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PubMed2005

[Methodology of mapping quantitative trait loci for discrete traits using maximum likelihood].

The maximum likelihood method was used to compare the efficiency of interval mapping with either the threshold model or the linear model. The irfluencing factors of quantitative trait loci (QTL) detection efficiency (e.g. QTL effect, heritability and incidence of categories) were simulated in our study. Daughter design with multiple families was applied, and the number of segregating population was 500. The results showed that the threshold model was superior in terms of parameter estimation. It was a more efficient and accurate model of QTL mapping for discrete traits. In addition, the accuracy of QTL mapping depended on the effect of the putative QTL, the value of heritability and incidence directly. With an increase of QTL effect, heritability and incidence of categories, the accuracy of QTL mapping improved correspondingly.

Algorithms↗
PubMed1999

Preweanling sensorial and motor development in laboratory mice: quantitative trait loci mapping.

Chromosomal mapping of genes linked with 19 measures of sensorial, motor, and body weight development were investigated. Chromosomal mapping is the first step towards gene identification. When a genomic region is shown to be linked to a trait, it is possible to select a reduced number of candidate genes that have been previously mapped on this region. The involvement of every gene can be individually tested either by molecular (transgenesis, homologous recombination) or traditional methods (congenicity). Mapping was performed using 389 males and females from two inbred strains of laboratory mice C57BL/6By and NZB/BlNJ, their reciprocal F1s and F2s. Thirty-six Quantitative Trait Loci (QTL) were mapped, 12 reached the 3.13 lod score, being thus considered as confirmed. These QTL were tentatively labeled: Cliff Drop Aversion (Cliff Qtl), Geotaxia (Geot Qtl), Vertical Clinging (VertCling Qtl), Bar Holding with the 4 paws (BH4P Qtl), Age at Eyelid Opening (Aeyo Qtl), Visual Placing (Vispl Qtl), Startle Response (Start Qtl1, Start Qtl2), Body Weight at Day 10 in Males pooled with Females (Bwefmd10 Qtl), and Body Weight at Day 30 in males (Bwemd30 Qtl). For the majority of the developmental measures, the QTL that were mapped contributed little to the phenotypic variance, even when mitochondrial DNA contribution was included: Righting Response (12.7%), Cliff Drop Aversion (10%), Crossed Extensor Response (18.1%), Geotaxia (16.2%), Bar Holding Response for 10 s (12.1%), Bar Holding Response with 4 paws (8.1%), Vertical Clinging (9.3%), Vertical Climbing (5%), Startle Response (21.2%), Eyelid Opening (14.6%), Visual Placing (22%), Body Weight at Day 10 (27%), Body Weight at Day 15 in Females (52.5%), Body Weight at Day 15 in Males (17%), Body Weight at Day 30 in Females (42%), and Body Weight at Day 30 in Males (48%). A factorial analysis of the correlations between the measures of development did not provide evidence of a general factor. A general genetic factor of development was also rejected because few common genetic correlates were discovered for the 19 measures of development (Body Weight at Days 15 and 30 in Females on Chromosome 2, Eyelid Opening and Body Weight at Day 10 on Chromosome 5 and mitochondrial genome for five measures). Co-identification of genes, the function of which were previously known thanks to newly discovered QTL, should help to explain the function of QTL. Present data help to highlight candidate regions including several genes that could be candidates for the QTL function. Large confidence intervals were obtained as usual from the F2 intercrossed population. More stringent methods are suggested for more efficient co-identification.

Animals↗
PubMed2002

Fine mapping of polymorphic alcohol-related quantitative trait loci candidate genes using interval-specific congenic recombinant mice.

BACKGROUND: The inbred long-sleep (ILS) and inbred short-sleep (ISS) strains of mice are widely studied as a model of initial sensitivity to alcohol. Recently, a large comparative DNA sequencing study of candidate genes located within the four Lore quantitative trait loci (QTLs) associated with the ethanol-induced loss of righting reflex in ILS and ISS mice has identified eight genes that contain coding region differences corresponding to amino acid changes. Here, recently developed interval-specific congenic recombinant mice (ISCRs) have been used to map these genes in relationship to newly narrowed QTL regions. METHODS: Regions of candidate genes containing DNA differences corresponding to previously identified amino acid changes between ISS and ILS mice were amplified from either genomic DNA or complementary DNA from ISCR mice using polymerase chain reaction. The products were purified and directly sequenced to determine the genotypes for each polymorphism. On the basis of these genotypic data, each candidate gene was determined to be located either within or outside of recently narrowed Lore QTL intervals. RESULTS: Of these eight candidates with protein-coding differences, five are now excluded from their respective Lore intervals. The other three (Znf142, Ptprn, and Znf133) have been localized to the narrowed QTL intervals. CONCLUSIONS: These three central nervous system genes (Znf142, Ptprn, and Znf133) represent promising candidates for involvement in the differential sensitivity to alcohol exhibited between ILS and ISS mice. This study also demonstrates how the combination of high-throughput comparative gene sequencing and concomitant genetic fine mapping of QTL regions with ISCRs can be an effective tool for accelerating the process of moving from QTL to gene.

Alcoholism↗
PubMed2004

Mapping quantitative trait loci with censored observations.

The existing statistical methods for mapping quantitative trait loci (QTL) assume that the phenotype follows a normal distribution and is fully observed. These assumptions may not be satisfied when the phenotype pertains to the survival time or failure time, which has a skewed distribution and is usually subject to censoring due to random loss of follow-up or limited duration of the experiment. In this article, we propose an interval-mapping approach for censored failure time phenotypes. We formulate the effects of QTL on the failure time through parametric proportional hazards models and develop efficient likelihood-based inference procedures. In addition, we show how to assess genome-wide statistical significance. The performance of the proposed methods is evaluated through extensive simulation studies. An application to a mouse cross is provided.

Chromosome Mapping↗
PubMed1999

Statistical methods for mapping quantitative trait loci from a dense set of markers.

Lander and Botstein introduced statistical methods for searching an entire genome for quantitative trait loci (QTL) in experimental organisms, with emphasis on a backcross design and QTL having only additive effects. We extend their results to intercross and other designs, and we compare the power of the resulting test as a function of the magnitude of the additive and dominance effects, the sample size and intermarker distances. We also compare three methods for constructing confidence regions for a QTL: likelihood regions, Bayesian credible sets, and support regions. We show that with an appropriate evaluation of the coverage probability a support region is approximately a confidence region, and we provide a theroretical explanation of the empirical observation that the size of the support region is proportional to the sample size, not the square root of the sample size, as one might expect from standard statistical theory.

Chromosome Mapping↗
PubMed1997

Assessment of locomotor activity, acoustic and tactile startle, and prepulse inhibition of startle in inbred mouse strains and F1 hybrids: implications of genetic background for single gene and quantitative trait loci analyses.

As the use of transgenic and null mutation techniques in the development of animal models of disorders increases, the importance of selecting the appropriate genetic background also increases. The genetic background of the mouse strains used as models for various disorders is critical because of the potential for epistatic effects on the expression of transgenes and null mutations. Twelve strains of inbred mice and seven F1 hybrids were tested in multiple behavioural tasks including open-field locomotor activity, Y-maze activity, auditory and tactile startle and prepulse inhibition of startle response. Differences across genotypes were found for all variables measured. The range of variability among genotypes was dependent on the specific measure so careful consideration must be made in selecting a strain for testing a particular behaviour. Because of the polygenic nature of each of the behavioural phenotypes, the impact of a single gene manipulation may vary depending on the genetic background on which it is expressed. Moreover, quantitative trait loci methods could be applied to these behaviours.

Acoustic Stimulation↗
PubMed2005

Molecular mapping of QTLs for resistance to Gibberella ear rot, in corn, caused by Fusarium graminearum.

Gibberella ear rot, caused by the fungus Fusarium graminearum Schwabe, is a serious disease of corn (Zea mays) grown in northern climates. Infected corn is lower yielding and contains toxins that are dangerous to livestock and humans. Resistance to ear rot in corn is quantitative, specific to the mode of fungal entry (silk channels or kernel wounds), and highly influenced by the environment. Evaluations of ear rot resistance are complex and subjective; and they need to be repeated over several years. All of these factors have hampered attempts to develop F. graminearum resistant corn varieties. The aim of this study was to identify molecular markers linked to the genes for resistance to Gibberella ear rot. A recombinant inbred (RI) population, produced from a cross between a Gibberella ear rot resistant line (CO387) and a susceptible line (CG62), was field-inoculated and scored for Gibberella ear rot symptoms in the F4, F6, and F7 generations. The distributions of disease scores were continuous, indicating that resistance is probably conditioned by multiple loci. A molecular linkage map, based on segregation in the F5 RI population, contained 162 markers distributed over 10 linkage groups and had a total length of 2237 cM with an average distance between markers of 13.8 cM. Composite interval mapping identified 11 quantitative trait loci (QTLs) for Gibberella ear rot resistance following silk inoculation and 18 QTLs following kernel inoculation in 4 environments that accounted for 6.7%-35% of the total phenotypic variation. Only 2 QTLs (on linkage group 7) were detected in more than 1 test for silk resistance, and only 1 QTL (on linkage group 5) was detected in more than 1 test for kernel resistance, confirming the strong influence of the environment on these traits. The majority of the favorable alleles were derived from the resistant parent (CO387). The germplasm and markers for QTLs with significant phenotypic effects may be useful for marker-assisted selection to incorporate Gibberella ear rot resistance into commercial corn cultivars.

Chromosome Mapping↗
PubMed2005

Quantitative trait locus analysis of candidate gene alleles associated with attention deficit hyperactivity disorder (ADHD) in five genes: DRD4, DAT1, DRD5, SNAP-25, and 5HT1B.

It has been widely postulated that the categorical diagnosis of attention deficit hyperactivity disorder (ADHD) should be seen as the extreme end of a set of traits quantitatively distributed in the general population. A consequence of this is that the genes associated with DSM-IV ADHD should also influence these underlying traits in non-affected individuals. The aim of this study was to examine if specific candidate loci previously shown to be associated with DSM-IV ADHD, also act as quantitative trait loci (QTLs) for ADHD-symptoms in the general population. We have genotyped five candidate markers in a population-based sample of male dizygous twin-pairs (n = 329 pairs). We found little evidence to support a role for the previously-nominated alleles of a DRD4 VNTR, a 5HT1B SNP, or a microsatellite marker near to DRD5, in the distribution of ADHD-symptoms scores; however, we found some evidence to suggest that the DAT1 3'UTR VNTR and weak evidence that a microsatellite in SNAP-25 may have a role in continuous measures of ADHD-symptoms hyperactivity above and beyond their role in clinical ADHD.

Alleles↗
PubMed2006

Relationships between the functional PPARalpha Leu162Val polymorphism and obesity, type 2 diabetes, dyslipidaemia, and related quantitative traits in studies of 5799 middle-aged white people.

Peroxisome proliferator-activated receptor-alpha (PPARalpha) is a nuclear receptor capable of regulating the expression of genes involved in peroxisomal and mitochondrial beta-oxidation pathways. The common Leu162Val polymorphism in the gene encoding PPARalpha has inconsistently shown association with quantitative traits related to obesity, type 2 diabetes, and dyslipidaemia. We genotyped the Leu162Val polymorphism in 1383 patients with type 2 diabetes and 4401 control subjects with normal glucose tolerance (NGT) without showing any association between diabetes and genotype. In addition, the Leu162Val polymorphism was not associated with WHO-defined obesity or dyslipidaemia in case-control settings involving 961 obese and 2563 lean subjects and 1399 dyslipidaemic and 4399 normolipidaemic subjects, respectively. Quantitative trait studies of metabolic variables were carried out in 5799 middle-aged, treatment-naïve subjects showing a difference in fasting serum triglyceride concentrations among homozygous Val-carriers (Leu/Leu+Leu/Val, n=5782, 1.33+/-1.35 mmol/l vs. Val/Val, n=17, 2.22+/-2.4 mmol/l, p=0.007). Similarly, Val/Val was associated with increased fasting serum total cholesterol concentrations (p=0.01). In conclusion, in a relative large-scale study of middle-aged whites we found no evidence of association between the PPARalpha Leu162Val polymorphism and obesity or type 2 diabetes. If replicated, the Val162Val variant may, however, confer an increase in fasting levels of serum lipids.

Aged↗
PubMed1999

Single- and multiple-trait mapping analysis of linked quantitative trait loci. Some asymptotic analytical approximations.

Estimating the resolution power of mapping analysis of linked quantitative trait loci (QTL) remains a difficult problem, which has been previously addressed mainly by Monte Carlo simulations. The analytical method of evaluation of the expected LOD developed in this article spreads the "deterministic sampling" approach for the case of two linked QTL for single- and two-trait analysis. Several complicated questions are addressed through this evaluation: the dependence of QTL detection power on the QTL effects, residual correlation between the traits, and the effect of epistatic interaction between the QTL for one or both traits on expected LOD (ELOD), etc. Although this method gives only an asymptotic estimation of ELOD, it allows one to get an approximate assessment of a broad spectrum of mapping situations. A good correspondence was found between the ELODs predicted by the model and LOD values averaged over Monte Carlo simulations.

Chromosome Mapping↗
PubMed2006

Characterization of the porcine acyl-CoA synthetase long-chain 4 gene and its association with growth and meat quality traits.

Summary Long-chain acyl-CoA synthetase (ACSL) catalyses the formation of long-chain acyl-CoA from fatty acid, ATP and CoA, activating fatty acids for subsequent reactions. Long-chain acyl-CoA synthetase thus plays an essential role in both lipid biosynthesis and fatty acid degradation. The ACSL4 gene was evaluated as a positional candidate gene for the quantitative trait loci (QTL) located between SW2456 and SW1943 on chromosome X. We have sequenced 4906 bp of the pig ACSL4 mRNA. Sequence analysis allowed us to identify 10 polymorphisms located in the 3'-UTR region and to elucidate two ACSL4 haplotypes. Furthermore, a QTL and an association study between polymorphisms of the ACSL4 gene and traits of interest were carried out in an Iberian x Landrace cross. We report QTL that have not been previously identified, and we describe an association of the ACSL4 polymorphisms with growth and percentage of oleic fatty acid. Finally, we have determined allelic frequencies in 140 pigs belonging to the Iberian, Landrace, Large White, Meishan, Pietrain, Duroc, Vietnamese, Peccary and Babirusa populations.

Animals↗
PubMedDate not supplied

[Genetic selection of mice for quantitative responsiveness of lymphocytes to phytohemagglutinin].

A two-way selection was performed in mice according to the quantitative response of small lymphocytes to the mitogenic activity of phytohaemagglutinin (PHA). The response of inguinal lymph node cells of each mouse to an optimal dose of PHA was measured by 3H-thymidine incorporation using a micro-plate method. Starting from four outbred mouse strains we mated on the one hand mice getting the best response and on the other hand mice getting the poorest response. A progressive separation of the two lines was observed. At the 7th generation a 3-fold difference was found between the two lines. A similar interline difference was observed when concanavalin A (ConA) was used as mitogen. The separation of the two lines was also evident when spleen cells or thymus cells were cultured with PHA or ConA.

Animals↗
PubMed2002

Models and tests of linkage and association studies of quantitative trait locus for multi-allele marker Loci.

In this paper, we explore models and tests for association and linkage studies of a quantitative trait locus (QTL) linked to a multi-allele marker locus. Based on the difference between an offspring's conditional trait means of receiving and not receiving an allele from a parent at marker locus, we propose three statistics T(m), T(m,row) and T(m,col) to test association or linkage disequilibrium between the marker locus and the QTL. These tests are composite tests, and use the offspring marginal sample means including offspring data of both homozygous and heterozygous parents. For the linkage study, we calculate the offspring's conditional trait mean given the allele transmission status of a heterozygous parent at the marker locus. Based on the difference between the conditional means of a transmitted and a nontransmitted allele from a heterozygous parent, we propose statistics T(parsi), T(satur), T(gen) and T(m,het) to perform composite tests of linkage between the marker locus and the quantitative trait locus in the presence of association. These tests only use the offspring data that are related to the heterozygous parents at the marker locus. T(parsi) is a parsimonious or allele-wise statistic, T(satur) and T(gen )are satured or genotype-wise statistics, and T(m,het) compares the row and column sample means for offspring data of heterozygous parents. After comparing the powers and the sample sizes, we conclude that T(parsi) has higher power than those of the bi-allele tests, T(satur), T(gen), and T(m,het). If there is tight linkage between the marker and the trait locus, T(parsi) is powerful in detecting linkage between the marker and the trait locus in the presence of association. By investigating the goodness-of-fit of T(parsi), we find that T(satur) does not gain much power compared to that of T(parsi). Moreover, T(parsi) takes into account the pattern of the data that is consistent with linkage and linkage disequilibrium. As the number of alleles at the marker locus increases, T(parsi) is very conservative, and can be useful even for sparse data. To illustrate the usefulness and the power of the methods proposed in this paper, we analyze the chromosome 6 data of the Oxford asthma data, Genetic Analysis Workshop 12.

Asthma↗
PubMed2005

QTL analysis of powdery mildew resistance in cucumber (Cucumis sativus L.).

A population of F7 recombinant inbred lines (RILs) was made from a cross between susceptible ('Santou') and resistant (PI197088-1) lines of cucumber in order to study powdery mildew resistance loci. Susceptibility to powdery mildew in the F7 RIL individuals showed a continuous distribution from susceptible to resistant, suggesting that powdery mildew resistance is controlled by quantitative trait loci (QTLs). A QTL analysis identified two and three loci for powdery mildew resistance under 26 and 20 degrees C conditions, respectively. One QTL was found in the same position under both temperature conditions. Therefore, it is more likely that one major QTL acts under both temperature conditions and that other QTLs are specific to the two temperature conditions. The above results suggest that the four QTLs are controlled in a different temperature manner, and that their combination played an important role in expressing a high level of resistance to powdery mildew in this cucumber population. Sequence-tagged site (STS) markers associated with each QTL were developed and would be useful for breeding a cucumber line with a high level of powdery mildew resistance.

Chromosome Segregation↗
PubMed2006

IL-6 promoter polymorphisms and quantitative traits related to the metabolic syndrome in KORA S4.

Interleukin-6 (IL-6) is a pleiotropic cytokine which has been proposed as "cytokine for gerontologists" and linked to age-related metabolic disturbances such as the metabolic syndrome or type 2 diabetes. Polymorphisms located in the promoter region of IL-6 have been reported to be involved in the regulation of IL-6 transcription. This study investigates whether IL-6 promoter variants -174 G/C and -573 G/C are associated with quantitative traits related to the metabolic syndrome (International Diabetes Federation criteria) in a population of normoglycemic subjects (n=878) from the latest KORA survey (KORA S4). Genotyping was performed using MALDI-TOF MS. Besides lower height (p=0.01) the -174 CC genotype was independently associated with lower waist (p=0.002) and hip (p=0.01) circumferences in men. Furthermore, the -174 CC genotype was associated with BMI (p=0.004) when adjusted for waist and hip circumference. The present study does not suggest associations with further components of the metabolic syndrome. The association with height seems to be the central factor indicating an influence of IL-6 on growth through impaired bone metabolism. However, the complex relationships need further investigation.

Aged↗
PubMed1998

Mapping quantitative trait loci for binary traits using a heterogeneous residual variance model: an application to Marek's disease susceptibility in chickens.

A typical problem in mapping quantitative trait loci (QTLs) comes from missing QTL genotype. A routine method for parameter estimation involving missing data is the mixture model maximum likelihood method. We developed an alternative QTL mapping method that describes a mixture of several distributions by a single model with a heterogeneous residual variance. The two methods produce similar results, but the heterogeneous residual variance method is computationally much faster than the mixture model approach. In addition, the new method can automatically generate sampling variances of the estimated parameters. We derive the new method in the context of QTL mapping for binary traits in a F2 population. Using the heterogeneous residual variance model, we identified a QTL on chromosome IV that controls Marek's disease susceptibility in chickens. The QTL alone explains 7.2% of the total disease variation.

Algorithms↗
PubMed2000

[Computer system for simulating population dynamic patterns of polygenes and mobile genetic elements upon truncation selection for a quantitative trait].

A computer system was developed for simulation of population dynamics of interacting polygene patterns and mobile genetic elements (MGEs) under selection for a quantitative trait. The system is stochastic (Monte Carlo) and takes into account the main sources of random change in the patterns (recombinations, transpositions, excisions), genetic drift, and determined trends of selection and other genetic processes in a finite population. Using this model, it is possible to analyze the dynamics of many population parameters that cannot be experimentally estimated: frequencies of polygenic alleles, proportions of adaptive and random fixations, average heterozygosities of polygenes and MGEs, coefficient of inbreeding, heritability, etc. In addition, the model can be used to test various hypotheses on polygene-MGE interaction.

Adaptation, Physiological↗
PubMed1996

Using multivariate genetic modeling to detect pleiotropic quantitative trait loci.

Large numbers of sibling pairs or other relatives are needed to detect linkage between a quantitative trait locus (QTL) and a marker, especially if the variance of the QTL is low relative to the total phenotypic variance of the trait. One strategy to increase the power to detect linkage is to reduce the environmental variance in the trait under analysis. This approach was explored by carrying out a series of simulation studies in which multivariate observations were used to estimate individual genotypic values at a QTL, that pleiotropically affected more than one trait. Simulations for different QTL allele frequencies with a completely informative marker showed that the power to detect the QTL increased substantially when estimates of individual genotypic values at the QTL were used in the linkage analysis instead of phenotypic observations. An advantage of this approach is that, rather than employing phenotypic selection, individuals with extreme genotypes may selected when ascertaining a sample of extreme families.

Adult↗