Sex dependent imprinting effects on complex traits in mice

Background  

Genomic imprinting is an epigenetic source of variation in quantitative traits that results from monoallelic gene expression, where commonly either only the paternally- or the maternally-derived allele is expressed. Imprinting has been shown to affect a diversity of complex traits in a variety of species. For several such quantitative traits sex-dependent genetic effects have been discovered, but whether imprinting effects also show such sex-dependence has yet to be explored. Moreover, theoretical work on the evolution of sex-dependent genomic imprinting effects makes specific predictions about the phenotypic patterns of such effects, which, however, have not been assessed empirically to date.     

Genetic and environmental effects on secondary sex traits in guppies (Poecilia reticulata)

Male guppies (Poecilia reticulata) exhibit extreme phenotypic and genetic variability for several traits that are important to male fitness, and several lines of evidence suggest that resource level affects phenotypic expression of these traits in nature. We tested the hypothesis that genetic variation for male secondary sex traits could be maintained by genotype-specific effects of variable resource levels (genotype-environment interaction). To do this, we measured genetic variation and covariation under two environmental conditions--relatively low and relatively high food availability. We found high levels of genetic variation for most traits, but we only found a significant G x E interaction across food levels for one trait (body size) for one population. The across-environment correlations for size were large and positive, indicating that the reaction norms for size did not cross. We also found that male colour pattern elements had nearly an order of magnitude more genetic variation than did male size. Heritability estimates indicated that Y-linked genes are responsible for some of the genetic variation in male size and colour traits. We discuss implications of these results for theories of the maintenance of genetic variation in male secondary sexual traits in guppies.     

Genetic prediction of complex traits: integrating infinitesimal and marked genetic effects

Genetic prediction for complex traits is usually based on models including individual (infinitesimal) or marker effects. Here, we concentrate on models including both the individual and the marker effects. In particular, we develop a “Mendelian segregation” model combining infinitesimal effects for base individuals and realized Mendelian sampling in descendants described by the available DNA data. The model is illustrated with an example and the analyses of a public simulated data file. Further, the potential contribution of such models is assessed by simulation. Accuracy, measured as the correlation between true (simulated) and predicted genetic values, was similar for all models compared under different genetic backgrounds. As expected, the segregation model is worthwhile when markers capture a low fraction of total genetic variance.     

Genetic and environmental influence on the asymmetry of dermatoglyphic traits

Fluctuating asymmetry (FA) is defined as random deviations from bilateral symmetry of the body. Thus, its magnitude is often used to evaluate developmental homeostasis. In this study we evaluate the following hypotheses: 1) FA of dermatoglyphic traits has a significant genetic component; 2) prenatal maternal environment (PME) has a significant effect on the FA of dermatoglyphic traits in developmentally healthy individuals; and 3) genetic or environmental factors affect FA on organismal or systemic levels. Therefore, their effect is better seen in composite scores of FA rather than in FA indices for single traits. We analyzed 15 dermatoglyphic traits from 140 pairs of monozygous twins, 120 pairs of dizygous twins, and 106 pairs of mothers and daughters. All individuals were developmentally healthy. The influence of genetic and environmental factors on FA was evaluated by analysis of variance and regression analysis. For a majority of the traits in our study, FA showed significant but weak heritabilities, with values falling within the 0.20-0.35 range. None of the traits taken separately demonstrated the effect of PME on FA to be significantly greater than zero. The composite score of FA tended to have greater heritability values than individual traits. One of them, obtained in principal components analysis, showed a significant PME effect, supporting the hypothesis that FA is a systemic property.     

Change in maternal environment induced by cross-fostering alters genetic and epigenetic effects on complex traits in mice

The interaction between maternally provided environment and offspring genotype is a major determinant of offspring development and fitness in many organisms. Recent research has demonstrated that not only genetic effects, but also epigenetic effects may be subject to modifications by the maternal environment. Genomic imprinting resulting in parent-of-origin-dependent gene expression is among the best studied of epigenetic effects. However, very little is known about the degree to which genomic imprinting effects can be modulated by the maternally provided environment, which has important implications for phenotypic plasticity. In this study, we investigated this unresolved question using a cross-fostering design in which mouse pups were nursed by either their own or an unrelated mother. We scanned the entire genome to search for quantitative trait loci whose effects depend on cross-fostering and detected 10 of such loci. Of the 10 loci, 4 showed imprinting by cross-foster interactions. In most cases, the interaction effect was due to the presence of an effect in either cross-fostered or non-cross-fostered animals. Our results demonstrate that genomic imprinting effects may often be modified by the maternal environment and that such interactions can impact key fitness-related traits suggesting a greater plasticity of genomic imprinting than previously assumed.     

Genomic imprinting and genetic effects on muscle traits in mice

ABSTRACT: BACKGROUND: Genomic imprinting refers to parent-of-origin dependent gene expression caused by differential DNA methylation of the paternally and maternally derived alleles. Imprinting is increasingly recognized as an important source of variation in complex traits, however, its role in explaining variation in muscle and physiological traits, especially those of commercial value, is largely unknown compared with genetic effects. RESULTS: We investigated both genetic and genomic imprinting effects on key muscle traits in mice from the Berlin Muscle Mouse population, a key model system to study muscle traits. Using a genome scan, we first identified loci with either imprinting or genetic effects on phenotypic variation. Next, we established the proportion of phenotypic variation explained by additive, dominance and imprinted QTL and characterized the patterns of effects. In total, we identified nine QTL, two of which show large imprinting effects on glycogen content and potential, and body weight. Surprisingly, all imprinting patterns were of the bipolar type, in which the two heterozygotes are different from each other but the homozygotes are not. Most QTL had pleiotropic effects and explained up to 40% of phenotypic variance, with individual imprinted loci accounting for 4-5% of variation alone. CONCLUSION: Surprisingly, variation in glycogen content and potential was only modulated by imprinting effects. Further, in contrast to general assumptions, our results show that genomic imprinting can impact physiological traits measured at adult stages and that the expression does not have to follow the patterns of paternal or maternal expression commonly ascribed to imprinting effects.     

Genetic and environmental pathways to complex diseases

Background  

Pathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches.     

Genetic and epigenetic effects of environmental arsenicals

Environmental arsenic compounds and their methylated metabolites do not form adducts with DNA, but do cause oxidative DNA damage. Chromosome aberrations are seen at toxic concentrations. Genetic effects that occur at non-toxic concentrations include aneuploidy, comutagenesis (resulting from indirect effects on DNA repair), and delayed mutagenesis (probably secondary to aneuploidy and/or epigenetic effects). Effects of trivalent arsenicals on poly(ADP ribose) polymerase and P53 activation may mediate effects on DNA repair and aneuploidy. A growing literature points to the epigenetic effects of arsenic compounds in cells and in vivo. A review of the current literature on DNA methylation, histone modifications and microRNA effects is presented.     

Genetic variants affecting meat and milk production traits appear to have effects on reproduction traits in cattle

Polymorphisms located in the genes ABCG2, DGAT1, LEP, PRLR, RORC, CAPN1 and CAST previously have been associated with milk or meat production traits. In this study, these polymorphisms were examined for significant effects on reproductive traits [age at puberty (AGECL), post-partum anoestrus interval (PPAI) and the ability ovulate prior to weaning (PW)] and on a panel of correlated traits such as weight, growth and serum concentration of insulin-like growth factor I. The effects of the polymorphisms were examined in two samples of tropically adapted beef cattle: Brahman (N = 932) and Tropical Composites (N = 1097). A polymorphism in the gene DGAT1 was associated with age at puberty in the combined sample (P = 0.042), and two polymorphisms in CAPN1 were associated with PPAI (P = 0.033) and with the ability ovulate PW (P = 0.017). The favourable allele for reproductive traits was not always the favourable allele associated with production traits. The effects of these polymorphisms on reproductive traits were small compared to their effects on the traits for which they were originally discovered.     

Genomic imprinting effects on complex traits: A phenotype-based perspective

Parent-of-origin dependent gene expression associated with genomic imprinting is expected to result in the phenotypic signature of a difference between the average phenotypes of the reciprocal heterozygotes.     

Genetic association studies of complex traits: design and analysis issues

Most common diseases and many important quantitative traits are complex genetic traits, with multiple genetic and environmental variables contributing to the observed phenotype. Because of the multi-factorial nature of complex traits, each individual genetic variant generally has only a modest effect, and the interaction of genetic variants with each other or with environmental factors can potentially be quite important in determining the observed phenotype. It remains largely unknown what sort of genetic variants explain inherited variation in complex traits, but recent evidence suggests that common genetic variants will explain at least some of the inherited variation in susceptibility to common disease. Genetic association studies, in which the allele or genotype frequencies at markers are determined in affected individuals and compared with those of controls (either population- or family-based), may be an effective approach to detecting the effects of common variants with modest effects. With the explosion in single nucleotide polymorphism (SNP) discovery and genotyping technologies, large-scale association studies have become feasible, and small-scale association studies have become plentiful. We review the different types of association studies and discuss issues that are important to consider when performing and interpreting association studies of complex genetic traits. Heritable and accurately measured phenotypes, carefully matched large samples, well-chosen genetic markers, and adequate standards in genotyping, analysis, and interpretation are all integral parts of a high-quality association study.     

Genetic and nutritional effects on male traits and reproductive performance in Tribolium flour beetles

In Tribolium flour beetles and other organisms, individuals migrate between heterogeneous environments where they often encounter markedly different nutritional conditions. Under these circumstances, theory suggests that genotype-by-environment interactions (GEI) may be important in facilitating adaptation to new environments and maintaining genetic variation for male traits subject to directional selection. Here, we used a nested half-sib breeding design with Tribolium castaneum to partition the separate and joint effects of male genotype and nutritional environment on phenotypic variation in a comprehensive suite of life-history traits, reproductive performance measures across three sequential sexual selection episodes, and fitness. When male genotypes were tested across three nutritional environments, considerable phenotypic plasticity was found for male mating and insemination success, longevity and traits related to larval development. Our results also revealed significant additive genetic variation for male mating rate, sperm offence ability (P(2)), longevity and total fitness and for several traits reflecting both larval and adult resource use. In addition, we found evidence supporting GEI for sperm defence ability (P(1)), adult longevity and larval development; thus, no single male genotype outperforms others in every nutritional environment. These results provide insight into the potential roles of phenotypic plasticity and GEI in facilitating Tribolium adaptation to new environments in ecological and evolutionary time.     

Large-scale in silico mapping of complex quantitative traits in inbred mice

Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA) scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs) from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity) as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.     

Parental environmental effects on life history traits in Arabidopsis thaliana (Brassicaceae)

Environmentally induced maternal effects on offspring phenotype are well known in plants. When genotypes or maternal lineages are replicated and raised in different environmental conditions, the phenotype of their offspring often depends on the environment in which the parents developed. However, the degree to which such maternal effects are maintained over subsequent generations has not been documented in many taxa. Here we report the results of a study designed to assess the effects of parental environment on vegetative and reproductive traits, using glasshouse-raised maternal lines sampled from natural populations of Arabidopsis thaliana . Replicates of five highly selfed lines from each of four wild populations were cultivated in two abiotic environments in the glasshouse, and the quality and performance of seeds derived from these two environments were examined over two generations. We found that offspring phenotype was strongly influenced by parental environment, but because the parental environments differed with respect to the time of seed harvest, it was not possible to distinguish clearly between parental environmental effects and the possible (but unlikely) effects of seed age on offspring phenotype. We observed a rapid decline in the expression of ancestral environmental effects, and no main environmental effects on progeny phenotype persisted in the second generation. The mechanism of transmission of environmental effects did not appear to be associated with the quantity or quality of reserves in the seeds, suggesting that environmental effects may be transmitted across subsequent generations via some mechanism that generates environment-specific gene expression.     

Genetic traits

Recognizing that all traits are the result of an interaction between genes and environment, I offer a set of criteria for nevertheless making sense of our practice of singling out certain traits as genetic ones, in effect making a distinction between causes and mere conditions. The central criterion is that a trait is genetic if it is genetic differences that make the differences in that trait variable in a given population. A second criterion requires that genetic traits be individuated in a way that matches what some genetic factors cause specifically. Clarifying our causal and classificatory language here can help us to avoid confusions of both theoretical and practical significance.     

Genetic and environmental effects on morphology and fluctuating asymmetry in nestling barn swallows

A barn swallow Hirundo rustica partial cross‐fostering experiment with simultaneous brood size manipulation was conducted in two years with contrasting weather conditions, to estimate heritable variation in tarsus, tail and wing size and fluctuating asymmetry. Environmental stress had contrasting effects depending on trait type. Significant heritabilities for tarsus, tail and wing size were found only in enlarged broods irrespective of year effects, while tarsus asymmetry was significantly heritable in the year with benign weather conditions irrespective of brood size manipulation effects. Tail, wing and composite (multicharacter) asymmetry were never significantly heritable. The environment with the higher heritability generally had higher additive genetic variance and lower environmental variance, irrespective of trait type. Heritability was larger for trait size than for trait asymmetry. Patterns of genetic variation in nestlings do not necessarily translate to the juvenile or adult stage, as indicated by lack of correlation between nestling and fledgling traits.