, compiled code, documentation and GDPC Browser are freely available at: www.maizegenetics.net/gdpc/index.html the current release of GDPC is version 1.0, with updated releases planned for the future. Comments are welcome.

Database Management Systems↗
PubMed1991

Computer-aided quantification of RNA levels detected by in situ hybridization of tissue sections.

A semi-automatic program, designed for non-computer scientists, was developed for quantification of RNA levels detected by in situ hybridization in heterogeneous tissues. A video camera was used to acquire microscopic images of autoradiographed tissue sections which are then digitized on a video monitor for semi-automated quantification of silver grains. We describe a data entry and analysis procedure for systematic quantification of RNA levels in which about 300 cells per tissue sample can be analysed within 10 min. When compared with visual counting, computer-aided quantification was found to be more objective and reliable, with the highest variation coefficient between individuals being 7.5% using computer-aided quantification, compared to 24% with manual counting of the same section areas. A comparative study of c-myc oncogene expression in 11 mammary adenocarcinomas from 3 independent experiments showed the good reproducibility of results using the computer-aided method, with an 18% maximum variation between experiments. The program, with its simple user-interface, reliability and rapidity, is convenient for measuring specific genetic expression levels in clinical studies requiring large numbers of specimens.

Autoradiography↗
PubMed2006

Identification of quantitative trait loci affecting corpora lutea and number of teats in a Meishan x Duroc F2 resource population.

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome-wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning.

Alleles↗
PubMed1989

RFrAP: a computer program for analysis of complex HLA RFLPs. Assignment of restriction fragments to haplotypes by segregation analysis.

The availability of HLA class II cDNA probes has led to the development of a powerful method for the discrimination of genetic variation in this region of the major histocompatibility complex. There are problems with this approach which reduce its usefulness, including the hybridization of a probe with multiple restriction fragments (RFs) from the same locus or of two different cDNA probes with the same RF (cross-hybridizing). These problems may now be largely overcome by the relatively simple computer program presented here, which allows the entry, storage, and editing of phenotype data. It includes utilities for the automatic assignment of bands to haplotypes and also statistical functions to determine several types of correlations. The outputs are presented in a format familiar to HLA serologists and immunogeneticists. In addition, the data is stored in a manner that allows the user to easily prepare "ad hoc" figures and tables that illustrate the more complex relationships among bands and between them and other variables.

Computers↗
PubMed2003

Canine parvovirus enteritis, canine distemper, and major histocompatibility complex genetic variation in Mexican wolves.

The endangered Mexican wolf (Canis lupus baileyi) was recently reintroduced into Arizona and New Mexico (USA). In 1999 and 2000, pups from three litters that were part of the reintroduction program died of either canine parvovirus or canine distemper. Overall, half (seven of 14) of the pups died of either canine parvovirus or canine distemper. The parents and their litters were analyzed for variation at the class II major histocompatibility complex (MHC) gene DRB1. Similar MHC genes are related to disease resistance in other species. All six of the surviving pups genotyped for the MHC gene were heterozygous while five of the pups that died were heterozygous and one was homozygous. Resistance to pathogens is an important aspect of the management and long-term survival of endangered taxa, such as the Mexican wolf.

Animals↗
PubMed2026

A cross-sectional study of oxidative stress pathway genotypes and their interactions with environmental pollutant levels identifies associations with gene expression and lung function.

BACKGROUND: Asthma is a heterogeneous disease influenced by genetic and environmental factors. Fine particulate matter (PM2.5) exacerbates asthma, likely through oxidative stress pathways, but whether genetic variation modifies this effect remains unclear. METHODS: We analysed data on 948 adults with asthma from the Severe Asthma Research Program (SARP), linking ZIP-code-level PM2.5 exposure with whole-genome sequencing data. We tested 4337 single nucleotide polymorphisms (SNPs) in 120 oxidative stress pathway genes for gene-environment (GxE) interactions with PM2.5 on lung function (forced expiratory volume in 1 s [FEV1] % predicted) using weighted linear regression. Gene expression data from bronchial epithelial cells (n = 170) were used to assess cis-expression quantitative trait loci (eQTLs). FINDINGS: Higher PM2.5 exposure was associated with lower FEV1% predicted (&#x3b2; per &#x3bc;g/m3 = -0.7, p = 0.01). We identified 20 SNPs across seven genes (OXSR1, PXDN, TPO, LRRK2, APP, MSRA, MSRB2) with significant GxE interactions after multiple-testing correction. Five SNPs were also eQTLs, linking PM2.5-modified gene expression to lung function. Minor alleles in OXSR1 and PXDN were associated with reduced gene expression and worsened FEV1% under high PM2.5 exposure. Conversely, TPO variants were associated with higher baseline expression and lower lung function, but under increasing PM2.5 exposure, minor allele carriers showed suppressed TPO expression and improved FEV1%. INTERPRETATION: This study identified 20 SNPs in oxidative stress pathway genes that modify the effect of PM2.5 on lung function in asthma. These findings highlight the importance of integrating environmental context in genetic studies and suggest potential therapeutic targets for pollution-sensitive asthma phenotypes. FUNDING: Supported by NIH grants.

Cross-Sectional Studies↗
PubMed1974

The effects of r- and K-selection on components of variance for two quantitative traits.

The genetic and environmental components of variance for two quantitative characters were measured in the descendants of Drosophila melanogaster populations which had been grown for several generations at densities of 100, 200, 300, and 400 eggs per vial. Populations subject to intermediate densities had a greater proportion of phenotypic variance available for selection than populations from either extreme. Selection on either character would be least effective under pure r-selection, a frequent attribute of selection programs.

Alleles↗
PubMed1982

Factors affecting stability of contemporary comparison evaluations of sires for milk yield.

Evaluations of sires for milk yield by contemporary comparison were used to determine factors associated with changes of evaluation over time. Changes in paired evaluations for 160 Holstein sires were final evaluations (Repeatability exceeding 90%) minus initial evaluations (Repeatability less than 70%). Multiple regression procedures were used to relate characteristics of initial sampling programs to changes in evaluations. Characteristics of initial evaluations associated with more stable evaluations included greater Repeatability for sires evaluated and for sires of contemporaries, higher producing, smaller sized herds with lower genetic merit of contemporaries, and less variation across herd-year-seasons in number of contemporary sires and producing ability of mates. Initial evaluations tending to increase over time were those from large herds of below average genetic merit (for contemporary sires) with greater than average variation in Repeatability of contemporary sires and less than average variance in number of contemporary sires and producing abilities of mates. Results suggested that most changes in evaluations of sires are from Mendelian sampling but that modest increases in stability of evaluations may be achieved through altered design of initial progeny testing programs.

Animals↗
PubMed2003

Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica.

We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.

Bayes Theorem↗
PubMed2002

The genetic diversity of Apulian apricot genotypes (Prunus armeniaca L.) assessed using AFLP markers.

Apricot is an important crop in Italy and, especially in Southern regions, in the last five years numerous plantings using new cultivars and appropriate cultural management have been established. The cultivars available were created in different environments (USA, France, New Zealand, etc), they then often show low adaptability to Italian conditions. However, in the South of Italy, it is still possible to safeguard and to exploit a considerable amount of the apricot genetic variation available in ecotypes often characterised both by useful bio-agronomic traits and by good environmental adaptation. These genetic materials could be used in breeding programs aimed at broadening the harvest period and obtaining high fruit quality and resistance to the main biotic and abiotic stresses.

Crops, Agricultural↗
PubMed2004

Genetic parameters for stillbirth in Danish Holstein cows using a Bayesian threshold model.

The objective of this study was to make an inference about the direct and maternal genetic variation of stillbirth for first-calving Holstein cows and to estimate the effect of breed and heterosis for original Danish black and white and Holstein-Friesian. A Bayesian threshold model, which included correlated genetic effects of sires and maternal grandsires was used. Marginal posterior distributions of effects were obtained using Gibbs sampling. Point estimates were compared with results from a linear model using REML. Data with and without twins were analyzed and models with and without effects of breed and heterosis were fitted, but estimates of genetic parameters were almost identical. In all the analyses with threshold models, the marginal posterior mean (and standard deviation) was 0.10 (0.014) for the direct heritability, 0.13 (0.015) for the maternal heritability, and 0.05 (0.10) for the genetic correlation between direct and maternal effects. The stillbirth rate tended to increase with a higher proportion of Holstein-Friesian in the calf and in the dam, but no effects of breed and heterosis were significant. Joint sampling of all location parameters was found superior to univariate sampling in terms of much better mixing properties of the fixed effects. Based on the results showing genetic variation for stillbirth at first calving, both the direct and the maternal effect could be included in the breeding program.

Animals↗
PubMed1975

Ethnic variation in genetic disease: possible roles of hitchhiking and epistasis.

The high incidence of some genetic diseases in certain ethnic groups is important in planning of medical genetic programs. Simple interaction models predict that at least some lethal recessive alleles will have "hitchhiked" to increased frequencies because of linkage to genes whose alleles have been favored by selection for other reasons in certain populations. In the absence of linkage or epistasis with a gene favored by selection, heterozygote advantage for a recessive lethal may produce the same phenomenon. In the hitchhiking model (linkage), the increase in the gene frequency is temporary, but the length of time that the increased gene frequency is at least double the base frequency may be quite long. Changes in gene frequency for the unlinked epistatic model result in a new equilibrium with a possibly higher gene frequency. The most likely chromosomal regions in which hitchhiked lethal recessives would be found are in the vicinity of genes whose allelic frequencies vary substantially among human racial groups (e.g., Gm, Rh, Duffy, lactose tolerance, or HL-A). There will be a hitchhiking effect if recombination distance is less than the selective advantage. The closer the linkage of two loci, the easier hitchhiking effects will be to detect. Hitchhiking is suggested by nonrandom association of the recessive disease and one of the selected markers, as in the case of Gm and cystic fibrosis. However, there is so far insufficient evidence of linkage between them. More pedigree information is necessary than is now available.

Alleles↗
PubMed1995

Genetic variation in body temperature and its response to short-term acute heat stress in broilers.

Genetic variation in body temperature of broilers and its response to short-term acute (43.5 C for 45 min) heat stress was studied. Body temperatures before (T0) and after (T45) heat exposure were recorded and the changes in body temperature (T delta) were calculated for 5-wk-old chicks from 32 broiler sire families. The T0 data were utilized to rank the families as to their relative body temperature and used to conduct a one-generation divergent family selection program for high basal body temperature (H-BT) and low basal body temperature (L-BT). A control (C) line was established by random selection from the nonselected birds. There was little genetic variation in the base broiler population for body temperature, and one generation of selection for divergence in T0 did not result in differences. There were also no differences among lines in T45. Low realized heritability estimates of .09 and .17 were obtained for T0 in the L-BT and H-BT lines. Phenotypic correlations between body temperature and body weight were very low for all groups. Highly significant negative correlations were observed between T0 and T delta after heat exposure. The T0 fluctuated during the course of each day and between days. The adjustment of the data to eliminate this variation did not result in increased heritability estimates.

Animals↗