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PubMed2006

A quantitative trait locus on chromosome 6 regulates the onset of puberty in mice.

Puberty is a fundamental developmental process experienced by all reproductively competent adults, yet the specific factors that regulate variation in its timing remain elusive. Using a new approach to identifying these factors, we have performed a survey among a panel of chromosome substitution strains (for inbred strains C57BL/6J and A/J) followed by linkage analysis to map a quantitative trait locus (QTL) on the distal end of chromosome 6 that regulates pubertal timing (as assessed by vaginal opening) in mice. The location of the QTL was then refined to a region between marker D6MIT59 and the end of the chromosome by generating and phenotyping a panel of 12 congenic strains, each with a unique and overlapping homozygous segment of the A/J chromosome on an otherwise uniform C57BL/6J genomic background. Additional characterization of the QTL indicated that the effects of the responsible gene(s) are gender specific and inherited in a codominant manner without parent-of-origin effects. These findings represent an important advancement toward identification of novel factors that regulate maturation of the hypothalamic-pituitary-gonadal axis and determine the timing of puberty.

Animals↗
PubMed2003

Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana.

Phenotypic plasticity and genotype-environment interactions (GEI) play a prominent role in plant morphological diversity and in the potential functional capacities of plant life-history traits. The genetic basis of plasticity and GEI, however, is poorly understood in most organisms. In this report, inflorescence development patterns in Arabidopsis thaliana were examined under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations (Ler x Col and Cvi x Ler) using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Plasticity and GEI were regularly observed for the majority of 13 inflorescence traits. These observations can be attributable (at least partly) to variable effects of specific QTL. Pooled across traits, 12/44 (27.3%) and 32/62 (51.6%) of QTL exhibited significant QTL x environment interactions in the Ler x Col and Cvi x Ler lines, respectively. These interactions were attributable to changes in magnitude of effect of QTL more often than to changes in rank order (sign) of effect. Multiple QTL x environment interactions (in Cvi x Ler) clustered in two genomic regions on chromosomes 1 and 5, indicating a disproportionate contribution of these regions to the phenotypic patterns observed. High-resolution mapping will be necessary to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.

Arabidopsis↗
PubMed2002

A quantitative trait locus influencing type 2 diabetes susceptibility maps to a region on 5q in an extended French family.

Type 2 diabetes is a heterogeneous disorder of glucose metabolism characterized by insulin resistance, beta-cell dysfunction, and increased glucose production by the liver. Given the high degree of genetic heterogeneity, multiple genes with small to moderate effects may influence susceptibility to diabetes. To circumvent this limitation, we searched for quantitative trait loci (QTLs) that explain the variation in susceptibility of type 2 diabetes in a single extended family, as these individuals are likely to share polymorphisms. We collected genotypic and phenotypic data on 152 individuals ascertained through a multimedia campaign in France to find diabetes-prone families for genetic studies. The effects of genes and covariates (age and sex) on diabetes status were estimated using a threshold model and a maximum likelihood variance component approach. We obtained suggestive evidence of linkage (logarithm of odds [LOD] = 2.4) for diabetes status on chromosome 5q. Within the 1-LOD unit support interval, there are two strong candidates: PCSK1 and CAST. Furthermore, we have obtained a replication (LOD = 1.6) for a QTL for type 2 diabetes on chromosome 11 detected by Hanson and colleagues (1998).

Chromosome Mapping↗
PubMed2005

Quantitative trait loci that determine BMD in C57BL/6J and 129S1/SvImJ inbred mice.

UNLABELLED: BMD is highly heritable; however, little is known about the genes. To identify loci controlling BMD, we conducted a QTL analysis in a (B6 x 129) F2 population of mice. We report on additional QTLs and also narrow one QTL by combining the data from multiple crosses and through haplotype analysis. INTRODUCTION: Previous studies have identified quantitative trait loci (QTL) that determine BMD in mice; however, identification of genes underlying QTLs is impeded by the large size of QTL regions. MATERIALS AND METHODS: To identify loci controlling BMD, we performed a QTL analysis of 291 (B6 x 129) F2 females. Total body and vertebral areal BMD (aBMD) were determined by peripheral DXA when mice were 20 weeks old and had consumed a high-fat diet for 14 weeks. RESULTS AND CONCLUSIONS: Two QTLs were common for both total body and vertebral aBMD: Bmd20 on chromosome (Chr) 6 (total aBMD; peak cM 26, logarithm of odds [LOD] 3.8, and vertebral aBMD; cM 32, LOD 3.6) and Bmd22 on Chr 1 (total aBMD; cM 104, LOD 2.5, and vertebral aBMD; cM 98, LOD 2.6). A QTL on Chr 10 (Bmd21, cM 68, LOD 3.0) affected total body aBMD and a QTL on Chr 7 (Bmd9, cM 44, LOD 2.7) affected vertebral aBMD. A pairwise genome-wide search did not reveal significant gene-gene interactions. Collectively, the QTLs accounted for 21.6% of total aBMD and 17.3% of vertebral aBMD of the F(2) population variances. Bmd9 was previously identified in a cross between C57BL/6J and C3H/HeJ mice, and we narrowed this QTL from 34 to 22 cM by combining the data from these crosses. By examining the Bmd9 region for conservation of ancestral alleles among the low allele strains (129S1/SvImJ and C3H/HeJ) that differed from the high allele strain (C57BL/6J), we further narrowed the region to approximately 9.9 cM, where the low allele strains share a common haplotype. Identifying the genes for these QTLs will enhance our understanding of skeletal biology.

Animals↗
PubMed1999

Mapping quantitative trait loci for complex binary traits in outbred populations.

Complex binary traits have a dichotomous phenotypic expression but do not show a simple Mendelian segregation ratio. These traits are considered to be jointly controlled by the actions of several genes and a random environmental effect. The binary phenotype and the underlying factor are assumed to be linked through a threshold model. The underlying factor, referred to as the liability, is treated as a regular but unobservable quantitative character. Mapping quantitative trait loci (QTL) can be performed directly on the liability. Methods of QTL mapping for the liability of a complex binary trait have been well developed in line-crossing experiments. However, such a method is not available in outbred populations which usually consist of many independent pedigrees (families). In this study, we develop a method to analyse jointly multiple families of an outbred population. The method is developed based on a fixed-model approach, i.e. the QTL effects, rather than the variance, are estimated and tested. After the test, the estimated effects are then converted into a single estimate of the QTL variance by taking into consideration errors in the estimated effects. The QTL effects and variance-covariance matrix of the estimates are obtained by a fast Fisher-scoring method. Monte Carlo simulations show that the method is not only powerful but also generates very accurate estimates of QTL variances.

Algorithms↗
PubMed1997

Mapping quantitative trait loci for body weight on the X chromosome in mice. II. Analysis of congenic backcrosses.

In a QTL mapping study with an F2 population of mice, we have shown that one or more sex-linked factors account for a large part of the divergence between mouse lines selected for high and low body weight. Here, we describe a study undertaken to map the putative X-linked quantitative trait loci (QTLs) by backcrossing segments of chromosome from the high line onto an inbred line derived from the low line, thereby removing possible contributions from the autosomes and linked segments of the X chromosome. Sublines containing a regional at the proximal end of the X chromosome were found to be associated with large differences in body weight, and to account for almost all the difference between the lines. A Markov chain Monte Carlo based multipoint linkage analysis incorporating the available marker and phenotypic information from the backcross pedigree was used to map the QTL to a region of about 6 cM. There was no evidence for QTLs elsewhere on the chromosome. The estimated QTL effect is approximately 20% of mean body weight in males and females at 10 weeks. From results obtained from this study and the accompanying F2 analysis, we conclude the presence of a single factor for body weight localizing to about position (+/- SE) 26.4 +/- 1.2 cM on the X chromosome, which increases body weight by approximately 18% at 10 weeks. A strategy to positionally clone the QTL is discussed.

Animals↗
PubMed1999

Chromosomal mapping of quantitative trait loci that influence renal hemodynamic functions.

BACKGROUND: Impaired renal hemodynamic function has been suspected to be responsible for hypertension in the spontaneously hypertensive rat (SHR). METHODS AND RESULTS: We measured renal hemodynamic functions, including the glomerular filtration rate, renal plasma flow, and renal vascular resistance, in an F2 rat population derived from spontaneously hypertensive and Wistar-Kyoto (WKY) rats and performed a genome-wide screening to map quantitative trait loci that influence these functions to gain insight into the relationship between renal hemodynamic functions and blood pressure control. The D1 Mit7 locus was identified as a major locus that influenced renal hemodynamic functions, and we transferred the SHR chromosomal segment around the D1 Mit7 locus into the WKY strain. The congenic rats exhibited impaired renal hemodynamic functions. The systolic blood pressure of the congenic rats was significantly higher than that of age-matched WKY rats, but only at nighttime. No significant differences in systolic blood pressure during daytime or diastolic blood pressure were observed between the 2 strains. CONCLUSIONS: We have identified a chromosome segment that influences renal hemodynamic function. The SHR chromosome segment around the D1 Mit7 locus had significant, but not dramatic, effects in increasing blood pressure in the WKY genetic background. However, further studies will be necessary to determine the significance of this locus in SHR hypertension.

Animals↗
PubMed2006

A statistical model to analyse quantitative trait locus interactions for HIV dynamics from the virus and human genomes.

Viruses can be considered 'parasites' because they cannot survive outside of a host. The progression rate to AIDS caused by human immunodeficiency virus type-1 (HIV-1) is therefore a consequence of HIV-host cell interactions. In this article, we present an innovative statistical model for detecting the effects of genetic interactions on HIV-1 dynamics triggered by different quantitative trait loci (QTL) from the HIV and human genomes. Our model integrates the principles of functional mapping for longitudinal traits and of linkage disequilibrium analysis for high-resolution mapping of QTL within the maximum likelihood context and is implemented with the EM algorithm. We performed Monte Carlo simulation studies to investigate the impacts of different heritability levels and sample sizes on the power to detect interacting QTL. Our model allows for the tests of a number of clinically meaningful hypotheses and provides a powerful tool for unravelling the genetic architecture of HIV-1 dynamics and therefore AIDS progression rate.

Algorithms↗
PubMed1998

A major quantitative trait locus co-localizing with cholecystokinin type A receptor gene influences poor pancreatic proliferation in a spontaneously diabetogenic rat.

The Otsuka Long-Evans Tokushima Fatty (OLETF) rat is an animal model for obese-type, non-insulin-dependent diabetes mellitus (NIDDM) in humans. The OLETF rat has poor capacity for pancreatic proliferation, which may be the critical pathogenetic event in NIDDM development. Our investigation was designed to identify quantitative trait loci (QTLs) responsible for poor pancreatic proliferation by examining compensatory proliferation of the pancreatic remnant after partial pancreatectomy and performing a genome-wide scan in an F2 intercross obtained by mating the OLETF and the Fischer-344 (F344) rats. We identified a highly significant QTL on rat Chromosome 14 with a maximum lod score of 16.7, which accounts for 55% of the total variance. The QTL co-localizes with the gene encoding cholecystokinin type A receptor (CCKAR) which is likely to mediate the trophic effect of cholecystokinin on pancreas and is defective in the OLETF rat.

Animals↗
PubMed2005

Expression quantitative trait loci analysis of 13 genes in the rat prostate.

Differential expression of mRNA among animal strains is one of the mechanisms for their diversity. cDNA microarray analysis of the prostates of BUF/Nac (BUF) and ACI/N (ACI) rats, which show different susceptibility to prostate cancers, found 195 differentially expressed genes. To identify loci that control differential expression of 13 genes with diverse expression levels, their expression levels were measured by quantitative RT-PCR in 89 backcross rats, and expression quantitative trait locus (eQTL) analysis was performed. Nine genes [Aldh1a1, Aldr1, Bmp6, Cdkn1a (p21), Cntn6, Ghr, Jund, Nupr1, and RT1-M3] were controlled by cis-acting loci. Cdkn1a, a cell cycle regulator and a candidate for a prostate cancer susceptibility gene, was mapped to its own locus and had polymorphisms, including a 119-bp insertion in the 5' upstream region in BUF rats. Four genes (Kclr, Pbsn, Psat1, and Ptn) were controlled by trans-acting loci. Pbsn, a prostate-specific gene on chromosome X, was controlled by a QTL on chromosome 8. Depending upon which gene that we selected from the genes widely used for normalization (Actb, Gapd, or Ppia), different QTL were mapped for Kclr, Psat1, and Ptn. Normalization using Actb most appropriately explained the expression levels in a congenic strain for chromosome 3. eQTL analysis with precise measurement of expression levels and appropriate normalization was shown to be effective for mapping loci that control gene expression in vivo.

Animals↗
PubMed2005

Pleiotropic quantitative trait loci contribute to population divergence in traits associated with life-history variation in Mimulus guttatus.

Evolutionary biologists seek to understand the genetic basis for multivariate phenotypic divergence. We constructed an F2 mapping population (N = 539) between two distinct populations of Mimulus guttatus. We measured 20 floral, vegetative, and life-history characters on parents and F1 and F2 hybrids in a common garden experiment. We employed multitrait composite interval mapping to determine the number, effect, and degree of pleiotropy in quantitative trait loci (QTL) affecting divergence in floral, vegetative, and life-history characters. We detected 16 QTL affecting floral traits; 7 affecting vegetative traits; and 5 affecting selected floral, vegetative, and life-history traits. Floral and vegetative traits are clearly polygenic. We detected a few major QTL, with all remaining QTL of small effect. Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained. We also compared the genetic architecture controlling floral trait divergence both within (our intraspecific study) and between species, on the basis of a previously published analysis of M. guttatus and M. nasutus. Eleven of our 16 floral QTL map to approximately the same location in the interspecific map based on shared, collinear markers, implying that there may be a shared genetic basis for floral divergence within and among species of Mimulus.

Flowers↗
PubMed2006

Independent quantitative trait loci influence ventral and dorsal hippocampal volume in recombinant inbred strains of mice.

Anatomical and functional studies support segregation of the hippocampus into ventral and dorsal components along its septotemporal axis. However, it is unknown whether the development of these two components of the hippocampus is influenced by common or separate genetic factors. In this study, we used recombinant inbred strains of mice to determine whether the same or different quantitative trait loci (QTL) influence ventral and dorsal hippocampal volume. Using two sets of strains of recombinant inbred mice (BXD and AXB/BXA), we identified separate QTLs for ventral and dorsal hippocampal volume. In BXD mice, suggestive QTLs for ventral hippocampus were identified on chromosomes 2, 8 and 13, and a significant QTL for dorsal hippocampal volume was identified on chromosome 15. There was also a suggestive QTL for dorsal hippocampal volume on chromosome 13. In AXB/BXA mice, there were no significant or suggestive QTLs for ventral hippocampal volume, but a significant QTL for dorsal hippocampus was identified on chromosome 5. These findings suggest that the development of the ventral and dorsal components of the hippocampus is influenced by separate genetic loci.

Age Factors↗
PubMed2003

Genomic imprinting and linkage test for quantitative-trait Loci in extended pedigrees.

Genomic imprinting is a mechanism in which only one of the two copies of a gene is expressed. Some genes that affect development and behavior in mammals are known to be imprinted. Deregulation of imprinted genes has been found in a number of human diseases. Incorporating imprinting information into linkage analysis results in a more powerful test for linkage. Here, we propose an efficient method to test for linkage and imprinting of quantitative traits in extended pedigrees. We compared the results obtained by using the extended-pedigree-analysis approach proposed in this study with other existing approaches. We found that the proposed method is more powerful and uses extended-pedigree information most efficiently.

Female↗
PubMed2005

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

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

Alleles↗
PubMed2005

A genomewide scan for intelligence identifies quantitative trait loci on 2q and 6p.

Between 40% and 80% of the variation in human intelligence (IQ) is attributable to genetic factors. Except for many rare mutations resulting in severe cognitive dysfunction, attempts to identify these factors have not been successful. We report a genomewide linkage scan involving 634 sibling pairs designed to identify chromosomal regions that explain variation in IQ. Model-free multipoint linkage analysis revealed evidence of a significant quantitative-trait locus for performance IQ at 2q24.1-31.1 (LOD score 4.42), which overlaps the 2q21-33 region that has repeatedly shown linkage to autism. A second region revealed suggestive linkage for both full-scale and verbal IQs on 6p25.3-22.3 (LOD score 3.20 for full-scale IQ and 2.33 for verbal IQ), overlapping marginally with the 6p22.3-21.31 region implicated in reading disability and dyslexia.

Adolescent↗
PubMed2004

Adult gonadal hormones selectively regulate sexually dimorphic quantitative traits observed in experimental allergic encephalomyelitis.

Experimental allergic encephalomyelitis (EAE) and multiple sclerosis (MS) are characterized by strong sexual dimorphisms, many of which may be due to genetically controlled sex hormone effects on the immune system, the central nervous system (CNS), or both. In the present study we used 487 gonadectomized and 376 intact age-matched F(2) mice generated through crosses of B10.S/SgMcdJ and SJL/J mice to assess the role of adult gonadal hormones in regulating clinical and histopathological quantitative traits (QT) associated with EAE in the context of genetic heterogeneity. We found that gonadectomy resulted in different effects, depending on the QT and the sex of the mouse. Ovariectomized mice on average had lower cumulative clinical disease scores, shorter duration of clinical signs, and increased peak disease scores. This trend was accompanied by a significant increase in the incidence of acute, progressive EAE which is more frequently seen in intact and orchiectomized males. Although spinal cord (SC) inflammation was the better predictor of clinical signs of EAE in both sexes, ovariectomized females had considerable reductions in nearly all histopathological QT in both the brain and SC. Orchiectomy resulted in modestly significant increases in disease severity and peak score and earlier onset of clinical signs. With the exception of SC demyelination and lesion scores, orchiectomy had no effect on histopathological QT. Importantly, gonadectomy reduced but did not completely abolish any of the sexually dimorphic clinical QT seen in intact mice. It did however, lead to a significant sexual dimorphism in incidence and severity not seen in intact mice. For histopathological QT, no sexual dimorphism was detected for brain lesions in either intact or gonadectomized mice. In contrast, SC histopathological QT exhibited significant sexual dimorphisms, which were impacted by gonadectomy. The results from this study indicate that within the context of genetic heterogeneity, circulating gonadal hormones influence both clinical and histopathological QT in this model of MS, but they do not solely account for the sexual dimorphisms seen in these traits. Thus, additional mechanisms must play a role in regulating gender differences in autoimmune disease of the CNS.

Animals↗
PubMed2002

A method for computing identity by descent probabilities and quantitative trait loci mapping with dominant (AFLP) markers.

Amplified fragment length polymorphisms (AFLPs) are a widely used marker system: the technique is very cost-effective, easy and rapid, and reproducibly generates hundreds of markers. Unfortunately, AFLP alleles are typically scored as the presence or absence of a band and, thus, heterozygous and dominant homozygous genotypes cannot be distinguished. This results in a significant loss of information, especially as regards mapping of quantitative trait loci (QTLs). We present a Monte Carlo Markov Chain method that allows us to compute the identity by descent probabilities (IBD) in a general pedigree whose individuals have been typed for dominant markers. The method allows us to include the information provided by the fluorescent band intensities of the markers, the rationale being that homozygous individuals have on average higher band intensities than heterozygous individuals, as well as information from linked markers in each individual and its relatives. Once IBD probabilities are obtained, they can be combined into the QTL mapping strategy of choice. We illustrate the method with two simulated populations: an outbred population consisting of full sib families, and an F2 cross between inbred lines. Two marker spacings were considered, 5 or 20 cM, in the outbred population. There was almost no difference, for the practical purpose of QTL estimation, between AFLPs and biallelic codominant markers when the band density is taken into account, especially at the 5 cM spacing. The performance of AFLPs every 5 cM was also comparable to that of highly polymorphic markers (microsatellites) spaced every 20 cM. In economic terms, QTL mapping with a dense map of AFLPs is clearly better than microsatellite QTL mapping and little is lost in terms of accuracy of position. Nevertheless, at low marker densities, AFLPs or other biallelic markers result in very inaccurate estimates of QTL position.

Algorithms↗
PubMed2006

Identification of quantitative trait loci for larval morphological traits in interspecific hybrids of Ochlerotatus triseriatus and Ochlerotatus hendersoni (Diptera: Culicidae).

Ochlerotatus triseriatus is the natural vector of La Crosse virus, a common cause of pediatric encephalitis in the United States; the closely related Ochlerotatus hendersoni transmits this virus at low frequency. Adults of these mosquito species are difficult to distinguish morphologically; however, the larval stages show species-specific differences in several characters. We identified genomic regions contributing to the differences between the larvae of these species through interspecific hybridizations. Quantitative trait loci (QTL) were identified by standard interval mapping techniques and by univariate marker association analyses. We examined 159 F(2) progeny from an Oc. hendersoni female by Oc. triseriatus male interspecific cross for variation in the number of saddle and siphon hair branches, attachment of the acus, and morphology of the anal papillae. At least one putative QTL was identified for each of the phenotypes examined. QTL most commonly mapped to linkage group (LG) III, although QTL were identified on LGI and LGII for three phenotypes each. Several of these QTL, and particularly those on LGIII, also map to genome regions controlling adult female body size and ability to orally transmit La Crosse virus. Further studies are required to elucidate the relationships among these traits and the impact they may have had on the ecological specialization and speciation of these mosquitoes.

Alleles↗