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PubMed1980

A simulation study of truncation selection for a quantitative trait opposed by natural selection.

A quantitative character controlled at one locus with two alleles was submitted to artificial (mass) selection and to three modes of opposing natural selection (directional selection, overdominance and underdominance) in a large random-mating population. The selection response and the limits of the selective process were studied by deterministic simulation. The lifetime of the process was generally between 20 and 100 generations and did not appear to depend on the mode of natural selection. However, depending on the values of the parameters (initial gene frequency, selection intensity, ratio of the effect of the gene to the environmental standard deviation, fitness values) the following outcomes of selection were observed: fixation of the allele favored by artificial selection, stable nontrivial equilibrium, unstable equilibrium and loss of the allele favored by artificial selection. Finally, the results of the simulation were compared to the results of selection experiments.

Alleles↗
PubMed2003

Segregation analysis comparing liability and quantitative trait models for hypertension using the Genetic Analysis Workshop 13 simulated data.

Discrete (qualitative) data segregation analysis may be performed assuming the liability model, which involves an underlying normally distributed quantitative phenotype. The appropriateness of the liability model for complex traits is unclear. The Genetic Analysis Workshop 13 simulated data provides measures on systolic blood pressure, a highly complex trait, which may be dichotomized into a discrete trait (hypertension). We perform segregation analysis under the liability model of hypertensive status as a qualitative trait and compare this with results using systolic blood pressure as a quantitative trait (without prior knowledge at that stage of the true underlying simulation model) using 1050 pedigrees ascertained from four replicates on the basis of at least one affected member. Both analyses identify models with major genes and polygenic components to explain the family aggregation of systolic blood pressure. Neither of the methods estimates the true parameters well (as the true model is considerably more complicated than those considered for the analysis), but both identified the most complicated model evaluated as the preferred model. Segregation analysis of complex diseases using relatively simple models is unlikely to provide accurate parameter estimates but is able to indicate major gene and/or polygenic components in familial aggregation of complex diseases.

Adult↗
PubMed2003

On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals.

Although genetic association studies using unrelated individuals may be subject to bias caused by population stratification, alternative methods that are robust to population stratification such as family-based association designs may be less powerful. Recently, various statistical methods robust to population stratification were proposed for association studies, using unrelated individuals to identify associations between candidate markers and traits of interest (both qualitative and quantitative). Here, we propose a semiparametric test for association (SPTA). SPTA controls for population stratification through a set of genomic markers by first deriving a genetic background variable for each sampled individual through his/her genotypes at a series of independent markers, and then modeling the relationship between trait values, genotypic scores at the candidate marker, and genetic background variables through a semiparametric model. We assume that the exact form of relationship between the trait value and the genetic background variable is unknown and estimated through smoothing techniques. We evaluate the performance of SPTA through simulations both with discrete subpopulation models and with continuous admixture population models. The simulation results suggest that our procedure has a correct type I error rate in the presence of population stratification and is more powerful than statistical association tests for family-based association designs in all the cases considered. Moreover, SPTA is more powerful than the Quantitative Similarity-Based Association Test (QSAT) developed by us under continuous admixture populations, and the number of independent markers needed by SPTA to control for population stratification is substantially fewer than that required by QSAT.

Analysis of Variance↗
PubMed2004

Disease-associated qualitative and quantitative trait loci in proteoglycan-induced arthritis and collagen-induced arthritis.

Two autoimmune murine models--proteoglycan (aggrecan)-induced arthritis (PGIA) and collagen-induced arthritis (CIA)--were developed in parent strains, F1 and F2 hybrids of major histocompatibility complex (MHC)-matched (H-2) BALB/c x DBA/2 and MHC-unmatched (H-2/H-2) BALB/c x DBA/1 intercrosses. The major goal of this comparative study was to identify disease (model)-specific (PGIA or CIA) and shared clinical and immunologic loci in 2 types of genetic intercrosses. Qualitative (binary/susceptibility) and quantitative (severity and onset) clinical trait loci were separated and analyzed independently or together with various pathophysiologic/immunologic traits, such as antigen-specific T- and B-cell responses and cytokine production. The major quantitative trait locus (QTL) was the MHC on chromosome 17, which was especially dominant in CIA. In addition, chromosomes 3, 5, 10, and X contained shared clinical loci in both models, and a total of 8 QTLs (clinical traits together with immunologic traits) were colocalized in PGIA and CIA.

Animals↗
PubMed1997

Quantitative trait loci controlling halothane sensitivity in Caenorhabditis elegans.

Genetic analysis is an essential tool for defining the molecular mechanisms whereby volatile anesthetics (VA) disrupt nervous system function. However, the degree of natural variation of the genetic determinants of VA sensitivity has not been determined nor have mutagenesis approaches been very successful at isolating significantly resistant mutant strains. Thus, a quantitative genetic approach was taken toward these goals. Recombinant-inbred strains derived from two evolutionarily distinct lineages of the nematode Caenorhabditis elegans were tested for sensitivity to clinically relevant concentrations (0.3-0.5 mM) of the VA halothane. The halothane sensitivities of coordinated movement and male mating behavior were highly variant among the recombinant-inbred strains with a range of EC50 values of 13- and 4-fold, respectively. Both traits were highly heritable (H2 = 0.82, 0.87, respectively). Several strains were found to be significantly resistant to halothane when compared with the wild-type strain N2. A major locus or loci mapping to the middle of chromosome V accounted for more than 40% of the phenotypic variance for both traits. Five weaker loci, four of which interact, explained most of the remaining variance. None of the halothane-sensitivity quantitative trait loci significantly affected behavior in the absence of halothane or halothane's potency for C. elegans immobilization, which requires 5-fold higher drug concentrations. Thus, the quantitative trait loci are unlikely to result from differences in halothane-independent (native) behavior or differences in halothane metabolism or permeability. Rather, these loci may code for targets and/or downstream effectors of halothane in the C. elegans nervous system or for modifiers of such gene products.

Anesthetics, Inhalation↗
PubMed2005

A male-specific quantitative trait locus on 1p21 controlling human stature.

BACKGROUND: Many genome-wide scans aimed at complex traits have been statistically underpowered due to small sample size. Combining data from several genome-wide screens with comparable quantitative phenotype data should improve statistical power for the localisation of genomic regions contributing to these traits. OBJECTIVE: To perform a genome-wide screen for loci affecting adult stature by combined analysis of four previously performed genome-wide scans. METHODS: We developed a web based computer tool, Cartographer, for combining genetic marker maps which positions genetic markers accurately using the July 2003 release of the human genome sequence and the deCODE genetic map. Using Cartographer, we combined the primary genotype data from four genome-wide scans and performed variance components (VC) linkage analyses for human stature on the pooled dataset of 1417 individuals from 277 families and performed VC analyses for males and females separately. RESULTS: We found significant linkage to stature on 1p21 (multipoint LOD score 4.25) and suggestive linkages on 9p24 and 18q21 (multipoint LOD scores 2.57 and 2.39, respectively) in males-only analyses. We also found suggestive linkage to 4q35 and 22q13 (multipoint LOD scores 2.18 and 2.85, respectively) when we analysed both females and males and to 13q12 (multipoint LOD score 2.66) in females-only analyses. CONCLUSIONS: We strengthened the evidence for linkage to previously reported quantitative trait loci (QTL) for stature and also found significant evidence of a novel male-specific QTL on 1p21. Further investigation of several interesting candidate genes in this region will help towards characterisation of this first sex-specific locus affecting human stature.

Adult↗
PubMed1986

[Testing of a monogenic hypothesis in pedigrees of an arbitrary structure selected for a proband. III. Quantitative traits].

Methods of the Mendelian analysis of quantitative characters by pedigrees selected for proband are discussed. The method is illustrated on the example of the familial hypercholesterinemia in man. The estimations of parameters of monogenic hypothesis of inheritance, obtained by the maximum likelihood method, are considered, their adequacy discussed, and prognostic criteria of fitness of the genetic hypothesis introduced.

Adolescent↗
PubMed2003

[Analysis of the effects of parental genotypes of rye lines on the development of quantitative traits in primary octaploid triticale. Plant height].

When breeding the primary spring octoploid triticale derived from crosses of various inbred rye lines to wheat Chinese Spring, the effects of the rye genotype and growth conditions on the plant height and proportion of the first, second, and final (pedicle) internodes to the entire stem length were studied. Two triticale groups were examined: homozygotes for the dominant (Ddw1) and recessive (ddw1) alleles of the gene responsible for short stem in rye. In the short stem triticale lines carrying the Ddw1 alleles, the plants were 20 cm shorter on average than those in the ddw1-carrying lines, and the distribution of the two triticale groups overlapped significantly. In both groups, the lines significantly differing in plant height could be differentiated, because of allelic diversity of the additional genes controlling this trait along with the Ddw gene. In most triticale lines, especially in the Ddw1-carrying ones, the plant height was much reduced under unfavorable growth conditions. At the same time, a short-stem line was isolated, which is characterized by ecological plasticity, like the maternal wheat cultivar. In the triticale studied, the stem structure depended on the short-stem rye genotype. The two-year study showed that in the triticale carrying the dominant allele of this gene, the first internode is significantly extended, whereas the upper (pedicle) internode is reduced, which increases plant lodging resistance. The differences revealed between the rye lines as well as their effect on the quantitative triticale traits are discussed in view of a variant of the hybridological analysis, which had been previously proposed for identification and mapping of the correspondent rye genes.

Alleles↗
PubMed2005

Quantitative trait loci and the study of plant domestication.

Plant domestication ranks as one of the most important developments in human history, giving human populations the potential to harness unprecedented quantities of the earth's resources. But domestication has also played a more subtle historical role as the foundation of the modern study of evolution and adaptation. Until recently, however, researchers interested in domestication were limited to studying phenotypic changes or the genetics of simple Mendelian traits, when often the characters of most interest--fruit size, yield, height, flowering time, etc.--are quantitative in nature. The goals of this paper are to review some of the recent work on the quantitative genetics of plant domestication, identify some of the common trends found in this literature, and offer some novel interpretations of the data that is currently available.

Breeding↗
PubMed2003

Fine mapping of the alpha-T catenin gene to a quantitative trait locus on chromosome 10 in late-onset Alzheimer's disease pedigrees.

Using plasma amyloid beta protein (Abeta42) levels as an intermediate, quantitative phenotype for late onset Alzheimer's disease (LOAD), we previously obtained significant linkage at approximately 80 cM on chromosome 10. Linkage to the same region was obtained independently in a study of affected LOAD sib-pairs. Together, these two studies provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta42. VR22 is a large (1.7 Mb) gene located at 80 cM that encodes alpha-T catenin, which is a binding partner of beta catenin. This makes VR22 an attractive candidate gene because beta catenin interacts with presenilin 1, which has many mutations that elevate Abeta42 and cause early onset familial AD. We identified two intronic VR22 SNPs (4360 and 4783) in strong linkage disequilibrium (LD) that showed highly significant association (P=0.0001 and 0.0006) with plasma Abeta42 in 10 extended LOAD families. This association clearly contributed to the linkage at approximately 80 cM because the lod scores decreased when linkage analysis was performed conditional upon the VR22 association. This association replicated in another independent set of 12 LOAD families (P=0.04 for 4783 and P=0.08 for 4360). Bounding of the association region using multiple SNPs showed VR22 to be the only confirmed gene within the region of association. These findings indicate that VR22 has variant(s) which influence Abeta42 and contribute to the previously reported linkage for plasma Abeta42 in LOAD families.

Adult↗
PubMed1986

Identifying single genes of large effect in quantitative traits using best linear unbiased prediction.

The recent discovery of a major gene for rapid postweaning growth has reinforced the hypothesis that other quantitative continuous traits may be influenced by single genes of large effect. However, most methods for the detection of such genes rely on the discovery of multimodality in the population frequency distribution. The complicating effects of environment and artificial selection make the identification of such genes with field-collected data a formidable problem. An index is proposed that may serve as an indicator that a major gene is segregating within a population. The index is based on the assumption that under polygenic inheritance, an offspring's deviation from the midparent average is smaller than the deviation from either parent. Whereas, for the Mendelian segregation of a major gene, the opposite would be expected. A proposed class of indices is then based on the ratio [O - .5(S + D)]k/([O - S]k/2 [O - D]k/2) where O, S and D are the additive genetic values of an offspring and its sire and dam estimated via best linear unbiased prediction. Values of the index greater than 1. would be indicative of major gene inheritance. Simulation of small populations indicates that the index is quite sensitive to the existence of segregating major genes even in the absence of multimodality of the phenotypic distribution. However, the index remains dependent on the accuracy of genetic value estimation.

Animals↗
PubMed2006

Family based association analysis of statistically derived quantitative traits for drug use in ADHD and the dopamine transporter gene.

OBJECTIVE: To determine whether SNPs within the dopamine transporter gene (DAT) are associated with quantitative phenotypes generated from drug frequency variables in an ADHD sample. METHOD: 35 SNPs were genotyped in and around DAT. We developed a quantitative phenotype at each SNP by weighting the drug frequency variables. The weights were selected to maximize the heritability at each SNP. Once a quantitative phenotype was generated at each SNP, a screening procedure was used to select and test the SNPs with the greatest power to detect an association in DAT. RESULTS: No SNPs in DAT were associated with the quantitative phenotypes generated from the drug frequency variables after the multiple comparisons adjustment; however, some SNPs achieved nominal significance. A sliding window of analysis of 3 SNPs also resulted in only nominal associations. CONCLUSIONS: SNPs in DAT do not appear to be associated with the phenotypes generated from drug frequency variables among individuals with ADHD.

Adolescent↗