SEARCH · PubMed Health

Results for “QTL mapping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29Linked to original sources

PubMed2004

An efficient resampling method for assessing genome-wide statistical significance in mapping quantitative trait Loci.

Assessing genome-wide statistical significance is an important and difficult problem in multipoint linkage analysis. Due to multiple tests on the same genome, the usual pointwise significance level based on the chi-square approximation is inappropriate. Permutation is widely used to determine genome-wide significance. Theoretical approximations are available for simple experimental crosses. In this article, we propose a resampling procedure to assess the significance of genome-wide QTL mapping for experimental crosses. The proposed method is computationally much less intensive than the permutation procedure (in the order of 10(2) or higher) and is applicable to complex breeding designs and sophisticated genetic models that cannot be handled by the permutation and theoretical methods. The usefulness of the proposed method is demonstrated through simulation studies and an application to a Drosophila backcross.

Animals↗

PubMed2003

Quantitative trait loci analysis of water and anion contents in interaction with nitrogen availability in Arabidopsis thaliana.

In plants, water and anion parameters are linked, for example through the integration of nutritional signaling and the response to diverse stress. In this work, Arabidopsis thaliana is used as a model system to dissect the genetic variation of these parameters by quantitative trait loci (QTL) mapping in the 415 recombinant inbred lines of the Bay-0 x Shahdara population. Water, nitrate, chloride, and phosphate contents were measured at the vegetative stage in the shoots of plants grown in controlled conditions. Two contrasting nitrogen (N) conditions were studied, one leading to the complete depletion of the nitrate pool in the plants. Most of the observed genetic variation was identified as QTL, with medium but also large phenotypic contributions. QTL colocalization provides a genetic basis for the correlation between water and nitrate contents in nonlimiting N conditions and water and chloride contents in limiting N conditions. The 34 new QTL described here represent at least 19 loci polymorphic between Bay-0 and Shahdara; some may correspond to known genes from water/anion transport systems, while others clearly identify new genes controlling or interacting with water/anion absorption and accumulation. Interestingly, flowering-time genes probably play a role in the regulation of water content in our conditions.

Anions↗

PubMed2002

Mapping of quantitative trait loci for body weight at three, six, and nine weeks of age in a broiler layer cross.

An F2 chicken population was established from a cross of a broiler sire-line and an egg laying (White Leghorn) line. There were two males and two females from both lines in the base population. The F1 progeny consisted of 8 males and 32 females. Over 500 F2 offspring from five hatches were reared to slaughter at a live weight of 2 kg at 9 wk of age. Body weights at 3, 6, and 9 wk were recorded. The DNA was extracted from blood samples, and genotypes for 101 microsatellite markers were determined. Data of 466 individuals from 30 families were available for analysis. Interval mapping QTL analyses were carried out. The QTL significant at the genome wide level that affected body weight at two ages were identified on chromosomes 1, 2, 4, 7, and 8 and a QTL on Chromosome 13 influenced body weight at all three ages. Genetic effects were generally additive, and the broiler allele increased body weight in all cases. The effects for significant individual QTL accounted for between 0.2 and 1.0 phenotypic standard deviations and the sum of the additive effects accounted for approximately 0.75 of the line difference in body weight at 6 wk of age. The largest single additive effect was on chromosome 4, and the effect of substituting one copy of the gene was an increase in weight of 249 g. Interactions of the QTL with sex or family were unimportant. There was no evidence for imprinting or of two or more QTL at the same location for any of the traits.

Aging↗

PubMed2005

Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.).

This paper aims at providing reliable and cost effective genotyping conditions, level of polymorphism in a range of genotypes and map position of newly developed microsatellite markers in order to promote broad application of these markers as a common set for genetic studies in pea. Optimal PCR conditions were determined for 340 microsatellite markers based on amplification in eight genotypes. Levels of polymorphism were determined for 309 of these markers. Compared to data obtained for other species, levels of polymorphism detected in a panel of eight genotypes were high with a mean number of 3.8 alleles per polymorphic locus and an average PIC value of 0.62, indicating that pea represents a rather polymorphic autogamous species. One of our main objectives was to locate a maximum number of microsatellite markers on the pea genetic map. Data obtained from three different crosses were used to build a composite genetic map of 1,430 cM (Haldane) comprising 239 microsatellite markers. These include 216 anonymous SSRs developed from enriched genomic libraries and 13 SSRs located in genes. The markers are quite evenly distributed throughout the seven linkage groups of the map, with 85% of intervals between the adjacent SSR markers being smaller than 10 cM. There was a good conservation of marker order and linkage group assignment across the three populations. In conclusion, we hope this report will promote wide application of these markers and will allow information obtained by different laboratories worldwide in diverse fields of pea genetics, such as QTL mapping studies and genetic resource surveys, to be easily aligned.

Chromosome Mapping↗

PubMed2001

QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane.

QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31 different probes were found in two interspecific F(1) populations. Most QTL alleles showed phenotypic effects consistent with the parental phenotypes, but occasional transgressive QTLs revealed opportunities to purge unfavorable alleles from cultivars or introgress valuable alleles from exotics. Several QTLs on homologous chromosomes appeared to correspond to one another-multiple doses of favorable 'alleles' at such chromosomal region(s) yielded diminishing returns-such negative epistasis may contribute to phenotypic buffering. Fewer sugar content QTLs were discovered from the highest-sugar genotype than from lower-sugar genotypes, perhaps suggesting that many favorable alleles have been fixed by prior selection, i.e. that the genes for which allelic variants (QTLs) persist in improved sugarcanes may be a biased subset of the population of genes controlling sugar content. Comparison of these data to mutations and QTLs previously mapped in maize hinted that seed and biomass crops may share a partly-overlapping basis for genetic variation in carbohydrate deposition. However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues.

Alleles↗

PubMed2004

Identification of QTLs for weight and cross-sectional area on cervical enlargement of spinal cord in mice.

Two inbred strains of mice, A/J, C57BL/6J and F2 intercross progenies,were used for QTL mapping for weight and cross-sectional area on cervical enlargement of spinal cord in mice. 13 QTLs located on Chromosome 2, 4, 8, 14, 15, 17, 18, 19 and X, respectively, for these two traits were found. Six QTLs were responsible for the cord weight, four for the cross-sectional area and three for both. Among 13 QTLs, three QTLs (P < 0.01) termed SC1 (located near D15Mit158) ,SC2 (DXMit140) and SC3 (DXMit64) accounted for 24%, 19% and 15% of the total variance in weight phenotype, and -3.78, 3.41 and 2.06 mg additive effect, respectively. The P value of other QTLs is between 0.01 and 0.05. SC1 is only one QTL that responsible for both weight and cross-sectional area in three QTLs above. This study revealed the location of major QTLs related size of spinal cord in mice, and may be helpful in fine mapping and ultimate identification of candidate genes.

Animals↗

PubMed2003

A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae).

Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5' end of the repeats.

Animals↗

PubMed1997

Identification of a sex-specific quantitative trait locus mediating nonopioid stress-induced analgesia in female mice.

It is increasingly appreciated that the sexes differ in their perception of noxious stimuli and in their responsivity to exogenous and endogenous analgesic manipulations. We previously reported the existence of qualitative sex differences in the neurochemical mediation of nonopioid (i.e., naloxone-insensitive) stress-induced analgesia (SIA) produced by forced swims and suggested that female mice possess a sex-specific SIA mechanism. This female-specific system is now known to be estrogen-dependent, to be ontogenetically organized, and to vary with reproductive status; however, its neurochemical identity remains obscure. In an attempt to identify candidate genes underlying SIA in both sexes, we performed a two-phase quantitative trait locus (QTL) mapping experiment using the BXD/Ty recombinant inbred (RI) set derived from DBA/2J (D2) and C57BL/6J (B6) inbred mouse strains and (B6xD2)F2 hybrid mice derived from these same progenitors. All mice were subjected to 3 min forced swims in 15 degrees C water; nociceptive sensitivity on the 54 degrees C hot-plate assay was assessed immediately before and 2 min after cessation of the swim. We report the localization of a QTL statistically associated with SIA magnitude [p = 0.00000012; logarithm of the odds (LOD) = 6.1] in female mice only. This female-specific QTL, which we name Fsia1, is located on chromosome 8 at 52-84 cM from the centromere and accounts for 17-26% of the overall trait variance in this sex. The present data provide further evidence of the existence of a female-specific SIA mechanism and highlight the important role of both genetic background and gender in the inhibition of pain.

Animals↗

PubMed2003

A major gene locus links early onset albuminuria with renal interstitial fibrosis in the MWF rat with polygenetic albuminuria.

The development of renal interstitial fibrosis (RIF) represents an important step in the progression of chronic proteinuric nephropathies. The Munich Wistar Frömter (MWF) rat represents a valuable model to study the progression in proteinuric renal disease. MWF animals demonstrate a significant increase of urinary albumin excretion (UAE) and RIF compared with the spontaneously hypertensive rat (SHR) with low UAE. The aim of this study was to analyze the genetic basis and the relation between UAE and RIF by genetic linkage and quantitative trait loci (QTL) mapping analysis. The authors generated a backcross population between MWF and SHR including 215 male animals. UAE was determined in young backcross animals at 8 wk, and at 14 and 24 wk of age, respectively. RIF was evaluated by Sirius red staining of kidney sections and quantified by computer-assisted image analysis at 24 wk. Total genome scan analysis identified in total eight QTL linked to UAE and a major locus on chromosome 6. At this locus, homozygosity for the MWF allele exhibited a strong effect on UAE levels (threefold elevation) and displayed significant linkage already at 8 wk (logarithm of odds [LOD] = 4.3) with increasing significance at 14 and 24 wk (LOD = 7.8 and 10.1, respectively). In addition, this was the only QTL that was linked to the amount of RIF (P = 0.0009, LOD = 2.4). These data establish a genetic link between early onset albuminuria and progression of RIF at the QTL on RNO6. This study demonstrates the power of genetic linkage analysis for the dissection of physiologic pathways involved in renal disease progression.

Albuminuria↗

PubMed2003

Mapping blood pressure loci in (A/J x B6)F2 mice.

Although the genetics of rare, monogenic, forms of human hypertension are fairly well defined, the genetics of the common polygenic form of human essential hypertension is only emerging. With the ability to control environmental variables, animal models have provided valuable tools with which to study blood pressure (BP) homeostasis. We have now studied BP genetics in a model consisting of 1,521 F2 mice from a series of (A/J x B6) intercrosses kept under standardized conditions. Using whole genome quantitative trait loci (QTL) mapping, we have identified four novel significant BP loci. These included Abbp1 on mouse chromosome MMU1 [maximum LOD score (MLS) at approximately 35 cM = 6.8], Abbp2 on MMU4 (MLS at approximately 25 cM = 9.8), Abbp3 on MMU7 (MLS at approximately 25 cM = 5.4), and Abbp4 on MMU11 (MLS at approximately 58 cM = 6.3). Compared with A/J homozygotes, homozygosity for the B6 alleles of Abbp1, Abbp2, or Abbp4 is independently associated with a 7-12 mmHg increase in BP. In contrast Abbp3 interacts epistatically with a locus on MMU17 (near D17Mit180) to modulate BPs in female (A/J x B6)F2 mice. Interestingly, Abbp4 on MMU11 is homologous to a major confirmed BP locus, BP1, on rat chromosome 10 and to a major confirmed BP locus, HYT1, on human chromosome 17. Defining the molecular differences between the A/J and the B6 alleles at these novel loci with major influences on the BP phenotype will contribute to our understanding of the complex genetics of BP control.

Animals↗

PubMed2005

Inferring gene transcriptional modulatory relations: a genetical genomics approach.

Bayesian network modeling is a promising approach to define and evaluate gene expression circuits in diverse tissues and cell types under different experimental conditions. The power and practicality of this approach can be improved by restricting the number of potential interactions among genes and by defining causal relations before evaluating posterior probabilities for billions of networks. A newly developed genetical genomics method that combines transcriptome profiling with complex trait analysis now provides strong constraints on network architecture. This method detects those chromosomal intervals responsible for differences in mRNA expression using quantitative trait locus (QTL) mapping. We have developed an efficient Bayesian approach that exploits the genetical genomics method to focus computational effort on the most plausible gene modulatory networks. We exploit a dense marker map for a genetic reference population (GRP) that consists of 32 BXD strains of mice made by intercrossing two progenitor strains--C57BL/6J and DBA/2J. These progenitors differ at approximately 1.3 million known single nucleotide polymorphisms (SNPs), all of which can be exploited to estimate the probability that a gene contains functional polymorphisms that segregate within the GRP. We constructed 66 candidate networks that include all the candidate modulator genes located in the 209 statistically significant trans-acting QTL regions. SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data.

Algorithms↗

PubMed2002

Genetic dissection of increased urinary albumin excretion in the munich wistar frömter rat.

An elevated urinary albumin excretion (UAE) is a risk factor for the development of chronic nephropathy and for cardiovascular mortality. The Munich Wistar Frömter (MWF) rat represents a genetic model that develops spontaneously mild hypertension and a 142-fold increased UAE compared with normal Lewis rats at 14 wk of age. The genetic basis of UAE in male MWF was analyzed in relation to BP by using a quantitative trait (QTL) mapping strategy. F1-hybrids generated from a cross between MWF and Lewis rats showed normal UAE rates similar to Lewis. A backcross strategy including 213 animals was therefore used. To account for age-of-onset effects, UAE was determined in young backcross animals at 8 wk and in adult animals at 14 and 24 wk of age, respectively. Total genome scan analysis identified three QTL with significant linkage to UAE and one QTL with suggestive linkage to UAE. These loci showed no linkage to BP, and BP explained only 2% of the total variance of UAE. Homozygosity for the MWF allele accounted for a similar mean increase in UAE in adult backcross animals at each UAE QTL. When single gene effects were analyzed, only one UAE QTL led to a significant increase in UAE. Early onset of albuminuria and a considerable increase of UAE in adult animals required homozygosity at three loci at least. This study demonstrates the polygenetic recessive determination of increased UAE by a set of genes that are unlinked to BP.

Albuminuria↗

PubMed2005

Female sterility in hybrids between Anopheles gambiae and A. arabiensis, and the causes of Haldane's rule.

Although F1 female hybrids between Anopheles gambiae and A. arabiensis are fully fertile, sterility is present in backcross females. Here we report the results of a study into the genetic basis of backcross female sterility. Using 23 markers, we performed quantitative trait loci (QTL) mapping analyses to identify chromosomal regions involved in hybrid female sterility. We found that female sterility in backcrosses in both directions is primarily caused by interspecific interactions between a heterozygous X chromosome and recessive autosomal factors. In addition, our data provide support for two theories implicated in Haldane's rule in a single taxon. A comparison with data from a previous study shows that male hybrid sterility QTL are present in higher numbers than female hybrid sterility QTL. Furthermore, autosomal female sterility factors tend to be recessive, supporting the dominance theory for female sterility. Finally, our data indicate a very large effect of the X chromosome from both species on hybrid female sterility, despite the fact that the X chromosome represents less than 9% of the genome. However, this could be the result of a lack of introgression of the X chromosome between A. gambiae and A. arabiensis, rather than a faster evolution of sterility factors on the X chromosome.

Animals↗

PubMedDate not supplied

Test for positional candidate genes for body composition on pig chromosome 6.

One QTL affecting backfat thickness (BF), intramuscular fat content (IMF) and eye muscle area (MA) was previously localized on porcine chromosome 6 in an F2 cross between Iberian and Landrace pigs. This work was done to study the effect of two positional candidate genes on these traits: H-FABP and LEPR genes. The QTL mapping analysis was repeated with a regression method using genotypes for seven microsatellites and two PCR-RFLPs in the H-FABP and LEPR genes. H-FABP and LEPR genes were located at 85.4 and 107 cM respectively, by linkage analysis. The effects of the candidate gene polymorphisms were analyzed in two ways. When an animal model was fitted, both genes showed significant effects on fatness traits, the H-FABP polymorphism showed significant effects on IMF and MA, and the LEPR polymorphism on BF and IMF. But when the candidate gene effect was included in a QTL regression analysis these associations were not observed, suggesting that they must not be the causal mutations responsible for the effects found. Differences in the results of both analyses showed the inadequacy of the animal model approach for the evaluation of positional candidate genes in populations with linkage disequilibrium, when the probabilities of the parental origin of the QTL alleles are not included in the model.

Animals↗

PubMed2002

Interacting QTLs for cholesterol gallstones and gallbladder mucin in AKR and SWR strains of mice.

We employed quantitative trait locus (QTL) mapping in a backcross between gallstone-susceptible SWR/J and gallstone-resistant AKR/J inbred mice to identify additional susceptibility loci for cholesterol gallstone formation. After 12 wk of feeding the mice a lithogenic diet, we phenotyped 330 backcross progeny for gallstones, gallbladder mucin accumulation, liver weight, and body weight. Marker-based regression analysis revealed significant single QTLs associated with gallstone formation on chromosome 9 and the liver weight/body weight ratio on chromosomes 5 and X. A search for gene pairs detected significant gene-gene interactions for mucin accumulation between loci on chromosomes 5 and 11 and suggestive gene-gene interactions linked to gallstone formation between the QTL on chromosome 9 and loci on chromosomes 6 and 15. These findings uncover new QTLs for cholesterol gallstones, reveal independent loci for mucin accumulation, and demonstrate the importance of considering gene-gene interactions in cholesterol cholelithiasis. According to standard nomenclature, the gallstone QTL on chromosome 9 is named Lith5.

Animals↗

PubMed2006

Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation.

Cryptococcus neoformans is a fungal human pathogen with a bipolar mating system. It undergoes a dimorphic transition from a unicellular yeast to hyphal filamentous growth during mating and monokaryotic fruiting. The traditional sexual cycle that leads to the production of infectious basidiospores involves cells of both alpha and a mating type. Monokaryotic fruiting is a modified form of sexual reproduction that involves cells of the same mating type, most commonly alpha, which is the predominant mating type in both the environment and clinical isolates. However, some a isolates can also undergo monokaryotic fruiting. To determine whether mating type and other genetic loci contribute to the differences in fruiting observed between alpha and a cells, we applied quantitative trait loci (QTL) mapping to an inbred population of F2 progeny. We discovered that variation in hyphal length produced during fruiting is a quantitative trait resulting from the combined effects of multiple genetic loci, including the mating type (MAT) locus. Importantly, the alpha allele of the MAT locus enhanced hyphal growth compared with the a allele. Other virulence traits, including melanization and growth at 39 degrees C, also are quantitative traits that share a common QTL with hyphal growth. The Mac1 transcription factor, encoded in this common QTL, regulates copper homeostasis. MAC1 allelic differences contribute to phenotypic variation, and mac1Delta mutants exhibit defects in filamentation, melanin production, and high temperature growth. Further characterization of these QTL regions will reveal additional quantitative trait genes controlling biological processes central to fungal development and pathogenicity.

Alleles↗

PubMed1998

Mapping quantitative trait loci for ordered categorical traits in four-way crosses.

Many quantitative traits of economical importance are ordinal in nature. Although methods of mapping quantitative trait loci (QTLs) for continuous quantitative characters are well developed, such methods for ordinal characters are generally lacking. In this paper, we develop a method based on the framework of a generalized linear model using four-way cross populations. The method estimates and tests the average effects of a gene substitution in the parents. All markers in the same linkage group are simultaneously used to infer the allelic transmission of a putative QTL. General results of the method are demonstrated by a few simulation experiments. We discuss extensions of the method to QTL mapping in full-sib families.

Animals↗

PubMed2002

Resolving the composite trait of hypertension into its pharmacogenetic determinants by acute pharmacological modulation of blood pressure regulatory systems.

Acute pharmacogenetic analysis was carried out in an intercross F2 population derived from Prague hypertensive-hypertriglyceridemic and Lewis rats. Quantitative trait loci (QTL) mapping was performed for baseline blood pressure (BP) and for BP after blockade of the renin-angiotensin system by losartan, of the sympathetic nervous system (SNS) by pentolinium, and of the nitric oxide system by N(G)-nitro- L-arginine methyl ester. Two significant loci for baseline BP were found on chromosome (Chr) 3 (logarithm of likelihood, LOD, 3.8) and Chr 5 (LOD 3.6), and one suggestive locus on Chr 1 (LOD 2.7). The QTL on Chr 3 persisted after treatment with the three agents while the QTL on Chr 5 and Chr 1 disappeared after pentolinium administration. This suggests independence of the locus on Chr 3 from each acute BP regulatory system examined, whereas the loci on Chr 5 and Chr 1 appeared to be controlled mainly by the SNS. Although not apparent at baseline, a significant locus appeared on Chr 8 (LOD 7.0) after blockade of the SNS, and NO system blockade led to the appearance of a new QTL on Chr 1 (LOD 3.6), indicating the contribution of the inhibited systems to these loci. Pharmacogenetic dissection of the BP trait is a powerful tool to unravel the underlying physiological mechanisms of QTL affecting baseline BP and to identify specific QTL for the response to drugs. This pharmocogenetic approach enabled us to determine the main causative acute BP regulatory systems and should lead to better selection of suitable antihypertensive drugs for individual patients.

Animals↗