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Results for “quantitative trait locus”

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PubMed2006

Fine mapping of the MAPT locus using quantitative trait analysis identifies possible causal variants in Alzheimer's disease.

In addition to senile plaques, neurofibrillary tangles are characteristic of Alzheimer's disease (AD) pathology, suggesting a clear involvement of the microtubule-associated protein tau (MAPT) in AD. Recent findings, suggesting that the H1c haplotype is associated with increased risk, now also implicate MAPT genetically. In this study, we aim to clarify this association by a fine mapping approach using both a traditional phenotypic association analysis and a quantitative trait (QT) analysis using cerebrospinal fluid (CSF) tau protein levels in the German population. Here, we report that both methodologies identify that the H1c haplotype may play important role in AD (AD risk, P=0.007, uncorrected; CSF tau levels, P=0.027, uncorrected). Further, the use of a sliding window approach in the QT analysis allowed for the narrowing down of the region where a probable causal variant may be located. The data suggest that this may lie at or within close proximity to the rs242557 single nucleotide polymorphism as association with CSF tau levels seems to be primarily driven by rs242557 in a gene dosage-dependent manner (trend model: P=0.002, uncorrected). These findings provide functional evidence to support the genetic association of MAPT with AD.

Aged↗

PubMed2005

Gene networks in hexaploid wheat: interacting quantitative trait loci for grain protein content.

In hexaploid wheat, single-locus and two-locus quantitative trait loci (QTL) analyses for grain protein content (GPC) were conducted using two different mapping populations (PI and PII). Main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL x environment interactions (QE, QQE) were detected using two-locus analyses in both the populations. Only a few QTLs were common in both the analyses, and the QTLs and the interactions detected in the two populations differed, suggesting the superiority of two-locus analysis and the need for using several mapping populations for QTL analysis. A sizable proportion of genetic variation for GPC was due to interactions (28.59% and 54.03%), rather than to M-QTL effects (7.24% and 7.22%), which are the only genetic effects often detected in the majority of QTL studies. Even E-QTLs made a marginal contribution to genetic variation (2.68% and 6.04%), thus suggesting that the major part of genetic variation is due to changes in gene networks rather than the presence or absence of specific genes. This is in sharp contrast to the genetic dissection of pre-harvest sprouting tolerance conducted by us earlier, where interaction effects were not substantial, suggesting that the nature of genetic variation also depends on the nature of the trait.

Plant Proteins↗

PubMed2005

A method for identifying genes related to a quantitative trait, incorporating multiple siblings and missing parents.

When studying either qualitative or quantitative traits, tests of association in the presence of linkage are necessary for fine-mapping. In a previous report, we suggested a polytomous logistic approach to testing linkage and association between a di-allelic marker and a quantitative trait locus, using genotyped triads, consisting of an individual whose quantitative trait has been measured and his or her two parents. Here we extend that approach to incorporate marker information from entire nuclear families. By computing a weighted score function instead of a maximum likelihood test, we allow for both an unspecified correlation structure between siblings and "informative" family size. Both this approach and our original approach allow for population admixture by conditioning on parental genotypes. The proposed method allows for missing parental genotype data through a multiple imputation procedure. We use simulations based on a population with admixture to compare our method to a popular non-parametric family-based association test (FBAT), testing the null of no association in the presence of linkage.

Alleles↗

PubMed2005

Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree.

Recent advances in genomics resources and tools are facilitating quantitative trait locus mapping. We developed a crossbreed pedigree for mapping quantitative trait loci for hip dysplasia in dogs by crossing dysplastic Labrador Retrievers and normal Greyhounds. We show that one advantage to using a crossbreed pedigree is the increased marker informativeness in the backcross/F2 population relative to the founder populations. We also discuss three factors that affect the detection power in the context of this crossbreed pedigree: being able to detect and correct genotyping errors, increasing marker density for chromosomes with a sparse coverage, and adding individuals to the mapping population as soon as they become available.

Alleles↗

PubMed2003

Combining quantitative trait Loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit.

Ecophysiological models predict quantitative traits of one genotype in any environment, whereas quantitative trait locus (QTL) models predict the contribution of alleles to quantitative traits under a limited number of environments. We have combined both approaches by dissecting into effects of QTLs the parameters of a model of maize (Zea mays) leaf elongation rate (LER; H. Ben Haj Salah, F. Tardieu [1997] Plant Physiol 114: 893-900). Response curves of LER to meristem temperature, water vapor pressure difference, and soil water status were established in 100 recombinant inbred lines (RILs) of maize in six experiments carried out in the field or in the greenhouse. All responses were linear and common to different experiments, consistent with the model. A QTL analysis was carried out on the slopes of these responses by composite interval mapping confirmed by bootstrap analysis. Most QTLs were specific of one response only. QTLs of abscisic acid concentration in the xylem sap colocalized with QTLs of response to soil water deficit and conferred a low response. Each parameter of the ecophysiological model was computed as the sum of QTL effects, allowing calculation of parameters for 11 new RILs and two parental lines. LERs were simulated and compared with measurements in a growth chamber experiment. The combined model accounted for 74% of the variability of LER, suggesting that it has a general value for any RIL under any environment.

Abscisic Acid↗

PubMed2002

Evidence of genetic interaction between the beta-globin complex and chromosome 8q in the expression of fetal hemoglobin.

During human development, the switch from fetal to adult hemoglobin (Hb) is not complete with the residual gamma-globin expression being restricted to a subset of erythrocytes termed "F cells" (FC). Statistical analyses have shown the FC trait to be influenced by a common sequence variant (C-->T) at position -158 upstream of the Ggamma-globin gene, termed the "XmnI-Ggamma polymorphism." The XmnI-Ggamma site is believed to be involved in the expression of the Ggamma-globin gene through interaction with transcription factors, and polymorphisms in the transcription factors could be influencing fetal Hb expression, conditional on the XmnI-Ggamma site. Using a two-locus model, in which the second locus was the known quantitative-trait locus (QTL) at the XmnI-Ggamma site, we showed suggestive linkage to chromosome 8q. A maximum single-point LOD score of 4.33 and a multipoint LOD score of 4.75 were found in a 15-20 cM region of chromosome 8q. A single-locus analysis failed to show linkage of FC to the region when the XmnI-Ggamma site was accounted for by removing its effects from the data or including it as a covariate. Results of the single-locus analysis were significant when the effects of the XmnI-Ggamma site were not accounted for in any way. The results of analysis in a large Indian kindred indicate that there is an interaction between the XmnI-Ggamma site and a QTL on chromosome 8q that is influencing the production of fetal Hb.

Chromosome Mapping↗

PubMed2006

Angiogenesis and capillary maturation phenotypes associated with the Edpm3 locus on rat chromosome 3.

The quantitative trait locus (QTL) Edpm3 is one of a group of additively acting QTL \responsible for the difference in estrogen-induced pituitary tumor growth between the tumor-susceptible F344 and tumor-resistant BN rat strains. The F344.BN-Edpm3(BN) rat strain was produced by moving the segment of rat Chr 3 between D3Mgh7 and D3Mgh13, which contains the Edpm3 QTL, from the BN strain into the F344 genetic background. In a previous study, we used this congenic line to find that the BN allele of the Edpm3 QTL reduces tissue mass and S-phase fraction in the estrogen-induced rat pituitary tumor. We now report on the use of this congenic line to investigate the linkage of Edpm3 to tumor angiogenesis. Contrary to expectation, the F344.BN-Edpm3(BN) strain has significantly greater angiogenic activity than does F344 in both treated and untreated rats. Microvessel count (MVC), perivascular space, and number of nonattached pericytes/pericapillary fibroblasts are all elevated in the pituitary by chronic estrogen treatment and their values are significantly greater in F344.BN-Edpm3(BN) than F344. Thus, although there is greater angiogenic activity in the pituitary of estrogen-treated F344.BN-Edpm3(BN) rats, there is a deficiency in capillary maturation compared with F344.

Animals↗

PubMed2003

Molecular dissection of a dormancy QTL region near the chromosome 7 (5H) L telomere in barley.

Moderate seed dormancy is desirable in barley (Hordeum vulgare L.). It is difficult for breeders to manipulate seed dormancy in practical breeding programs because of complex inheritance and large environmental effects. Quantitative trait locus (QTL) mapping opens a way for breeders to manipulate quantitative trait genes. A seed dormancy QTL, SD2, was mapped previously in an 8-cM interval near the chromosome 7 (5H) L telomere from a cross of 'Steptoe' (dormant)/'Morex' (non-dormant) by the North American Barley Genome Project using an interval mapping method and a relatively low-resolution genetic map. SD2 has a moderate dormancy effect, which makes it a promising candidate gene for moderate seed dormancy in barley cultivar development. The fine mapping of SD2 is required for efficient manipulation of SD2 in breeding and would facilitate the study of dormancy in barley. Ten different Morex isolines were generated, including regenerated Morex, of which nine lines had duplicates. The isolines together with Steptoe and Morex were grown in growth room and field environments for 2 years (2000 and 2001). In the growth room, relatively low growing temperatures (25 degrees C day/15 degrees C night) were employed to promote seed dormancy development. Seed germination percentage, determined at different post-harvest after-ripening periods, was used to measure seed dormancy. Fine mapping using the substitution mapping method based on differences among isolines resolved the SD2 QTL into an 0.8-cM interval between molecular markers MWG851D and MWG851B near the chromosome 7 (5H) L telomere. Relatively low temperatures (< or =25 degrees C) during seed development promoted the expression of the SD2 dormancy QTL. The chromosome region above the MWG851D-MWG851B interval might play a role in reducing barley seed dormancy during after-ripening.

Chromosome Mapping↗

PubMed2001

Detection of closely linked multiple quantitative trait loci using a genetic algorithm.

The existence of a quantitative trait locus (QTL) is usually tested using the likelihood of the quantitative trait on the basis of phenotypic character data plus the recombination fraction between QTL and flanking markers. When doing this, the likelihood is calculated for all possible locations on the linkage map. When multiple QTL are suspected close by, it is impractical to calculate the likelihood for all possible combinations of numbers and locations of QTL. Here, we propose a genetic algorithm (GA) for the heuristic solution of this problem. GA can globally search the optimum by improving the "genotype" with alterations called "recombination" and "mutation." The "genotype" of our GA is the number and location of QTL. The "fitness" is a function based on the likelihood plus Akaike's information criterion (AIC), which helps avoid false-positive QTL. A simulation study comparing the new method with existing QTL mapping packages shows the advantage of the new GA. The GA reliably distinguishes multiple QTL located in a single marker interval.

Algorithms↗

PubMed1989

Identifying pedigrees segregating at a major locus for a quantitative trait: an efficient strategy for linkage analysis.

Having found evidence for segregation at a major locus for a quantitative trait, a logical next step is to identify those pedigrees in which major-locus segregation is occurring. If the quantitative trait is a risk factor for an associated disease, identifying such segregating pedigrees can be important in classifying families by etiology, in risk assessment, and in suggesting treatment modalities. Identifying segregating pedigrees can also be helpful in selecting pedigrees to include in a subsequent linkage study to map the major locus. Here, we describe a strategy to identify pedigrees segregating at a major locus for a quantitative trait. We apply this pedigree selection strategy to simulated data generated under a major-locus or mixed model with a rare dominant allele and sampled according to one of several fixed-structure or sequential sampling designs. We demonstrate that for the situations considered, the pedigree selection strategy is sensitive and specific and that a linkage study based only on the pedigrees classified as segregating extracts essentially all the linkage information in the entire sample of pedigrees. Our results suggest that for large-scale linkage studies involving many genetic markers, the savings from this strategy can be substantial and that, compared with fixed-structure sampling, sequential sampling of pedigrees can greatly improve the efficiency for linkage analysis of a quantitative trait.

Genetic Linkage↗

PubMed1994

Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs.

Tuber shape in potato is commonly regarded as displaying continuous variation, yet at the diploid level phenotypes can be discerned visually, having round or long tubers. Inheritance of qualitative tuber shape can be explained by a single locus Ro, round being dominant to long. With restriction fragment length polymorphisms (RFLPs) the Ro locus was mapped on chromosome 10. Tuber shape was also studied as a quantitative trait, using the length/width ratio as trait value. The estimated broad sense heritability was h2 = 0.80. The morphologically mapped Ro locus explained 75% of the genetic variation, indicating the presence of a major quantitative trait locus (QTL) at the Ro locus and minor genetic factors. RFLP alleles linked with Ro alleles were used to divide the progeny into four genotypic classes: RofemaleRomale:Rofemalero:roRomale:roro = 1:1:1:1. The recessive ro allele is identical by descent in both parents. The significantly different effects (P = 0.0157) of the non-identical alleles Rofemale and Romale provided evidence for multiallelism at the Ro locus. Linkage mapping of the Ro locus was compared with QTL mapping. Only those markers which are polymorphic in both parents allow accurate QTL mapping when genetic factors segregate from both parents. This finding applies to QTL mapping in all outbreeders without homozygous inbred strains.

Alleles↗

PubMed1998

In search of hypertension genes in Dahl salt-sensitive rats.

Quantitative trait loci in Dahl rats Genetic and crude physical mapping have yielded chromosome regions containing quantitative trait loci for blood pressure in Dahl salt-sensitive rats. So far, the molecular identities of these loci are largely unknown. Intriguing still is how these quantitative trait loci would interact with each other to achieve an overall blood pressure effect Alleles of some loci previously identified as blood pressure quantitative trait loci in other rat strains appear to be the same between Dahl salt-sensitive and salt-resistant rats. Why do Dahl salt-resistant rats have low blood pressure whereas Dahl salt-sensitive rats develop high blood pressure? Recent findings With the use of congenic strains and 'double' congenics, these issues have begun to unravel. Certain quantitative trait loci exert major blood pressure effects (>20 mmHg) and each of them can be dissected as a monogenic trait Some appear to be located close to each other in the same chromosome region. Different quantitative trait loci interact epistatically to produce their combined blood pressure effects. 'Low' blood pressure alleles of one quantitative trait locus can compensate for the 'high' blood pressure alleles of other quantitative trait loci in the Dahl salt-resistant rat By integrating fine mapping and positional cloning strategies, blood pressure quantitative trait loci are being elucidated. Work in the rat may also facilitate genetic mapping of quantitative trait loci in humans.

Animals↗

PubMed2001

Phenotyping of individual pancreatic islets locates genetic defects in stimulus secretion coupling to Niddm1i within the major diabetes locus in GK rats.

The major diabetes quantitative trait locus (Niddm1), which segregates in crosses between GK rats affected with spontaneous type 2-like diabetes and normoglycemic F344 rats, encodes at least two different diabetes susceptibility genes. Congenic strains for the two subloci (Niddm1f and Niddm1i) have been generated by transfer of GK alleles onto the genome of F344 rats. Whereas the Niddm1f phenotype implicated insulin resistance, the Niddm1i phenotype displayed diabetes related to insulin deficiency. Individual islets from 16-week-old congenic rats were characterized for insulin release and oxygen tension (pO(2)). In the presence of 3 mmol/l glucose, insulin release from Niddm1f and Niddm1i islets was approximately 5 pmol. g(-1). s(-1) and pO(2) was 120 mmHg. Similar recordings were obtained from GK and F344 islets. When glucose was raised to 11 mmol/l, insulin release increased significantly in Niddm1f and F344 islets but was essentially unchanged in islets from GK and Niddm1i. The high glucose concentration lowered pO(2) to the same extent in islets from all strains. Addition of 1 mmol/l tolbutamide to the perifusion medium further increased pulsatile insulin release threefold in all islets. The pulse frequency was approximately 0.4 min(-1). alpha-Ketoisocaproate (11 mmol/l) alone increased pulsatile insulin release eightfold in islets from Niddm1f, Niddm1i, and control F344 rats but had no effect on insulin release from GK islets. These secretory patterns in response to alpha-ketoisocaproate were paralleled by reduction of pO(2) in Niddm1f, Niddm1i, and control F344 islets and no change of pO(2) in GK islets. The results demonstrate that Niddm1i carries alleles of gene(s) that reduce glucose-induced insulin release and that are amenable to molecular identification by genetic fine mapping.

Alleles↗

PubMed2026

Multi-Ancestry Genome-Wide Association with Fine-Mapping Identifies Novel Loci for Pigment Dispersion Syndrome and Pigmentary Glaucoma.

PURPOSE: Pigment dispersion syndrome and pigmentary glaucoma are important causes of ocular hypertension and glaucomatous optic neuropathy, yet their genetic determinants remain incompletely defined, particularly across diverse ancestries. This study aimed to use a large multi-ancestry cohort from the All of Us Research Program to investigate the genetic basis of pigment dispersion syndrome and pigmentary glaucoma. DESIGN: Case-control study. PARTICIPANTS: In total, 572 cases and 37 808 controls with array genotyping and 537 cases and 35 493 controls with whole-genome sequencing. METHODS: Using electronic health record phenotyping in the All of Us Research Program, we performed multi-ancestry genome-wide association analyses using both array-based data and whole-genome sequencing-based data, comparing patients with pigment dispersion syndrome or pigmentary glaucoma to those without either condition. We also performed Firth penalized regression and Fisher analyses, and we performed principal component analyses to assess effect sizes across genetic ancestries. We applied statistical fine-mapping, examined for cross-trait overlap, and assessed expression quantitative trait locus associations for lead variants. MAIN OUTCOME MEASURES: P values and odds ratios of lead loci from genome-wide association analyses; size of credible sets determined from fine-mapping; allele frequency of lead variants in cases, controls, and the general population; expression quantitative trait loci effect size and P values linking lead variants to gene expression. RESULTS: We identified 4 loci reaching genome-wide significance across analyses, including signals near EPHA7 (which mediates cell-cell signaling), within TYR (involved in melanin synthesis and replicated from prior studies), within LINC01138, and near OTX2. Statistical fine-mapping refined 3 of these loci to single-variant 95% credible sets and narrowed the TYR locus to small credible sets, prioritizing possible causal variants. Effect estimates were broadly consistent across genetic ancestry clusters. Lead variants showed regulatory evidence in expression quantitative trait locus, including reduced EPHA7 expression. CONCLUSIONS: These findings implicate both melanogenesis and cell-cell adhesion and signaling pathways in pigment dispersion syndrome and pigmentary glaucoma. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Genome-wide association study↗

PubMed2003

A maize QTL for silk maysin levels contains duplicated Myb-homologous genes which jointly regulate flavone biosynthesis.

The maize p1 locus coincides with a major QTL (quantitative trait locus) determining levels of maysin, a C-glycosyl flavone that deters feeding by corn ear-worm. The p1 gene is tightly linked with a second gene, p2, and both genes encode similar Myb-domain proteins. We show here that maize cell cultures transformed with either the p1 or p2 genes expressed under a constitutive promoter accumulate transcripts for flavonoid biosynthetic genes, and synthesize phenylpropanoids and C-glycosyl flavones related to maysin. Additionally, maize plants that are deleted for the p1 gene have reduced maysin levels and moderate silk-browning reaction, whereas plants with a deletion of both p1 and p2 have non-detectable silk maysin and non-browning silks. We conclude that both p1 and p2 induce maysin biosynthesis in silk, although the two genes differ in their expression and pigmentation effects in other tissues. These results show that a QTL for flavone biosynthesis actually comprises two tightly linked genes with related functions.

Flavones↗

PubMed2004

Quantitative trait loci affecting natural variation in Drosophila longevity.

Limited life span and senescence are universal phenomena, controlled by genetic and environmental factors whose interactions both limit life span and generate variation in life span between individuals, populations and species. To understand the genetic architecture of longevity it is necessary to know what loci affect variation in life span, what are the allelic effects at these loci and what molecular polymorphisms define quantitative trait locus (QTL) alleles. Here, we used quantitative complementation tests to determine whether genes that regulate longevity also contribute to naturally occurring variation in Drosophila life span. Inbred strains derived from a natural population were crossed to stocks containing null mutations (m) or deficiencies (Df) uncovering the candidate genes, maintained over a Balancer (Bal) chromosome. We measured the life span of the resulting F(1) genotypes, +(i)/m (Df) and +(i)/Bal, where +(i) denotes one of the i natural alleles. Failure of the QTL alleles to complement the candidate gene mutation is indicated by a significant cross (mutant versus wild-type allele of the candidate gene) by inbred line interaction term from analysis of variance of life span. Failure to complement indicates a genetic interaction between the candidate gene allele and the naturally occurring life span QTL, and implicates the candidate gene as potential cause of variation in longevity. Of the 16 candidate regions and genes tested, Df(2L)c17, Df(3L)Ly, Df(3L)AC1 and Df(3R)e-BS2 showed significant failure to complement wild-type alleles in both sexes, and an Alcohol dehydrogenase mutant failed to complement in females. Several genes that regulate life span (e.g., Superoxide dismutase, Catalase, and rosy) complemented the life span effects of wild-derived alleles, suggesting little natural variation affecting longevity at these loci, at least in this sample of alleles. Quantitative complementation tests are therefore useful for identifying QTL contributing to segregating genetic variation in life span in nature.

Aging↗

PubMed2004

Fine mapping of a malting-quality QTL complex near the chromosome 4H S telomere in barley.

Malting quality has long been an active objective in barley (Hordeum vulgare L.) breeding programs.However, it is difficult for breeders to manipulate malting-quality traits because of inheritance complexity and difficulty in evaluation of these quantitative traits. Quantitative trait locus (QTL) mapping provides breeders a promising basis with which to manipulate quantitative trait genes. A malting-quality QTL complex, QTL2, was mapped previously to a 30-cM interval in the short-arm telomere region of barley chromosome 4H in a "Step-toe"/"Morex" doubled haploid population by the North American Barley Genome Project, using an interval mapping method with a relatively low-resolution genetic map. The QTL2 complex has moderate effects on several malting-quality traits, including malt extract percentage(ME), a-amylase activity (AA), diastatic power (DP), malt 13-glucan content (BG), and seed dormancy, which makes it a promising candidate gene source in malting barley-cultivar development. Fine mapping QTL2 is desirable for precisely studying barley malting-quality trait inheritance and for efficiently manipulating QTL2 in breeding. A reciprocal-substitution mapping method was employed to fine map QTL2. Molecular marker-assisted backcrossing was used to facilitate the generation of isolines. Fourteen different types of "Steptoe" isolines, including regenerated "Steptoe" and 13 different types of "Morex" isolines,including regenerated "Morex", were made within a 41.5-cM interval between MWG634 and BCD265B on chromosome 4H. Duplicates were identified for 12 "Steptoe" and 12 "Morex" isoline types. The isolines together with "Steptoe" and "Morex" were grown variously at three locations in 2 years for a total of five field environments.Four malting-quality traits were measured: ME, DP, AA,and BG. Few significant differences were found between duplicate isolines for these traits. A total of 15 putative QTLs were mapped; three for ME, four for DP, six for AA,and two for BG. Background genotype seemed to make a difference in expression/detection of QTLs. Of the 15 QTLs identified, ten were from the "Morex" and only five from the "Steptoe" background. By combining the results from different years, field environments, and genetic backgrounds and taking into account overlapping QTLsegments, six QTLs can be conservatively estimated: two each for ME and AA and one each for DP and BG with chromosome segments ranging from 0.7 cM to 27.9 cM. A segment of 15.8 cM from the telomere (MWG634-CDO669) includes all or a portion of all QTLs identified. Further study and marker-assisted breeding should focus on this 15.8-cM chromosome region.

Breeding↗

PubMed1994

Mapping quantitative trait loci for ethanol-induced anesthesia in LSxSS recombinant inbred and F2 mice: methodology and results.

QTL (quantitative trait locus) mapping is an exciting new technique currently being applied to many quantitative traits. We review the animal models and molecular genetic techniques of QTL mapping with particular reference to ethanol-induced anesthesia (sleep time). Sleep time is an easily obtained measure of initial sensitivity to ethanol. We are using three-stage strategy to map QTLs causing the difference in sleep time between selected strains of mice. This project has been expedited by the use of polymorphic genetic markers (simple sequence repeats) which are amplifiable by the polymerase chain reaction. Over 115 strain distribution patterns have been characterized in the 27 LSxSS recombinant inbred strains. Provisional QTLs have been identified in the RI strains and will be confirmed or rejected in an F2 population of 1063 mice. A new statistical technique, interval mapping, allows the use of all polymorphic markers simultaneously to locate QTLs.

Anesthesia↗