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Results for “Quantitative Trait, Heritable”

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PubMed2007

Heritability and shared environment estimates for myopia and associated ocular biometric traits: the Genes in Myopia (GEM) family study.

To examine the familial correlations, heritability (h(2)) and common environmental components (c(2)) of myopia and ocular biometric traits (all treated as continuous outcomes) in families collected through the Genes in Myopia (GEM) family study in Australia. A total of 132 pedigrees (723 participants) were recruited for this study. All individuals completed a risk factor questionnaire and underwent a detailed eye examination including spherical equivalent (SphE) and ocular biometric measurements of axial length (AL), anterior chamber depth (ACD) and corneal curvature (CC). Familial correlations were calculated and h(2) and c(2) were estimated using a variance component model that assumes a multivariate t distribution within each pedigree. Two definitions of common environments (c(2)) were considered: nuclear family (current) shared environment (Model 1) and sib-ship (childhood) shared environment (Model 2). Population ascertainment adjustment was performed using the Blue Mountains eye study dataset. The trends observed for familial correlations suggested that SphE is influenced by both environmental and genetic factors whereas AL, ACD and CC are predominantly genetically determined. This was largely confirmed by variance components modelling. Heritability estimates (adjusted for age, sex and years of education) from the best fitting ACE model (Model 2, childhood shared environment) were 0.50 +/- 0.05 for SphE, 0.73 +/- 0.04 for AL, 0.78 +/- 0.04 for ACD and 0.16 +/- 0.06 for CC. Childhood environmental effects were significant with c(2) estimated to be 0.33 +/- 0.04 for SphE, 0.06 +/- 0.03 for AL, 0.22 +/- 0.04 for ACD and 0.10 +/- 0.05 for CC. Age was associated with SphE, total years of education was associated with AL and sex was associated with all traits studied. We used a novel and conservative approach to account for and estimate common environmental effects by specifying either nuclear family or sib-ship environment when estimating heritability estimates and showed that all traits examined (SphE, AL, ACD and CC) are heritable, thus reflecting a genetic component. These traits therefore all represent candidates for quantitative trait linkage analyses.

Adult↗

PubMedDate not supplied

Divergent selection on 63-day body weight in the rabbit: response on growth, carcass and muscle traits.

The effects of selection for growth rate on weights and qualitative carcass and muscle traits were assessed by comparing two lines selected for live body weight at 63 days of age and a cryopreserved control population raised contemporaneously with generation 5 selected rabbits. The animals were divergently selected for five generations for either a high (H line) or a low (L line) body weight, based on their BLUP breeding value. Heritability (h2) was 0.22 for 63-d body weight (N = 4754). Growth performance and quantitative carcass traits in the C group were intermediate between the H and L lines (N = 390). Perirenal fat proportion (h2 = 0.64) and dressing out percentage (h2 = 0.55) ranked in the order L < H = C (from high to low). The weight and cross-sectional area of the Semitendinosus muscle, and the mean diameter of the constitutive myofibres were reduced in the L line only (N = 140). In the Longissimus muscle (N = 180), the ultimate pH (h2 = 0.16) and the maximum shear force reached in the Warner-Braztler test (h2 = 0.57) were slightly modified by selection.

Age Factors↗

PubMed1998

Developmental loss of effect of a Chromosome 15 QTL on alcohol acceptance.

Human alcohol abuse and alcoholism have clear developmental features, suggesting the possibility of changes over time in heritability and in quantitative genetic architecture, and raising prospects of identifying individual genes or quantitative trait loci (QTLs) that display different influence on alcohol-related phenotypes at different ages. The identification of specific loci showing such age-related changes will open up opportunities of focused association studies and of genotype manipulation by various mating procedures. Most animal model research in alcohol assesses the phenotypes of the animals at an early age; developmental studies are rare. Here we report on a QTL on Chromosome (Chr) 15 of the mouse that has been shown in several populations, including BXD recombinant inbred strains, an F2, and genotypically selected lines, to affect a measure of alcohol consumption. In the present study, we measured alcohol acceptance in the genotypically selected animals and in an F4 sample at about 100 days and again at about 300 days of age. In both groups, and in both sexes, significant differences were observed at 100 days between animals that were homozygous for the "increasing" haplotype defining the QTL region and those homozygous for the "decreasing" haplotype. At 300 days of age, the effect is absent in females and has diminished or disappeared in males. The results provide a further confirmation of the Chr 15 QTL in young mice, offer a new perspective on the development of alcohol-related phenotypes, and have strong implications for research design.

Alcohol Drinking↗

PubMed2006

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings.

The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036). The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within-family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will allow the estimation of genetic variation for disease susceptibility and quantitative traits that is free from confounding with non-genetic factors and will allow partitioning of genetic variation into additive and non-additive components.

Body Height↗

PubMed2006

Locus-specific heritability estimation via the bootstrap in linkage scans for quantitative trait loci.

BACKGROUND/AIMS: In genome-wide linkage analysis of quantitative trait loci (QTL), locus-specific heritability estimates are biased when the original data are used to both localize linkage and estimate effects, due to maximization of the LOD score over the genome. Positive bias is increased by adoption of stringent significance levels to control genome-wide type I error. We propose multi-locus bootstrap resampling estimators for bias reduction in the situation in which linkage peaks at more than one QTL are of interest. METHODS: Bootstrap estimates were based on repeated sample splitting in the original dataset. We conducted simulation studies in nuclear families with 0 to 5 QTLs and applied the methods in a genome-wide analysis of a blood pressure phenotype in extended pedigrees from the Framingham Heart Study (FHS). RESULTS: Compared to naïve estimates in the original simulation samples, bootstrap estimates had reduced bias and smaller mean squared error. In the FHS pedigrees, the bootstrap yielded heritability estimates as much as 70% smaller than in the original sample. CONCLUSIONS: Because effect estimates obtained in an initial study are typically inflated relative to those expected in an independent replication study, successful replication will be more likely when sample size requirements are based on bias-reduced estimates.

Cardiovascular Diseases↗

PubMed2005

Long-term repeatability makes basal metabolic rate a likely heritable trait in the zebra finch Taeniopygia guttata.

Basal metabolic rate (BMR) is a physiological trait believed to show adaptational changes. Few studies have tested whether BMR shows stable between-individual variations. Repeatability indicates that the trait might be heritable and therefore a possible target for natural selection. We tested whether BMR was repeatable over a considerable time of the lifespan of a small passerine bird: the zebra finch Taeniopygia guttata. BMR was measured six times over a 2.5 year period in captive zebra finches. BMR residuals showed significant repeatabilities over a short (1.5 months) and a long (2.5 years) period for each sex as well as for both sexes pooled. In contrast to earlier studies on metabolism, our calculated repeatability (R) did not change significantly from the short to the long period in either males (R from 0.501 to 0.465), females (R from 0.413 to 0.522) or the pooled data (R from 0.571 to 0.567). Our results show that there are consistent between-individual variations in BMR on which natural selection can work, provided that this trait is heritable.

Adaptation, Physiological↗

PubMed1999

Asymptotic power of likelihood-ratio tests for detecting quantitative trait loci using the COGA data.

We investigated the asymptotic power of the likelihood-ratio test for detecting linkage to a quantitative trait locus (QTL) using the data set from the Collaborative Study on the Genetics of Alcoholism (COGA). Assuming a total trait heritability of 50% as determined for the COGA Cz P300 phenotype, we determined the minimum QTL heritability required at each point in the genome to achieve 80% power to detect linkage with a lod of 3.0. We find that there are regions of the genome where it is not possible to detect a QTL of any effect with 80% power, and that the overall minimum detectable QTL heritability for the COGA data is 0.35-0.40.

Alcoholism↗

PubMedDate not supplied

A QTL for the degree of spotting in cattle shows synteny with the KIT locus on chromosome 6.

The proportion of unpigmented coat on the trunk was determined from photographs of 38 German Simmental and 627 German Holstein bulls distributed over three generations. All 665 animals were members of 18 Holstein and 3 Simmental half-sib families. A Bayesian estimation of heritability yielded a posterior mean of 0.88 and a standard error of 0.08. A quantitative trait loci (QTL) scan over all chromosomes covered by 229 microsatellite marker loci (2926 cM) was performed by fitting a multiple marker regression model to 625 observations from the youngest generation in 18 families. On chromosome 6 a QTL for the proportion of white coat with large effects (experiment-wise error probability < .0001) was found and a less important one on chromosome 3 (chromosome-wise error probability < .009). Chromosome 6 is known to harbor the KIT locus (receptor tyrosinase kinase), which is associated with various depigmentation phenotypes in mice, humans, and pigs. Similarity of phenotypic KIT effects in other species and synteny with the reported QTL suggest that KIT is a serious candidate gene for the degree of spotting in cattle. The results are also discussed with respect to resistance to solar radiation, heat stress, and photosensitization.

Animals↗

PubMed2001

Complex trait analysis of the hippocampus: mapping and biometric analysis of two novel gene loci with specific effects on hippocampal structure in mice.

Notable differences in hippocampal structure are associated with intriguing differences in development and behavioral capabilities. We explored genetic and environmental factors that modulate hippocampal size, structure, and cell number using sets of C57BL/6J (B6) and DBA/2J (D2) mice; their F1 and F2 intercrosses (n = 180); and 35 lines of BXD recombinant inbred (RI) strains. Hippocampal weights of the parental strains differ by 20%. Estimates of granule cell number also differ by approximately 20%. Hippocampal weights of RI strains range from 21 to 31 mg, and those of individual F2 mice range from 23 to 36 mg (bilateral weights). Volume and granule cell number are well correlated (r = 0.7-0.8). Significant variation is associated with differences in age and sex. The hippocampus increases in weight by 0.24 mg per month, and those of males are 0.55 mg heavier (bilateral) than those of females. Heritability of variation is approximately 50%, and half of this genetic variation is generated by two quantitative trait loci that map to chromosome 1 (Hipp1a: genome-wide p < 0.005, between 65 and 100 cM) and to chromosome 5 (Hipp5a, p < 0.05, between 15 and 40 cM). These are among the first gene loci known to produce normal variation in forebrain structure. Hipp1a and Hipp5a individually modulate hippocampal weight by 1.0-2.0 mg, an effect size greater than that generated by age or sex. The Hipp gene loci modulate neuron number in the dentate gyrus, collectively shifting the population up or down by as much as 200,000 cells. Candidate genes for the Hipp loci include Rxrg and Fgfr3.

Aging↗

PubMed2005

An exact form of the breeder's equation for the evolution of a quantitative trait under natural selection.

Starting with the Price equation, I show that the total evolutionary change in mean phenotype that occurs in the presence of fitness variation can be partitioned exactly into five components representing logically distinct processes. One component is the linear response to selection, as represented by the breeder's equation of quantitative genetics, but with heritability defined as the linear regression coefficient of mean offspring phenotype on parent phenotype. The other components are identified as constitutive transmission bias, two types of induced transmission bias, and a spurious response to selection caused by a covariance between parental fitness and offspring phenotype that cannot be predicted from parental phenotypes. The partitioning can be accomplished in two ways, one with heritability measured before (in the absence of) selection, and the other with heritability measured after (in the presence of) selection. Measuring heritability after selection, though unconventional, yields a representation for the linear response to selection that is most consistent with Darwinian evolution by natural selection because the response to selection is determined by the reproductive features of the selected group, not of the parent population as a whole. The analysis of an explicitly Mendelian model shows that the relative contributions of the five terms to the total evolutionary change depends on the level of organization (gene, individual, or mated pair) at which the parent population is divided into phenotypes, with each frame of reference providing unique insight. It is shown that all five components of phenotypic evolution will generally have nonzero values as a result of various combinations of the normal features of Mendelian populations, including biparental sex, allelic dominance, inbreeding, epistasis, linkage disequilibrium, and environmental covariances between traits. Additive genetic variance can be a poor predictor of the adaptive response to selection in these models. The narrow-sense heritability sigma2A/sigma2P should be viewed as an approximation to the offspring-parent linear regression rather than the other way around.

Biological Evolution↗

PubMed2000

Estimation of variance components of quantitative traits in inbred populations.

Use of variance-component estimation for mapping of quantitative-trait loci in humans is a subject of great current interest. When only trait values, not genotypic information, are considered, variance-component estimation can also be used to estimate heritability of a quantitative trait. Inbred pedigrees present special challenges for variance-component estimation. First, there are more variance components to be estimated in the inbred case, even for a relatively simple model including additive, dominance, and environmental effects. Second, more identity coefficients need to be calculated from an inbred pedigree in order to perform the estimation, and these are computationally more difficult to obtain in the inbred than in the outbred case. As a result, inbreeding effects have generally been ignored in practice. We describe here the calculation of identity coefficients and estimation of variance components of quantitative traits in large inbred pedigrees, using the example of HDL in the Hutterites. We use a multivariate normal model for the genetic effects, extending the central-limit theorem of Lange to allow for both inbreeding and dominance under the assumptions of our variance-component model. We use simulated examples to give an indication of under what conditions one has the power to detect the additional variance components and to examine their impact on variance-component estimation. We discuss the implications for mapping and heritability estimation by use of variance components in inbred populations.

Algorithms↗

PubMed2005

Quantitative analysis of production traits in saltwater crocodiles (Crocodylus porosus): I. reproduction traits.

Repeatability and phenotypic correlations were estimated for saltwater crocodile reproductive traits. No pedigree information was available to estimate heritability or genetic correlations, because the majority of breeder animals on farms were wild-caught. Moreover, as the age of the female breeders could not be accounted for, egg-size measurements were used as proxies. The reproductive traits investigated were clutch size (total number of eggs laid), number of viable eggs, number of eggs that produced a live, healthy hatchling, hatchability, average snout-vent length of the hatchlings and time of nesting. A second data set was also created comprising binary data of whether or not the female nested. Repeatability estimates ranged from 0.24 to 0.68 for the measurable traits, with phenotypic correlations ranging from -0.15 to 0.86. Repeatability for whether a female nested or not was 0.58 on the underlying scale. Correlations could not be estimated between the measurement and binary traits because of confounding. These estimates are the first published for crocodilian reproduction traits.

Age Factors↗

PubMed2003

Heritability of energetics in a wild mammal, the leaf-eared mouse (Phyllotis darwini).

As a first examination of the additive genetic variance of thermoregulatory traits in a natural population of endotherms, we studied the quantitative genetics of key physiological ecology traits in the leaf-eared mouse, Phyllotis darwini. We measured basal metabolic rate (BMR), nonshivering thermogenesis (NST), maximum metabolic rate for thermoregulation (MMR), thermal conductance (CT), body temperature (Tb), and factorial aerobic scope (FAS) in individuals acclimated to cold and warm conditions. For comparability with previous studies, we included the following morphological traits: foot length (FL), total length (TL), body mass (mb, at birth, sexual maturity, 6 months, and 8 months). Variance components were obtained from two different procedures: the expected variance component in an ANOVA Type III sum of squares and an animal model approach using restricted maximum likelihood. Results suggest the presence of additive genetic variance in FL (h2 = 0.47, P = 0.045), CT of cold-acclimated animals (h2 = 0.66, P = 0.041), and night body temperature, measured in cold-acclimated animals (h2 = 0.68, P = 0.080). Heritabilities of mb were near zero at all ages, but maternal effects and common environment effects were high and significant. We found no evidence of additive genetic variance in BMR, NST, MMR, or FAS (i.e., estimates were not significantly different from zero for all tests). Our results are in general agreement with previous studies of mammals that reported low heritability for: (1) BMR and MMR; (2) daytime body temperature; and (3) body mass for wild, but not laboratory or domestic, populations.

Acclimatization↗

PubMedDate not supplied

A QTL study of cattle behavioral traits in embryo transfer families.

Two behavioral traits, temperament and habituation, were measured in 130 calves from 17 full-sib families which comprise the Canadian Beef Cattle Reference Herd. Using variance components, heritability was calculated as 0.36 for temperament and 0.46 for habituation. Genotyping of 162 microsatellites at approximately 20 cM intervals allowed the detection of six quantitative trait loci (QTL) for behavior traits on cattle chromosomes 1, 5, 9, 11, 14, 15.

Animals↗

PubMed2005

Large, consistent estimates of the heritability of cognitive ability in two entire populations of 11-year-old twins from Scottish mental surveys of 1932 and 1947.

Twin studies provide estimates of genetic and environmental contributions to cognitive ability differences, but could be based on biased samples. Here we report whole-population estimates using twins from unique mental surveys in Scotland. The Scottish Mental Surveys of 1st June 1932 (SMS1932) and 4th June 1947 (SMS1947), respectively, administered the same validated verbal reasoning test to almost everyone born in 1921 or 1936 and attending school in Scotland. There were 572 twin pairs from the SMS1932, and 517 pairs from the SMS1947. Information on zygosity was unavailable. A novel application of a mixture distribution was used to estimate genetic and environmental components of verbal reasoning variation by maximum likelihood. We found consistent heritability (approximately 0.70) and shared environment (approximately 0.21) estimates. The estimates did not change substantially when additional quantitative traits (height and weight) were added in a multivariate analysis. More generally for studies in genetics, the methodological innovation developed here implies that large (national) data collections can provide sufficient information on twin pairs to estimate genetic parameters, even without zygosity.

Analysis of Variance↗

PubMed2006

Genetics of food intake and eating behavior phenotypes in humans.

This review summarizes the research advances of the past decade regarding the role of human genetic differences in energy and nutrient intake as well as in eating behavior phenotypes and selected eating disorders. The evidence for familial aggregation and heritability based on twin and nuclear family study designs is summarized. Genome-wide linkage scans and quantitative trait loci identified to date are discussed. DNA sequence variants in candidate genes are reviewed. Single genes associated with classical eating disorders are also incorporated. Epigenetic events will need to be incorporated in future studies designed to investigate the effects of DNA variants on dietary phenotypes. Understanding the relative contribution of global genetic variation and of DNA sequence variants in specific genes is important in the effort to influence dietary habits in a healthier direction.

Chromosome Mapping↗

PubMed2002

Quantitative trait loci for inflorescence development in Arabidopsis thaliana.

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.

Arabidopsis↗

PubMed2001

[Analysis of QTL x environment interaction for rice panicle characteristics].

The development of molecular genetic linkage map has accelerated the identification and mapping of genomics regions controlling quantitative trait loci. A recombinant inbred line population derived from Zhenshan 97/Minghui 63 was grown in two years. Mixed linear model approach was used to jointly identify QTLs and QTL x environment interactions for five panicle characteristics. Ten, three, six, eight and seven QTLs were detected for spiketets per panicle, grains per panicle, seed setting, panicle length and panicle setting density, respectively. They collectively explained 29.13%, 19.2%, 29.46%, 26.39% and 35.76% of phenotypic variations for these traits, respectively. For the five traits, QTLs with increasing effects and decreasing effects could be simultaneously identified in high value parent and low value parent. QTLs for correlative traits clustering located in the similar regions. One QTL for panicle length, two QTLs for spikelets per panicle and three QTLs for seed setting performed significant interactions with environment. The contributions from interactions were slightly larger than that from the QTLs involved in the interactions. No QTL x environment interaction was detected for traits with high heritabilities such as grains per panicle and panicle setting density.

Chromosome Mapping↗