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PubMed2002

Identification of quantitative trait loci for chemical/inflammatory nociception in mice.

Sensitivity to pain is widely variable, and much of this variability is genetic in origin. The specific genes responsible have begun to be identified, but only for thermal nociception. In order to facilitate the identification of polymorphic, pain-related genes with more clinical relevance, we performed quantitative trait locus (QTL) mapping studies of the most common assay of inflammatory nociception, the formalin test. QTL mapping is a technique that exploits naturally occurring variability among inbred strains for the identification of genomic locations containing genes contributing to that variability. An F2 intercross was constructed using inbred A/J and C57BL/6J mice as progenitors, strains previously shown to display resistance and sensitivity, respectively, to formalin-induced nociception. Following phenotypic testing (5% formalin, 25 microl intraplantar injection), mice were genotyped at 90 microsatellite markers spanning the genome. We provide evidence for two statistically significant formalin test QTLs - chromosomal regions whose inheritance is associated with trait variability - on distal mouse chromosomes 9 and 10. Identification of the genes underlying these QTLs may illuminate the basis of individual differences in inflammatory pain, and lead to novel analgesic treatment strategies.

Animals↗

PubMed2005

Stacking quantitative trait loci (QTL) for Fusarium head blight resistance from non-adapted sources in an European elite spring wheat background and assessing their effects on deoxynivalenol (DON) content and disease severity.

Fusarium head blight (FHB) is a devastating disease in wheat that reduces grain yield, grain quality and contaminates the harvest with deoxynivalenol (DON). As potent resistance sources Sumai 3 and its descendants from China and Frontana from Brazil had been analysed by quantitative trait loci (QTL) mapping. We introgressed and stacked two donor QTL from CM82036 (Sumai 3/Thornbird) located on chromosomes 3B and 5A and one donor QTL from Frontana on chromosome 3A in elite European spring wheat and estimated the effects of the three individual donor QTL and their four combinations on DON, Fusarium exoantigen content, and FHB rating adjusted to heading date. One class with the susceptible QTL alleles served as control. Each of the eight QTL classes was represented by 12-15 F(3)-derived lines tested in F(5) generation as bulked progeny possessing the respective marker alleles homozygously. Traits were evaluated in a field experiment across four locations with spray inoculation of Fusarium culmorum. All three individual donor-QTL alleles significantly reduced DON content and FHB severity compared to the marker class with no donor QTL. The only exception was the donor-QTL allele 3A that had a low, but non-significant effect on FHB severity. The highest effect had the stacked donor-QTL alleles 3B and 5A for both traits. They jointly reduced DON content by 78% and FHB rating by 55% compared to the susceptible QTL class. Analysis of Fusarium exoantigen content illustrates that lower disease severity is associated with less mycelium content in the grain. In conclusion, QTL from non-adapted sources could be verified in a genetic background of German elite spring wheat. Within the QTL classes significant (P<0.05) genotypic differences were found among the individual genotypes. An additional phenotypic selection would, therefore, be advantageous after performing a marker-based selection.

Alleles↗

PubMed2004

Robust multipoint identical-by-descent mapping for affected relative pairs.

The genetic mapping of complex traits has been challenging and has required new statistical methods that are robust to misspecified models. Liang et al. proposed a robust multipoint method that can be used to simultaneously estimate, on the basis of sib-pair linkage data, both the position of a trait locus on a chromosome and its effect on disease status. The advantage of their method is that it does not require specification of an underlying genetic model, so estimation of the position of a trait locus on a specified chromosome and of its standard error is robust to a wide variety of genetic mechanisms. If multiple loci influence the trait, the method models the marginal effect of a locus on a specified chromosome. The main critical assumption is that there is only one trait locus on the chromosome of interest. We extend this method to different types of affected relative pairs (ARPs) by two approaches. One approach is to estimate the position of a trait locus yet allow unconstrained trait-locus effects across different types of ARPs. This robust approach allows for differences in sharing alleles identical-by-descent across different types of ARPs. Some examples for which an unconstrained model would apply are differences due to secular changes in diagnostic methods that can change the frequency of phenocopies among different types of relative pairs, environmental factors that modify the genetic effect, epistasis, and variation in marker-information content. However, this unconstrained model requires a parameter for each type of relative pair. To reduce the number of parameters, we propose a second approach that models the marginal effect of a susceptibility locus. This constrained model is robust for a trait caused by either a single locus or by multiple loci without epistasis. To evaluate the adequacy of the constrained model, we developed a robust score statistic. These methods are applied to a prostate cancer-linkage study, which emphasizes their potential advantages and limitations.

Chromosome Mapping↗

PubMed2003

QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance.

An F2 and an equivalent F3 population derived from a cross between a high salt-tolerance indica variety, Nona Bokra, and a susceptible elite japonica variety, Koshihikari, were produced. We performed QTL mapping for physiological traits related to rice salt-tolerance. Three QTLs for survival days of seedlings (SDSs) under salt stress were detected on chromosomes 1, 6 and 7, respectively, and explained 13.9% to 18.0% of the total phenotypic variance. Based on the correlations between SDSs and other physiological traits, it was considered that damage of leaves was attributed to accumulation of Na+ in the shoot by transport of Na+ from the root to the shoot in external high concentration. We found eight QTLs including three for three traits of the shoots, and five for four traits of the roots at five chromosomal regions, controlled complex physiological traits related to rice salt-tolerance under salt stress. Of these QTLs, the two major QTLs with the very large effect, qSNC-7 for shoot Na+ concentration and qSKC-1 for shoot K+ concentration, explained 48.5% and 40.1% of the total phenotypic variance, respectively. The QTLs detected between the shoots and the roots almost did not share the same map locations, suggesting that the genes controlling the transport of Na+ and K+ between the shoots and the roots may be different.

DNA, Plant↗

PubMed2000

Performance of Markov chain-Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of loci.

Markov chain-Monte Carlo (MCMC) techniques for multipoint mapping of quantitative trait loci have been developed on nuclear-family and extended-pedigree data. These methods are based on repeated sampling-peeling and gene dropping of genotype vectors and random sampling of each of the model parameters from their full conditional distributions, given phenotypes, markers, and other model parameters. We further refine such approaches by improving the efficiency of the marker haplotype-updating algorithm and by adopting a new proposal for adding loci. Incorporating these refinements, we have performed an extensive simulation study on simulated nuclear-family data, varying the number of trait loci, family size, displacement, and other segregation parameters. Our simulation studies show that our MCMC algorithm identifies the locations of the true trait loci and estimates their segregation parameters well-provided that the total number of sibship pairs in the pedigree data is reasonably large, heritability of each individual trait locus is not too low, and the loci are not too close together. Our MCMC algorithm was shown to be significantly more efficient than LOKI (Heath 1997) in our simulation study using nuclear-family data.

Algorithms↗

PubMed2006

SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values.

BACKGROUND: With the recent advances in high-throughput genotyping technologies that allow for large-scale association mapping of human complex traits, promising statistical designs and methods have been emerging. Efficient simulation software are key elements for the evaluation of the properties of new statistical tests. SLINK is a flexible simulation tool that has been widely used to generate the segregation and recombination processes of markers linked to, and possibly associated with, a trait locus, conditional on trait values in arbitrary pedigrees. In practice, its most serious limitation is the small number of loci that can be simulated, since the complexity of the algorithm scales exponentially with this number. RESULTS: I describe the implementation of a two-step algorithm to be used in conjunction with SLINK to enable the simulation of a large number of marker loci linked to a trait locus and conditional on trait values in families, with the possibility for the loci to be in linkage disequilibrium. SLINK is used in the first step to simulate genotypes at the trait locus conditional on the observed trait values, and also to generate an indicator of the descent path of the simulated alleles. In the second step, marker alleles or haplotypes are generated in the founders, conditional on the trait locus genotypes simulated in the first step. Then the recombination process between the marker loci takes place conditionally on the descent path and on the trait locus genotypes. This two-step implementation is often computationally faster than other software that are designed to generate marker data linked to, and possibly associated with, a trait locus. CONCLUSION: Because the proposed method uses SLINK to simulate the segregation process, it benefits from its flexibility: the trait may be qualitative with the possibility of defining different liability classes (which allows for the simulation of gene-environment interactions or even the simulation of multi-locus effects between unlinked susceptibility regions) or it may be quantitative and normally distributed. In particular, this implementation is the only one available that can generate a large number of marker loci conditional on the set of observed quantitative trait values in pedigrees.

Algorithms↗

PubMed2001

[Genetic analysis of important growth trait based on F-2 resource population in chicken].

A three-generation of chicken population is being constructed for mapping multi-economical trait loci where three extremely divergent breeds, including a broiler breed(A), a layer breed(B) and white-silk chicken(C) were employed for reciprocal cross. Four cross combinations of A Male x C Female, C Male x A Female; B Male x C Female, C Male x B Female were performed with 277 individuals in total parental population. According to the statistic analysis for growth trait, difference between parental lines is significant, F2 generation attains great variation. Correlations among body weight and daily gain traits are significant and relative coefficient are moderate or high. The number at QTL loci is expected to be no more than 10, and based on the theoretical computation the sample size of this resource population is sufficient for QTL mapping.

Animals↗

PubMed2000

Congenic strains developed for alcohol- and drug-related phenotypes.

Quantitative trait loci (QTLs) for many alcohol- and drug-related traits have been mapped using well-accepted mapping techniques. The ultimate goal of gene identification necessitates confirmation of the QTL and reduction of the interval surrounding the QTL; both can be accomplished in congenic strains. These strains carry a chromosomal region introgressed from a donor strain onto the genetic background of a second, recipient strain. Multiple generations of backcrossing reduce the unlinked donor genome to less than 0.1%. Then, phenotypic comparisons between mice congenic for the donor region and controls from the recipient strain allow confirmation of the QTL effect. Animals with recombinations in the donor region can be used to generate interval-specific congenic recombinant lines. Numerous congenic strains are currently being developed in which chromosomal regions carrying QTLs for alcohol- and drug-related traits have been transferred from one strain onto a second strain. The purpose of this review is to summarize the chromosomal regions, donor and recipient strains, and results obtained from these congenics. Most researchers developing such strains are willing to share these resources to facilitate localization of the genetic bases of other phenotypes.

Alcoholism↗

PubMed2001

Genetic factors involved in central nervous system/immune interactions.

Analysis of several inbred rat strains has led us to hypothesize that HPA axis abnormalities may contribute, in part, to susceptibility to both autoimmune disease and addiction. In this article we review the evidence for this hypothesis and describe our ongoing efforts to genetically characterize these traits. We have mapped the locations of 23 loci that regulate autoimmune disease in rats, and are currently constructing QTL congenic lines in which a genomic region from the resistant strain is transferred to the susceptible strain or vice versa. These QTL congenic lines will be valuable to test whether genes encoding autoimmune regulation also control neuroendocrine traits. Further genetic dissection and identification of the underlying genes will be necessary to infer a mechanistic link between autoimmune and neuroendocrine traits.

Animals↗

PubMed2000

Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data.

Optimal design of quantitative-trait loci (QTL) mapping studies requires a precise understanding of the power of QTL linkage versus QTL association analysis, under a range of different conditions. In this article, we investigate the power of QTL linkage and association analyses for simple random sibship samples, under the variance-components model proposed by Fulker et al. After a brief description of an extension of this variance-components model, we show that the powers of both linkage and association analyses are crucially dependent on the proportion of phenotypic variance attributable to the QTL. The main difference between the two tests is that, whereas the power of association is directly related to the QTL heritability, the power of linkage is related more closely to the square of the QTL heritability. We also describe both how the power of linkage is attenuated by incomplete linkage and incomplete marker information and how the power of association is attenuated by incomplete linkage disequilibrium.

Chi-Square Distribution↗

PubMed2005

QTL analysis and QTL-based prediction of flowering phenology in recombinant inbred lines of barley.

Combining ecophysiological modelling and genetic mapping has increasingly received attention from researchers who wish to predict complex plant or crop traits under diverse environmental conditions. The potential for using this combined approach to predict flowering time of individual genotypes in a recombinant inbred line (RIL) population of spring barley (Hordeum vulgare L.) was examined. An ecophysiological phenology model predicts preflowering duration as affected by temperature and photoperiod, based on the following four input traits: f(o) (the minimum number of days to flowering at the optimum temperature and photoperiod), theta1 and theta2 (the development stages for the start and the end of the photoperiod-sensitive phase, respectively), and delta (the photoperiod sensitivity). The model-input trait values were obtained from a photoperiod-controlled greenhouse experiment. Assuming additivity of QTL effects, a multiple QTL model was fitted for the model-input traits using composite interval mapping. Four to seven QTL were identified for each trait. Each trait had at least one QTL specific to that trait alone. Other QTL were shared by two or all traits. Values of the model-input traits predicted for the RILs from the QTL model were fed back into the ecophysiological model. This QTL-based ecophysiological model was subsequently used to predict preflowering duration (d) for eight field trial environments. The model accounted for 72% of the observed variation among 94 RILs and 94% of the variation among the two parents across the eight environments, when observations in different environments were pooled. However, due to the low percentage (34-41%) of phenotypic variation accounted for by the identified QTL for three model-input traits (theta1, theta2 and delta), the QTL-based model accounted for somewhat less variation among the RILs than the model using original phenotypic input trait values. Nevertheless, days to flowering as predicted from the QTL-based ecophysiological model were highly correlated with days to flowering as predicted from QTL-models per environment for days to flowering per se. The ecophysiological phenology model was thus capable of extrapolating (QTL) information from one environment to another.

Chromosome Mapping↗

PubMed1997

Progress in understanding the genetics of obesity.

Progress in understanding the genetics of obesity has moved rapidly in the past few years. The genes for all of the single gene defects that produce obesity in experimental animals have now been cloned. The new insights from these models are one spur for the examination of possible links to human obesity. In thinking about the biology of obesity produced by single gene defects, it must be kept in mind that adrenalectomy can prevent the phenotypic expression in all of the single gene models of obesity. Thus, nongenetic components can play a major role in regulating even single gene models of obesity. Transgenic mice have also expanded our understanding of obesity. Transgenic models that both increase and decrease body fat have been published. Of particular interest from the perspective of the physiological control of obesity is the destruction of the uncoupling protein in brown adipose tissue, which is followed by hyperphagia and obesity, suggesting that the sympathetic nervous system is involved in both modulation of food intake and energy storage. Gene mapping using quantitative trait loci and studies of candidate genes have been applied to experimental models of animals with differing susceptibilities to dietary fat and have been applied to the human genome in more detail.

Animals↗

PubMed2001

Quantitative genetic study of maximal electroshock seizure threshold in mice: evidence for a major seizure susceptibility locus on distal chromosome 1.

We conducted a quantitative trait locus (QTL) mapping study to dissect the multifactorial nature of maximal electroshock seizure threshold (MEST) in C57BL/6 (B6) and DBA/2 (D2) mice. MEST determination involved a standard paradigm in which 8- to 12-week-old mice received one shock per day with a daily incremental increase in electrical current until a maximal seizure (tonic hindlimb extension) was induced. Mean MEST values in parental strains were separated by over five standard deviation units, with D2 mice showing lower values than B6 mice. The distribution of MEST values in B6xD2 F2 intercrossed mice spanned the entire phenotypic range defined by parental strains. Statistical mapping yielded significant evidence for QTLs on chromosomes 1, 2, 5, and 15, which together explained over 60% of the phenotypic variance in the model. The chromosome 1 QTL represents a locus of major effect, accounting for about one-third of the genetic variance. Experiments involving a congenic strain (B6.D2-Mtv7(a)/Ty) enabled more precise mapping of the chromosome 1 QTL and indicate that it lies in the genetic interval between markers D1Mit145 and D1Mit17. These results support the hypothesis that the distal portion of chromosome 1 harbors a gene(s) that has a fundamental role in regulating seizure susceptibility.

Animals↗

PubMed2005

Gene expression differences in mice divergently selected for methamphetamine sensitivity.

In an effort to identify genes that may be important for drug-abuse liability, we mapped behavioral quantitative trait loci (bQTL) for sensitivity to the locomotor stimulant effect of methamphetamine (MA) using two mouse lines that were selectively bred for high MA-induced activity (HMACT) or low MA-induced activity (LMACT). We then examined gene expression differences between these lines in the nucleus accumbens, using 20 U74Av2 Affymetrix microarrays and quantitative polymerase chain reaction (qPCR). Expression differences were detected for several genes, including Casein Kinase 1 Epsilon (Csnkle), glutamate receptor, ionotropic, AMPA1 (GluR1), GABA B1 receptor (Gabbr1), and dopamine- and cAMP-regulated phosphoprotein of 32 kDa (Darpp-32). We used the www.WebQTL.org database to identify QTL that regulate the expression of the genes identified by the microarrays (expression QTL; eQTL). This approach identified an eQTL for Csnkle on Chromosome 15 (LOD = 3.8) that comapped with a bQTL for the MA stimulation phenotype (LOD = 4.5), suggesting that a single allele may cause both traits. The chromosomal region containing this QTL has previously been associated with sensitivity to the stimulant effects of cocaine. These results suggest that selection was associated with (and likely caused) altered gene expression that is partially attributable to different frequencies of gene expression polymorphisms. Combining classical genetics with analysis of whole-genome gene expression and bioinformatic resources provides a powerful method for provisionally identifying genes that influence complex traits. The identified genes provide excellent candidates for future hypothesis-driven studies, translational genetic studies, and pharmacological interventions.

Animals↗

PubMed2003

X-linked and lineage-dependent inheritance of coping responses to stress.

Coping-or how one routinely deals with stress-is a complex behavioral trait with bearing on chronic disease and susceptibility to psychiatric disorders. This complexity is a result of not only underlying multigenic factors, but also important non-genetic ones. The defensive burying (DB) test, although originally developed as a test of anxiety, can accurately measure differences in coping strategies by assaying an animal's behavioral response to an immediate threat with ethological validity. Using offspring derived from reciprocal crosses of two inbred rat strains differing in DB behaviors, we provide convergent phenotypic and genotypic evidence that coping styles are inherited in an X-linked fashion. We find that first-generation (F(1)) males, but not females, show maternally derived coping styles, and second-generation (F(2)) females, but not males, show significant differences in coping styles when separated by grandmaternal lineage. By using a linear modeling approach to account for covariate effects (sex and lineage) in QTL analysis, we map three quantitative trait loci (QTL) on the X Chromosome (Chr) ( Coping-1, Approach-1, and Approach-2) associated with coping behaviors in the DB paradigm. Distinct loci were associated with different aspects of coping, and their effects were modulated by both the sex and lineage of the animals, demonstrating the power of the general linear modeling approach and the important interplay of allelic and non-allelic factors in the inheritance of coping behaviors.

Adaptation, Psychological↗

PubMed1996

A locus on chromosome 7 determines myocardial cell necrosis and calcification (dystrophic cardiac calcinosis) in mice.

Dystrophic cardiac calcinosis, an age-related cardiomyopathy that occurs among certain inbred strains of mice, involves myocardial injury, necrosis, and calcification. Using a complete linkage map approach and quantitative trait locus analysis, we sought to identify genetic loci determining dystrophic cardiac calcinosis in an F2 intercross of resistant C57BL/6J and susceptible C3H/HeJ inbred strains. We identified a single major locus, designated Dyscalc, located on proximal chromosome 7 in a region syntenic with human chromosomes 19q13 and 11p15. The statistical significance of Dyscalc (logarithm of odds score 14.6) was tested by analysis of permuted trait data. Analysis of BxH recombinant inbred strains confirmed the mapping position. The inheritance pattern indicated that this locus influences susceptibility of cells both to enter necrosis and to subsequently undergo calcification.

Animals↗

PubMed2006

Quantitative trait loci analysis of mice administered the methionine-choline deficient dietary model of experimental steatohepatitis.

BACKGROUND: Nonalcoholic steatohepatitis (NASH) is a common disease with a poorly understood etiology, and the methionine-choline-deficient (MCD) diet is a nutritional model of NASH. Quantitative trait loci (QTL) analysis is a standard method for chromosomal mapping of polygenic disease traits. The purpose of this study is to administer mice an MCD diet in order to determine the strain-specific susceptibility for developing steatohepatitis, and to apply a computational methodology of QTL analysis to identify associated chromosomal susceptibility loci. METHODS: Inbred mice were fed an MCD diet and alanine aminotransferase (ALT), hepatic triglycerides, liver weight, and weight loss were measured as phenotypic markers of steatohepatitis. RESULTS: A/J mice developed the highest ALT and hepatic triglyceride levels. Using linear regression analysis, gene loci affecting serum ALT levels were identified on four chromosomes, and four loci that affect liver weight were also identified. In contrast, no QTLs for hepatic triglycerides or body weight were identified. Of note, loci for ALT and liver weight co-localized to proximal segments of chromosomes 2 and 15, in regions previously identified as QTLs for liver fibrosis. CONCLUSIONS: These data indicate that experimental steatohepatitis is a polygenic disease with genes determining ALT, liver weight, and liver fibrosis.

Animals↗

PubMed2005

Dipping and variability of blood pressure and heart rate at night are heritable traits.

BACKGROUND: Blunted nocturnal blood pressure dipping (NBPD) as well as high variability in blood pressure (BPV) and low variability in heart rate (HRV), are associated with increased cardiovascular morbidity and mortality. The aim of this study was to determine whether these traits are heritable. METHODS: We studied 260 healthy siblings without antihypertensive drugs from 118 Swedish families. The BPV and HRV were defined as the standard deviation of BP and heart rate values recorded during 24 h, daytime (6 am to 10 pm), and night-time (10 pm to 6 am). The NBPD was defined as the ratio between night-time and daytime BP. Heritability was estimated with a maximal likelihood method implemented in the Solar software package with and without adjustment for significant covariates. RESULTS: At night, significant heritability was found for systolic (33%, P < .05), diastolic (36%, P < .05), and mean (42%, P < .01) BPV. After covariate adjustment the corresponding heritability values were 23% (P = .08), 29% (P < .05), and 37% (P < .05). Daytime BPV was not heritable. The heritability of NBPD was 38% (P < .05) for systolic, 9% (P = .29) for diastolic, and 36% (P < .05) for mean BP, but after adjustment only systolic NBPD was significant (29%, P < .05). Heart rate was highly heritable both during daytime (57%, P < .001) and night-time (58%, P < .001), but the variability of heart rate, after adjustment, was only significant at night (37%, P < .05). CONCLUSIONS: Our data suggest that BPV and HRV are partially under genetic control and that genetic loci of importance for these traits could be mapped by linkage analysis.

Adult↗