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Results for “quantitative trait locus”

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PubMed2004

Locating Ath8, a locus for murine atherosclerosis susceptibility and testing several of its candidate genes in mice and humans.

A previous study revealed that the difference in susceptibility to atherosclerotic lesions between inbred mouse strains SM/J and NZB/BlNJ was determined by one major locus (Ath8). In this study a (SM/J x NZB/BlNJ) F(1) x SM/J backcross localized Ath8 by quantitative trait locus mapping to chromosome 4 with a suggestive LOD score of 2.7. This quantitative trait locus (QTL) was confirmed using an (SM/J x NZB/BlNJ) intercross; Ath8 mapped to a 23cM region with a significant LOD score of 3.6. The genes for toll-like receptor 4 (T1r4), arachidonic acid epoxygenase (Cyp2j5), and angiopoietin-like protein 3 (Angptl3) map to this region. These candidate genes were analyzed for expression and sequence differences in the mouse and for associations with cardiovascular traits in human. Sequence analysis of Angptl3 shows a base pair substitution in SM, the susceptible strain, giving rise to an amino acid change in the fibrinogen homology domain of the protein. We found a significant association between ANGPTL3 and atherosclerotic lesions (P < 0.05) in human. These results suggest that Angptl3 is involved in atherosclerosis susceptibility in both mouse and human.

Animals↗

PubMed1996

Marker-assisted selection for a sex-limited character in a nucleus breeding population.

The benefits of marker-assisted selection were examined by simulation of an adult multiple ovulation and embryo transfer nucleus breeding scheme. Animals were either typed for two polymorphic marker loci, 20 centimorgans apart, flanking a single biallelic quantitative trait locus and were evaluated using a model accounting for marker information, or animals were not typed but were evaluated by a conventional BLUP animal model. Selection was for a single trait measured on females, and each dam had 4 sons and 4 daughters. Nucleus foundation animals were chosen from a base population in linkage equilibrium. With the favorable allele at an initial frequency of 0.5, marker-assisted selection substantially increased responses at the quantitative trait locus but reduced the polygenic responses. Cumulative genetic gain increased by up to 3, 9, 12, and 6% after one, two, three, and six generations of selection, respectively. If the favorable allele was initially rare (frequency of 0.1), the merits of marker-assisted selection were even more pronounced (genetic gains increased by up to 9, 19, 24 and 15%, respectively). The superiority of marker-assisted selection over conventional BLUP increased when a restriction was placed on selection of full brothers and decreased when variance of the quantitative trait locus used in the evaluation model was overestimated.

Alleles↗

PubMed1997

Linkage of multilocus components of variance to polymorphic markers.

Haseman & Elston (1972) introduced a sib pair method using classical regression analysis to detect linkage between a polymorphic marker locus and any quantitative trait locus. Most of the diseases mapped to date follow simple Mendelian, single locus transmission. But there are many familial diseases that do not follow simple Mendelian segregation, for example diabetes, several forms of cancer, etc. In this paper, we extend Haseman and Elston's sib pair method to two unlinked quantitative trait loci each linked to one of two unlinked polymorphic marker loci. For the two-locus epistatic model, we give a general formulation of the complete regression model and details of the regression coefficients in terms of variance components.

Analysis of Variance↗

PubMed2004

Mapping quantitative trait loci affecting dairy conformation to chromosome 27 in two Holstein grandsire families.

Preliminary marker association results for quantitative trait loci affecting conformation traits using the granddaughter design and 8 large US Holstein grandsire families revealed strong associations in two families between the predicted transmitting abilities for dairy conformation and marker genotypes on bovine chromosome 27. Those results were based on single marker-trait associations in a genome-scan to identify broad chromosomal regions potentially containing genes affecting traits of interest. Results presented here describe continued study of quantitative trait loci on chromosome 27 for eventual incorporation into a marker-assisted selection program. Tests of marker associations for family 8 (91 sons) indicated an association with a microsatellite marker located near the telomere of chromosome 27. Interval analysis performed using additional marker genotypes generated for family 8 yielded further evidence for a quantitative trait locus in this region. No evidence was found for associations with milk production traits in this family in this region. An association was also detected in family 2 (240 sons) with a microsatellite marker located approximately 21 cM from the centromere of chromosome 27. Interval analysis performed for family 2 yielded evidence for a quantitative trait locus for dairy conformation near BMS689 with evidence of associations with fat percentage in the same region. Identification of quantitative trait loci affecting dairy conformation and fat components supports results reported by other groups, providing additional evidence that genes affecting fat metabolism are located on bovine chromosome 27.

Animals↗

PubMed1997

Host modifier genes affect mouse autoimmunity induced by the lpr gene.

A defect in apoptotic signal transmission through CD95 is an essential genetic mechanism for lymphoproliferation and autoimmunities in lpr or gld mice. However, disease manifestations are largely affected by the host genetic background. To identify and map such host genes modifying lpr gene effect, ie, the lpr modifier (Lprm) genes, 82 MRL/lpr x (MRL/lpr x C3H/lpr) F1 mice were subjected to immunopathological and genetical analyses. High-grade vasculitis and glomerulonephritis among backcross mice were observed in separate groups of mice. Microsatellite analysis revealed that there were two host genes affecting the occurrence of vasculitis, Lprm1 (chromosome 4) and Lprm2 (chromosome 3). A recessive MRL allele at Lprm1 enhanced vasculitis to occur in both sexes, whereas that of Lprm2 inhibited its development selectively in females. Genotype combinations of these two genes explained the severity of vasculitis in crosses of MRL/lpr and C3H/lpr mice and also the vasculitis-prone recombinant inbred strain McH5/lpr. A recessive MRL allele at Lprm3 (chromosome 14) suppressed glomerulonephritis. The weight of the spleen was increased by a recessive MRL allele at Lprm4 (chromosome 5) yielding a logarithm of odds score of 2.02 in a quantitative trait locus analysis. In contrast, the weight of axillary lymph nodes was increased by a recessive MRL allele at a locus on chromosome 2, but its presence was not supported by the quantitative trait locus analysis. The titer of anti-dsDNA autoantibody was controlled by the locus Lprm5 on chromosome 16, which had an logarithm of odds score of 3.41. Possible candidate genes for Lprm genes deduced from their map locations are discussed and compared with the autoimmunity genes reported thus far. In conclusion, autoimmune disease manifestations by the lpr mutation are affected by multiple host genes separately.

Animals↗

PubMed2000

Evidence for a gene influencing blood pressure on chromosome 17. Genome scan linkage results for longitudinal blood pressure phenotypes in subjects from the framingham heart study.

Hypertension is a leading cause of morbidity and mortality. Efforts to identify hypertension genes have focused on 3 approaches: mendelian disorders, candidate genes, and genome-wide scans. Thus far, these efforts have not identified genes that contribute substantively to overall blood pressure (BP) variation in the community. A 10-centiMorgan (cM) density genome-wide scan was performed in the largest families from 2 generations of Framingham Heart Study participants. Heritability and linkage for long-term mean systolic and diastolic BP phenotypes were analyzed by use of SOLAR software. Heritability estimates were based on BP measurements in 1593 families. Genotyping was performed on 1702 subjects from 332 large families, and BP data were available for 1585 (93%) genotyped subjects who contributed 12 588 longitudinal BP observations. The mean age was 47 years, and mean BP was 127/80 (systolic/diastolic) mm Hg. Long-term systolic and diastolic BP phenotypes had high heritability estimates, 0.57 and 0.56, respectively. For systolic BP, multipoint log-of-the-odds (LOD) scores >2.0 were located on chromosome 17 at 67 cM (LOD 4.7, P=0.0000016) and 94 cM (LOD 2.2). For diastolic BP, LOD scores >2.0 were identified on chromosome 17 (74 cM, LOD 2.1) and chromosome 18 (7 cM, LOD 2.1). Using a genome-wide scan, we found strong evidence for a BP quantitative trait locus on chromosome 17. Follow-up studies are warranted to identify the gene or genes in this quantitative trait locus that influence BP. Such knowledge could extend our understanding of the genetic basis of essential hypertension and have implications for the evaluation and treatment of patients with high BP.

Adolescent↗

PubMed2006

Experimental evidence for interspecific directional selection on moth pheromone communication.

The chemical composition of the sexual communication signals of female moths is thought to be under strong stabilizing selection, because females that produce atypical pheromone blends suffer lower success in finding mates. This intraspecific selection pressure cannot explain the high diversity of moth pheromone blends found in nature. We conducted experiments to determine whether communication interference from males of closely related species could exert strong enough directional selection to cause evolution of these signals. Attraction and mating success of Heliothis subflexa (Hs) females with a normal quantitative trait locus for production of acetate pheromone components (norm-OAc) were compared with Hs females with an introgressed quantitative trait locus from Heliothis virescens (Hv) that dramatically decreased the amount of acetate esters in their pheromone glands (low-OAc). In field experiments with natural Hv and Hs populations, 10 times more Hv males were captured in traps baited with live low-OAc Hs females than in traps with norm-OAc Hs females. This pattern was confirmed in mate-choice assays in cages. Hybrids resulting from Hv-Hs matings have effectively zero fitness in the field. Combining our results with the extensive data set gathered in the past 40 years on the reproductive biology of Hv, we can quantitatively estimate that the directional selection exerted by Hv males on Hs females to produce relatively high amounts (>5%) of acetates can range from 0.135 to 0.231. Such intense interspecific selection may counteract intraspecific stabilizing selection that impedes evolutionary changes in pheromone blends and could lead to diversification of sexual signals.

Animals↗

PubMed1999

Short communication: quantitative trait loci analysis on 17 nonproduction traits in the New Zealand dairy population.

Seven New Zealand Holstein-Friesian families and two Jersey families, a total of 274 sires, were analyzed in a granddaughter design for marker-quantitative trait loci associations. For 17 nonproduction traits (management, size, and conformation traits), an across-family analysis was undertaken using multimarker regression procedures. Threshold levels were set empirically by permuting the data. A quantitative trait locus for stature was identified on chromosome 14, which was significant at the 15% experimentwise level (suggestive linkage). The quantitative trait locus was identified to be segregating in three of the nine families.

Animals↗

PubMed2005

Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility.

Ath1 is a quantitative trait locus on mouse chromosome 1 that renders C57BL/6 mice susceptible and C3H/He mice resistant to diet-induced atherosclerosis. The quantitative trait locus region encompasses 11 known genes, including Tnfsf4 (also called Ox40l or Cd134l), which encodes OX40 ligand. Here we report that mice with targeted mutations of Tnfsf4 had significantly (P <or= 0.05) smaller atherosclerotic lesions than did control mice. In addition, mice overexpressing Tnfsf4 had significantly (P <or= 0.05) larger atherosclerotic lesions than did control mice. In two independent human populations, the less common allele of SNP rs3850641 in TNFSF4 was significantly more frequent (P <or= 0.05) in individuals with myocardial infarction than in controls. We therefore conclude that Tnfsf4 underlies Ath1 in mice and that polymorphisms in its human homolog TNFSF4 increase the risk of myocardial infarction in humans.

Aged↗

PubMed1998

Differential inspiratory timing is genetically linked to mouse chromosome 3.

Genetic control of differential inspiratory timing (TI) at baseline has been previously demonstrated among inbred mouse strains. The inheritance pattern for TI between C3H/HeJ (C3; 188 +/- 3 ms) and C57BL/6J (B6; 111 +/- 2 ms) progenitors was consistent with a two-gene model. By using the strain distribution pattern for recombinant inbred strains derived from C3 and B6 progenitors, 100% concordance was established between TI phenotypes and DNA markers on mouse chromosome 3. This genotype-phenotype hypothesis was tested by typing 52 B6C3F2 (F2) progeny by using simple sequence repeat DNA markers (n = 21) polymorphic between C3 and B6 strains on mouse chromosome 3. Linkage analysis compared marker genotypes to baseline ventilatory phenotypes by computing log-likelihood values. A putative quantitative trait locus located in proximity to D3Mit119 was significantly associated with baseline TI phenotypes. At the peak (log-likelihood = 3.3), the putative quantitative trait locus determined 25% of the phenotypic variance in TI among F2 progeny. In conclusion, this genetic model of ventilatory characteristics demonstrated an important linkage between differential baseline TI and a candidate genomic region on mouse chromosome 3.

Animals↗

PubMed2002

Serum- and glucocorticoid-regulated kinase (SGK1) gene and blood pressure.

The serum- and glucose-regulated kinase (SGK1) gene has recently been identified as an important aldosterone-induced protein kinase that mediates trafficking of the renal epithelial Na(+) channel (ENaC) to the cell membrane. Thus, SGK1 is an appealing candidate for blood pressure regulation and possibly essential hypertension. To test this hypothesis, we recruited monozygotic (126 pairs) and dizygotic (70 pairs) normotensive twin subjects and parents of dizygotic twins. Blood pressure was measured in a controlled fashion: recumbent, sitting, and upright. We documented genetic variance on blood pressure in all positions. We then relied on microsatellite markers at the SGK1 gene locus (D6S472, D6S1038, and D6S270) and 2 single nucleotide polymorphisms within the SGK1 gene. We found significant linkage of the SGK1 gene locus to diastolic blood pressure (P<0.0002) and suggestive evidence for linkage for systolic blood pressure (P<0.04), documenting the locus as a quantitative trait locus for blood pressure. We next performed association, using all dizygotic twins and a monozygotic member from each pair. We found significant associations between both single nucleotide polymorphism variants and blood pressure, as well as a significant interaction between the single nucleotide polymorphisms enhancing the effect. This combined effect of the polymorphisms was confirmed in an independent sample of 260 young normotensive men. We conclude that the SGK1 gene is relevant to blood pressure regulation and probably to hypertension in man.

Blood Pressure↗

PubMed2006

Gene by environment QTL mapping through multiple trait analyses in blood pressure salt-sensitivity: identification of a novel QTL in rat chromosome 5.

BACKGROUND: The genetic mechanisms underlying interindividual blood pressure variation reflect the complex interplay of both genetic and environmental variables. The current standard statistical methods for detecting genes involved in the regulation mechanisms of complex traits are based on univariate analysis. Few studies have focused on the search for and understanding of quantitative trait loci responsible for gene x environmental interactions or multiple trait analysis. Composite interval mapping has been extended to multiple traits and may be an interesting approach to such a problem. METHODS: We used multiple-trait analysis for quantitative trait locus mapping of loci having different effects on systolic blood pressure with NaCl exposure. Animals studied were 188 rats, the progenies of an F2 rat intercross between the hypertensive and normotensive strain, genotyped in 179 polymorphic markers across the rat genome. To accommodate the correlational structure from measurements taken in the same animals, we applied univariate and multivariate strategies for analyzing the data. RESULTS: We detected a new quantitative train locus on a region close to marker R589 in chromosome 5 of the rat genome, not previously identified through serial analysis of individual traits. In addition, we were able to justify analytically the parametric restrictions in terms of regression coefficients responsible for the gain in precision with the adopted analytical approach. CONCLUSION: Future work should focus on fine mapping and the identification of the causative variant responsible for this quantitative trait locus signal. The multivariable strategy might be valuable in the study of genetic determinants of interindividual variation of antihypertensive drug effectiveness.

Animals↗

PubMed1997

An index of information content for genotype probabilities derived from segregation analysis.

A genotype probability index (GPI) is proposed to indicate the information content of genotype probabilities derived from a segregation analysis. Typically, some individuals are genotyped at a marker locus or a quantitative trait locus, and segregation analysis is used to make genotype inferences about ungenotyped relatives. Genotype probabilities for a two-allele autosomal locus are plotted on a triangular surface. The GPI has a value of zero at the point corresponding to Hardy-Weinberg frequencies, and a value of 100% at the vertices of the triangle. Trigonometric functions are used to help calculate intermediate index values. It is proposed that such an index can be useful to help identify which ungenotyped individuals or loci should be genotyped to maximize the benefit/cost of genotyping operations.

Genotype↗

PubMed1993

Linkage between amylase-1 locus and a major gene for milk fat content in cattle.

Linkage between the amylase-1 (Am-1) locus and a quantitative trait locus influencing fat content in milk was studied in offspring from heterozygous sires of the Swedish Red and White dairy breed. The effect on bull breeding values for fat content was estimated as interactions between sire and paternal Am-1 allele using a model eliminating the direct effects of sire and Am-1 allele. There were strong indications of linkage, confirming results of previous studies. The interaction was caused by strong associations in 7 out of 14 site families. A test for within-family variance heterogeneity performed on the whole population of breeding bulls also supported the presence of a major gene for fat content in milk. The results indicate that there is genetic linkage between the Am-1 locus and a locus with large effect on milk fat content.

Amylases↗

PubMed2003

Population-wide analysis of a QTL affecting milk-fat production in the Israeli Holstein population.

A population-wide linkage disequilibrium on bovine chromosome 14 between microsatellite ILSTS039 and DGAT1, a putative quantitative trait locus affecting milk production traits, was found in the Israeli Holstein population. A total of 394 bulls were genotyped for both DGAT1 and ILSTS039, and 1747 cows were genotyped for ILSTS039. The ILSTS039 allele termed "225," and the DGAT1 K allele (substitution of a lysine residue with alanine), were associated with decreased milk production, and increased fat production and fat and protein percent. The number of 225 ILSTS039 and K DGAT1 alleles per individual were the same for 80% of the bulls genotyped. From the effects associated with cows homozygous for the 225 allele, the effect of the quantitative trait locus appears to be approximately codominant. The substitution effect was 0.16% fat. Genotype probabilities for the quantitative gene were determined for the entire Israeli Holstein milk-recorded population, including 507,725 cows and 1442 bulls, using segregation analysis. Overall frequency of the allele that increased fat percent was 8.9% in cows and 15.5% in bulls. The frequency of this allele decreased from 1981 until 1990, from 15 to 5%, and since has increased to 10%. The effects estimated on the population-wide analyses of both cows and bulls were similar to the effect associated with DGAT1 in the daughters of genotyped bulls. Modified animal model evaluations were computed for the entire population with the effect of this gene included in the model. The correlations between the modified and standard animal model evaluations for all traits were > 0.99.

Acyltransferases↗

PubMed1998

Genetics of experimental hypertension.

Experimental models of genetic hypertension are used to develop paradigms to study human essential hypertension while removing some of the complexity inherent in the study of human subjects. Since 1991 several quantitative trait loci responsible for blood pressure regulation have been identified in various rat crosses. More recently, a series of interesting quantitative trait loci influencing cardiac hypertrophy, stroke, metabolic syndrome and renal damage has also been described. It is recognized that the identification of large chromosomal regions containing a quantitative trait locus is only a first step towards gene identification. The next step is the production of congenic strains and substrains to confirm the existence of the quantitative trait locus and to narrow down the chromosomal region of interest. Several congenic strains have already been produced, with further refinement of the methodology currently in progress. The ultimate goal is to achieve positional cloning of the causal gene, a task which has so far been elusive. There are several areas of cross-fertilization between experimental and human genetics of hypertension, with a successful transfer of two loci directly from rats to humans and with new pharmacogenetic approaches which may be utilized in both experimental and clinical settings.

Animals↗

PubMed2001

fw2.2 directly affects the size of developing tomato fruit, with secondary effects on fruit number and photosynthate distribution.

fw2.2 is a quantitative trait locus responsible for approximately 30% of the difference in fruit size between large, domesticated tomatoes (Lycopersicon esculentum Mill.) and their small-fruited wild relatives. The gene underlying this quantitative trait locus was cloned recently and shown to be associated with altered cell division in ovaries (Frary et al., 2000). However, it was not known whether the change in fruit size is associated with other changes in plant morphology or overall fruit yield-changes that could potentially cause the fruit weight phenotype. To shed light on this issue, a detailed comparison was made between nearly isogenic lines differing for alleles at this locus to search for pleiotropic effects associated with fw2.2. Field observations show that although the small-fruited nearly isogenic line produced smaller ovaries and fruit as expected, this was compensated by a larger number of fruit-due mainly to a significantly greater number of inflorescences-but with no net change in total fruit mass yield. This strongly suggests that fw2.2 may have a pleiotropic effect on how the plant distributes photosynthate among fruit. In a flower removal experiment to control for differences in inflorescence size and number, fruit size remained significantly different between the nearly isogenic lines. These observations indicate that the primary effect of fw2.2 is in controlling ovary and fruit size, and that other associated phenotypic effects are secondary.

Alleles↗

PubMed2005

Quantitative trait analysis of the development of pulmonary tolerance to inhaled zinc oxide in mice.

BACKGROUND: Individuals may develop tolerance to the induction of adverse pulmonary effects following repeated exposures to inhaled toxicants. Previously, we demonstrated that genetic background plays an important role in the development of pulmonary tolerance to inhaled zinc oxide (ZnO) in inbred mouse strains, as assessed by polymorphonuclear leukocytes (PMNs), macrophages, and total protein in bronchoalveolar lavage (BAL) phenotypes. The BALB/cByJ (CBy) and DBA/2J (D2) strains were identified as tolerant and non-tolerant, respectively. The present study was designed to identify candidate genes that control the development of pulmonary tolerance to inhaled ZnO. METHODS: Genome-wide linkage analyses were performed on a CByD2F2 mouse cohort phenotyped for BAL protein, PMNs, and macrophages following 5 consecutive days of exposure to 1.0 mg/m3 inhaled ZnO for 3 hours/day. A haplotype analysis was carried out to determine the contribution of each quantitative trait locus (QTL) and QTL combination to the overall BAL protein phenotype. Candidate genes were identified within each QTL interval using the positional candidate gene approach. RESULTS: A significant quantitative trait locus (QTL) on chromosome 1, as well as suggestive QTLs on chromosomes 4 and 5, for the BAL protein phenotype, was established. Suggestive QTLs for the BAL PMN and macrophage phenotypes were also identified on chromosomes 1 and 5, respectively. Analysis of specific haplotypes supports the combined effect of three QTLs in the overall protein phenotype. Toll-like receptor 5 (Tlr5) was identified as an interesting candidate gene within the significant QTL for BAL protein on chromosome 1. Wild-derived Tlr5-mutant MOLF/Ei mice were tolerant to BAL protein following repeated ZnO exposure. CONCLUSION: Genetic background is an important influence in the acquisition of pulmonary tolerance to BAL protein, PMNs, and macrophages following ZnO exposure. Promising candidate genes exist within the identified QTL intervals that would be good targets for additional studies, including Tlr5. The implications of tolerance to health risks in humans are numerous, and this study furthers the understanding of gene-environment interactions that are likely to be important factors from person-to-person in regulating the development of pulmonary tolerance to inhaled toxicants.

Air Pollutants↗