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At least 1,423 records · Page 79Linked to original sources
PubMed2004

The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats.

We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local adaptation in shaping population differences. We derived a mapping population from a cross between a coastal Mediterranean population and a steppe inland population from Israel and assessed F3 progeny fitness in the natural growing environments of the two parental populations. Dilution of the local gene pool, estimated as the proportion of native alleles at 96 marker loci in the recombinant lines, negatively affected fitness traits at both sites. QTLs for fitness traits tended to differ in the magnitude but not in the direction of their effects across sites, with beneficial alleles generally conferring a greater fitness advantage at their native site. Several QTLs showed fitness effects at one site only, but no opposite selection on individual QTLs was observed across the sites. In a common-garden experiment, we explored the hypothesis that the two populations have adapted to divergent nutrient availabilities. In the different nutrient environments of this experiment, but not under field conditions, fitness of the F3 progeny lines increased with the number of heterozygous marker loci. Comparison of QTL-effects that underlie genotype x nutrient interaction in the common-garden experiment and genotype x site interaction in the field suggested that population differentiation at the field sites may have been driven by divergent nutrient availabilities to a limited extent. Also in this experiment no QTLs were observed with opposite fitness effects in contrasting environments. Our data are consistent with the view that adaptive differentiation can be based on selection on multiple traits changing gradually along ecological gradients. This can occur without QTLs showing opposite fitness effects in the different environments, that is, in the absence of genetic trade-offs in performance between environments.

Adaptation, Biological↗
PubMed1975

Immunochemical characterization of murine H-2 controlled Ss (serum substance) protein through identification of its human homologue as the fourth component of complement.

The S region of the mouse H-2 complex is genetically defined by a series of alleles, or pseudoalleles, which control the level of a serum globulin, Ss, and of its allotypic vairatn, Slp. In contrast with the products of other genes in the complex, no homologue of the Ss protein has been found in other species, except the rat. In the present study, a component in human plasma was identified which cross-reacts with anti-mouse Ss, and which also displays electrophoretic and size similarities to the mouse Ss protein. This component was isolated and characterized immunochemically as the fourth component of human complement (C'4 or beta1E globulin). Several antisera monospecific for human C'4 cross-react with the mouse Ss protein and detect its genetically determined quantitative variations.

Animals↗
PubMed1997

A two-stage half-sib design for mapping quantitative trait loci in food animals.

Daughter and granddaughter half-sib designs for mapping quantitative trait loci were modified to increase experimental power. This new design includes a two-stage procedure, in contrast to conventional one-step half-sib designs. In stage 1, a few progeny of each sire are genotyped for marker loci. Based on the analyses of stage 1 data, some sires are chosen to continue genotyping more progeny for stage 2. When multiple chromosomes are under investigation, chromosomes and sires for stage 2 are selected based on the analysis of stage 1 data. Sire selection results in increased frequency of heterozygous genotypes of interest in stage 2 if the markers are linked to those genes. Chromosome selection can increase the proportion of chromosomes with segregating quantitative trait loci in stage 2 if not all of the chromosomes evaluated in stage 1 have segregating quantitative trait loci. Numerical results indicated that two-stage half-sib designs are generally more powerful than conventional designs when 1) the noncentrality parameter is moderate or larger, 2) larger quantitative trait loci are mapped using tightly linked markers in larger families, and 3) variation is large in numbers and sizes of segregating quantitative trait loci among the chromosomes evaluated in stage 1.

Animals↗
PubMed2002

Application of non-parametric bootstrap methods to estimate confidence intervals for QTL location in a beef cattle QTL experimental population.

Empirical confidence intervals (CIs) for the estimated quantitative trait locus (QTL) location from selective and non-selective non-parametric bootstrap resampling methods were compared for a genome scan involving an Angus x Brahman reciprocal fullsib backcross population. Genetic maps, based on 357 microsatellite markers, were constructed for 29 chromosomes using CRI-MAP V2.4. Twelve growth, carcass composition and beef quality traits (n = 527-602) were analysed to detect QTLs utilizing (composite) interval mapping approaches. CIs were investigated for 28 likelihood ratio test statistic (LRT) profiles for the one QTL per chromosome model. The CIs from the non-selective bootstrap method were largest (87 7 cM average or 79-2% coverage of test chromosomes). The Selective II procedure produced the smallest CI size (42.3 cM average). However, CI sizes from the Selective II procedure were more variable than those produced by the two LOD drop method. CI ranges from the Selective II procedure were also asymmetrical (relative to the most likely QTL position) due to the bias caused by the tendency for the estimated QTL position to be at a marker position in the bootstrap samples and due to monotonicity and asymmetry of the LRT curve in the original sample.

Animals↗
PubMed2005

Large-scale, multibreed, multitrait analyses of quantitative trait loci experiments: the case of porcine X chromosome.

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10(-43)), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10(-15)) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.

Adipose Tissue↗
PubMed2001

Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs.

Identification of genes involved in complex traits by traditional (lod score) linkage analysis is difficult due to many complicating factors. An unfortunate drawback of non-parametric procedures in general, though, is their low power to detect genetic effects. Recently, Dudoit and Speed [2000] proposed using a (likelihood-based) score test for detecting linkage with IBD data on sib pairs. This method uses the likelihood for theta, the recombination fraction between a trait locus and a marker locus, conditional on the phenotypes of the two sibs to test the null hypothesis of no linkage (theta = (1/2)). Although a genetic model must be specified, the approach offers several advantages. This paper presents results of simulation studies characterizing the power and robustness properties of this score test for linkage, and compares the power of the test to the Haseman-Elston and modified Haseman-Elston tests. The score test is seen to have impressively high power across a broad range of true and assumed models, particularly under multiple ascertainment. Assuming an additive model with a moderate allele frequency, in the range of p = 0.2 to 0.5, along with heritability H = 0.3 and a moderate residual correlation rho = 0.2 resulted in a very good overall performance across a wide range of trait-generating models. Generally, our results indicate that this score test for linkage offers a high degree of protection against wrong assumptions due to its strong robustness when used with the recommended additive model.

Computer Simulation↗
PubMed2005

Quantitative trait locus-specific genotype x alcoholism interaction on linkage for evoked electroencephalogram oscillations.

We explored the evidence for a quantitative trait locus (QTL)-specific genotype x alcoholism interaction for an evoked electroencephalogram theta band oscillation (ERP) phenotype on a region of chromosome 7 in participants of the US Collaborative Study on the Genetics of Alcoholism. Among 901 participants with both genotype and phenotype data available, we performed variance component linkage analysis (SOLAR version 2.1.2) in the full sample and stratified by DSM-III-R and Feighner-definite alcoholism categories. The heritability of the ERP phenotype after adjusting for age and sex effects in the combined sample and in the alcoholism classification sub-groups ranged from 40% to 66%. Linkage on chromosome 7 was identified at 158 cM (LOD = 3.8) in the full sample and at 108 in the non-alcoholic subgroup (LOD = 3.1). Further, we detected QTL-specific genotype x alcoholism interaction at these loci. This work demonstrates the importance of considering the complexity of common complex traits in our search for genes that predispose to alcoholism.

Alcoholism↗
PubMed1997

Mapping of selective rat chromosome regions using mouse microsatellite markers.

Four hundred eighty mouse microsatellite markers distributed in discrete regions on five mouse chromosomes were screened for producing PCR products in the rat. Ninety-eight of these markers or 20% give distinctive PCR products. Among these ninety-eight markers, twenty-three are polymorphic between the inbred hypertensive Dahl salt-sensitive (S) rat strain and several normotensive rat strains of interest. Fourteen of these polymorphic markers have been mapped to the homologous chromosome regions of the rat, and have further been utilized to localize quantitative trait loci (QTL) for blood pressure in the S rat.

Animals↗
PubMed2002

hairy: A quantitative trait locus for drosophila sensory bristle number.

Advances in medicine, agriculture, and an understanding of evolution depend on resolving the genetic architecture of quantitative traits, which is challenging since variation for complex traits is caused by multiple interacting quantitative trait loci (QTL) with small and conditional effects. Here, we show that the key developmental gene, hairy (h), is a QTL for Drosophila sternopleural bristle number, a model quantitative trait. Near-isoallelic lines (NIL) for the h gene region exhibited significant variation in bristle number and failed to complement a hairy mutation. Sequencing 10 h alleles from a single population revealed 330 polymorphic sites in approximately 10 kb. Genotypes for 25 of these and 14 additional sites in the flanking regions were determined for the 57 NIL and associated with variation in bristle number in four genetic backgrounds. A highly significant association was found for a complicated insertion/deletion polymorphism upstream of the transcription start site. This polymorphism, present in 17.5% of the h alleles, was associated with an increase of 0.5 bristle and accounted for 31% of the genetic variance in bristle number in the NIL.

Animals↗
PubMed2005

Pathophysiology of beta thalassemia--a guide to molecular therapies.

The central mechanism underlying the pathophysiology of the beta thalassemias can be related to the deleterious effects of imbalanced globin chain synthesis on erythroid maturation and survival. An imbalance of the alpha/non-alpha globin chains leads to an excess of unmatched alpha globin which precipitates out, damaging membrane structures leading to accelerated apoptosis and premature destruction of the erythroid precursors in the bone marrow (ineffective erythropoiesis). Close observation of the genotype/phenotype relationships confirms the pathophysiological mechanism and provides clues to molecular therapies, all of which aim to reduce the alpha/non-alpha chain imbalance. They include inheritance of the milder forms of beta thalassemia, co-inheritance of alpha thalassemia, or genetic factors (quantitative trait loci, QTLs) for increasing gamma globin expression. Currently, the most promising molecular therapeutic approaches include increasing beta globin gene expression by stem cell gene therapy and increasing gamma globin expression using pharmacological agents or by transduction of the gamma globin genes.

Erythropoiesis↗
PubMed2003

Quantitative study of the response to genetic selection of the Wistar audiogenic rat strain (WAR).

To study the relationship between genetics and epilepsy, Wistar rats susceptible to audiogenic seizure were selected from the main breeding stock of the Ribeirão Preto School of Medicine at the University of São Paulo, Brazil, and inbred. The criteria for selection were the highest seizure severity index (SI) and shortest latencies of the first running fit (LI). Because behavioral response to sound stimulation (120 dB) at 70 to 78 days of age was very stable, SI and LI were evaluated within this age range. Analysis of 9450 observations in 1575 animals from the 3rd to 17th generations demonstrated significant effects of generation, parity, and litter on SI and of generation and litter on LI. The SI and LI averages were, respectively, 37.13 and 22.82 s in the 3rd generation and 83.06 and 7.84 in the 17th generation. Heritabilities of both characters were estimated, by maximum likelihood, as 0.37 +/- 0.066 and 0.44 +/- 0.059, respectively. Because a significant regression related individual breeding values for both SI and LI to generation number, we concluded that genetic selection has a positive impact on the traits analyzed. Therefore, the Wistar audiogenic rat (WAR) strain appears, as per the 17th to 20th generations of genetic selection to be an audiogenic rat strain suitable for epilepsy studies.

Acoustic Stimulation↗
PubMedDate not supplied

Real-time quantitative polymerase chain reaction methods for four genetically modified maize varieties and maize DNA content in food.

Quantitative detection methods are needed for enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients. This labeling threshold, which is set to 1% in the European Union and Switzerland, must be applied to all approved GMOs. Four different varieties of maize are approved in the European Union: the insect-resistant Bt176 maize (Maximizer), Btl 1 maize, Mon810 (YieldGard) maize, and the herbicide-tolerant T25 (Liberty Link) maize. Because the labeling must be considered individually for each ingredient, a quantitation system for the endogenous maize content is needed in addition to the GMO-specific detection systems. Quantitative real-time polymerase chain reaction detection methods were developed for the 4 approved genetically modified maize varieties and for an endogenous maize (invertase) gene system.

DNA, Plant↗
PubMed2003

Inferences regarding the numbers and locations of QTLs under multiple-QTL models using interval mapping and composite interval mapping.

This paper examines the properties of likelihood maps generated by interval mapping (IM) and composite interval mapping (CIM), two widely used methods for detecting quantitative trait loci (QTLs). We evaluate the usefulness of interpretations of entire maps, rather than only evaluating summary statistics that consider isolated features of maps. A simulation study was performed in which traits with varying genetic architectures, including 20-40 QTLs per chromosome, were examined with both IM and CIM under different marker densities and sample sizes. IM was found to be an unreliable tool for precise estimation of the number and locations of individual QTLs, although it has greater power for simply detecting the presence of QTLs than CIM. The ability of CIM to resolve the correct number of QTLs and to estimate their locations correctly is good if there are three or fewer QTLs per 100 centiMorgans, but can lead to erroneous inferences for more complex architectures. When the underlying genetic architecture of a trait consists of several QTLs with randomly distributed effects and locations likelihood profiles were often indicative of a few underlying genes of large effect. Studies that have detected more than a few QTLs per chromosome should be interpreted with caution.

Animals↗
PubMed1998

Trait-based analysis in dairy cattle using blood group polymorphisms.

The potential of trait-based analysis to detect quantitative trait loci was investigated using blood group polymorphisms as the marker systems and milk and type traits in Holstein cattle as the quantitative traits. Within large half-sib families, animals were ranked on their predicted transmitted abilities or phenotypes, and blood group allele frequencies were compared between the upper and lower 5% tails of the distributions. Genotype frequencies within large families were also examined for evidence of selection. All of the major effects that had previously been detected using linear model analyses were identified by the trait-based analyses of a C blood group effect on rump angle, an L effect on milk yield and composition traits, an S effect on milk fat yield, and a direct effect of the M locus on milk and protein yields. These results provide additional support for the biological validity of these associations and also demonstrate the utility of trait-based analysis for the detection of quantitative trait loci within existing dairy breeding programs. However, just as in the linear model analyses, an analytical strategy should be utilized that allows the identification of the effects that are consistent across environments and genetic backgrounds.

Alleles↗
PubMed2000

Bayesian mapping of quantitative trait loci for complex binary traits.

A complex binary trait is a character that has a dichotomous expression but with a polygenic genetic background. Mapping quantitative trait loci (QTL) for such traits is difficult because of the discrete nature and the reduced variation in the phenotypic distribution. Bayesian statistics are proved to be a powerful tool for solving complicated genetic problems, such as multiple QTL with nonadditive effects, and have been successfully applied to QTL mapping for continuous traits. In this study, we show that Bayesian statistics are particularly useful for mapping QTL for complex binary traits. We model the binary trait under the classical threshold model of quantitative genetics. The Bayesian mapping statistics are developed on the basis of the idea of data augmentation. This treatment allows an easy way to generate the value of a hypothetical underlying variable (called the liability) and a threshold, which in turn allow the use of existing Bayesian statistics. The reversible jump Markov chain Monte Carlo algorithm is used to simulate the posterior samples of all unknowns, including the number of QTL, the locations and effects of identified QTL, genotypes of each individual at both the QTL and markers, and eventually the liability of each individual. The Bayesian mapping ends with an estimation of the joint posterior distribution of the number of QTL and the locations and effects of the identified QTL. Utilities of the method are demonstrated using a simulated outbred full-sib family. A computer program written in FORTRAN language is freely available on request.

Algorithms↗
PubMed2000

Rapid determination of zygosity and common aneuploidies from amniotic fluid cells using quantitative fluorescent polymerase chain reaction following genetic amniocentesis in multiple pregnancies.

Following second-trimester twin amniocentesis, we used quantitative fluorescent polymerase chain reaction (QF-PCR) assays and polymorphic small tandem repeats (STR) for rapid determination of zygosity and common aneuploidies from amniotic fluid (AF) cells in four pregnancies with like-sex twins, fused placentae and inconclusive chorionicity. The first and the second cases were suspected to have inadvertent sampling of the same amniotic cavity twice. The first case showed a dizygotic (DZ) pattern and repeat amniocentesis was thus avoided. The second case was monozygotic (MZ) and was complicated by discordant fetal growth and twin-twin transfusion syndrome. The third case was associated with a co-twin malformation, occipital encephalocele. DNA studies revealed MZ twinning with a discordant structural defect. The fourth case was associated with co-twin abnormalities of cystic hygroma and hydrops fetalis. DNA studies showed DZ twinning with discordant structural and chromosomal defects. The QF-PCR assay with STR has the advantages of rapid determination of zygosity and common aneuploidies in AF cells. This simple test appears to be useful in the instances of possible inadvertent puncture of the same amniotic cavity twice during amniocentesis and of discordant fetal structural and/or chromosomal abnormalities following genetic amniocentesis in multiple pregnancies with uncertain chorionicity.

Adult↗