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PubMed2003

A strategy for the integration of QTL, gene expression, and sequence analyses.

Although hundreds if not thousands of quantitative trait loci (QTL) have been described for a wide variety of complex traits, only a very small number of these QTLs have been reduced to quantitative trait genes (QTGs) and quantitative trait nucleotides (QTNs). A strategy, Multiple Cross Mapping (MCM), is described for detecting QTGs and QTNs that is based on leveraging the information contained within the haplotype structure of the mouse genome. As described in the current report, the strategy utilizes the six F(2) intercrosses that can be formed from the C57BL/6J (B6), DBA/2J (D2), BALB/cJ (C), and LP/J (LP) inbred mouse strains. Focusing on the phenotype of basal locomotor activity, it was found that in all three B6 intercrosses, a QTL was detected on distal Chromosome (Chr) 1; no QTL was detected in the other three intercrosses, and thus, it was assumed that at the QTL, the C, D2, and LP strains had functionally identical alleles. These intercross data were used to form a simple algorithm for interrogating microsatellite, single nucleotide polymorphism (SNP), brain gene expression, and sequence databases. The results obtained point to Kcnj9 (which has a markedly lower expression in the B6 strain) as being the likely QTG. Further, it is suggested that the lower expression in the B6 strain results from a polymorphism in the 5'-UTR that disrupts the binding of at least three transcription factors. Overall, the method described should be widely applicable to the analysis of QTLs.

Algorithms↗
PubMed1996

Genes and aggressiveness. Behavioral genetics.

Four strains of 'knockout' mice, each with a different gene inactivated, have been found to show increased aggressive behavior. The generation of such knockout strains and quantitative trait locus analysis will help identify the genetic determinants of this complex trait.

Aggression↗
PubMed2005

Novel pheochromocytoma susceptibility loci identified by integrative genomics.

Pheochromocytomas are catecholamine-secreting tumors that result from mutations of at least six different genes as components of distinct autosomal dominant disorders. However, there remain familial occurrences of pheochromocytoma without a known genetic defect. We describe here a familial pheochromocytoma syndrome consistent with digenic inheritance identified through a combination of global genomics strategies. Multipoint parametric linkage analysis revealed identical LOD scores of 2.97 for chromosome 2cen and 16p13 loci. A two-locus parametric linkage analysis produced maximum LOD score of 5.16 under a double recessive multiplicative model, suggesting that both loci are required to develop the disease. Allele-specific loss of heterozygosity (LOH) was detected only at the chromosome 2 locus in all tumors from this family, consistent with a tumor suppressor gene. Four additional pheochromocytomas with a similar genetic pattern were identified through transcription profiling and helped refine the chromosome 2 locus. High-density LOH mapping with single nucleotide polymorphism-based array identified a total of 18 of 62 pheochromocytomas with LOH within the chromosome 2 region, which further narrowed down the locus to <2 cM. This finding provides evidence for two novel susceptibility loci for pheochromocytoma and adds a recessive digenic trait to the increasingly broad genetic heterogeneity of these tumors. Similarly, complex traits may also be involved in other familial cancer syndromes.

Adrenal Gland Neoplasms↗
PubMed1999

Identification of quantitative trait loci influencing traits related to energy balance in selection and inbred lines of mice.

Energy balance is a complex trait with relevance to the study of human obesity and maintenance energy requirements of livestock. The objective of this study was to identify, using unique mouse models, quantitative trait loci (QTL) influencing traits that contribute to variation in energy balance. Two F2 resource populations were created from lines of mice differing in heat loss measured by direct calorimetry as an indicator of energy expenditure. The HB F2 resource population originated from a cross between a noninbred line selected for high heat loss and an inbred line with low heat loss. Evidence for significant QTL influencing heat loss was found on chromosomes 1, 2, 3, and 7. Significant QTL influencing body weight and percentage gonadal fat, brown fat, liver, and heart were also identified. The LH F2 resource population originated from noninbred lines of mice that had undergone divergent selection for heat loss. Chromosomes 1 and 3 were evaluated. The QTL for heat loss identified on chromosome 1 in the HB population was confirmed in the LH population, although the effect was smaller. The presence of a QTL influencing 6-wk weight was also confirmed. Suggestive evidence for additional QTL influencing heat loss, percentage subcutaneous fat, and percentage heart was found for chromosome 1.

Adipose Tissue↗
PubMed2005

Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping.

Rodent inbred line crosses are widely used to map genetic loci associated with complex traits. This approach has proven to be powerful for detecting quantitative trait loci (QTL); however, the resolution of QTL locations, typically approximately 20 cM, means that hundreds of genes are implicated as potential candidates. We describe analytical methods based on linear models to combine information available in two or more inbred line crosses. Our strategy is motivated by the hypothesis that common inbred strains of the laboratory mouse are derived from a limited ancestral gene pool and thus QTL detected in multiple crosses are likely to represent shared ancestral polymorphisms. We demonstrate that the combined-cross analysis can improve the power to detect weak QTL, can narrow support intervals for QTL regions, and can be used to separate multiple QTL that colocalize by chance. Moreover, combined-cross analysis can establish the allelic states of a QTL among a set of parental lines, thus providing critical information for narrowing QTL regions by haplotype analysis.

Cholesterol, HDL↗
PubMed2003

Bone density in sheep: genetic variation and quantitative trait loci localisation.

Bone density (BD) is an important factor in osteoporotic fracture risk in humans. However, BD is a complex trait confounded by environmental influences and polygenic inheritance. Sheep provide a potentially useful model for studying differences in BD, as they provide a means of circumventing complex environmental factors and are a similar weight to humans. The aims of this study were to establish whether there is genetic variation in BD in sheep and then to localise quantitative trait loci (QTLs) associated with this variation. We also aimed to evaluate the relationship between fat and muscle body components and BD in sheep. Results showed that there was significant (P < 0.01) genetic variation among Coopworth sheep sires for BD. This genetic difference was correlated (P < 0.01) with body weight and muscle mass. A number of QTLs exceeding the suggestive threshold were identified (nine in total). Of these, two (chromosomes 1, P < 0.05; chromosome 24, P < 0.01) were significant using genome-wide permutation significance thresholds (2000 iterations). The position of the QTL on chromosome 24 coincided with a number of other body composition QTLs, indicating possible pleiotropic effects or the presence of multiple genes affecting body composition at that site. This study shows that sheep are potentially a useful model for studying the genetics of BD.

Animals↗
PubMed1995

Molecular dissection of quantitative traits: progress and prospects.

QTL mapping is an increasingly useful approach to the study and manipulation of complex traits important in agriculture, evolution, and medicine. The molecular dissection of quantitative phenotypes, supplementing the principles of classical quantitative genetics, is accelerating progress in the manipulation of plant and animal genomes. A growing appreciation of the similarities among different organisms and the usefulness of comparative genetic information is making genome analysis more efficient, and providing new opportunities for using model systems to overcome the limitations of less-favorable systems. The expanding repertoire of techniques and information available for studying heredity is removing obstacles to the cloning of QTLs. Although QTL mapping alone is limited to a resolution of 0.1%-1.0% of a genome, use of QTL mapping in conjunction with a search for mapped candidate genes, with emerging technologies for isolation of genes expressed under conditions likely to account for the quantitative phenotype, and with ever more efficient megabase DNA manipulation and characterization bodes well for the prospect of isolating the genetic determinants of QTLs in the foreseeable future. In the words of Thoday (1961), "An extensive attack on quantitative genetics made from this point of view as well as the biometric approach should be a great help in answering questions concerning the nature of polygenes...."

Animals↗
PubMed2003

Notch4, a non-HLA gene in the MHC is strongly associated with the most severe form of alopecia areata.

Alopecia areata (AA) is a disorder primarily affecting the hair and nails in which associated autoimmune or atopic disease is common. Genetically, it is a complex trait with evidence of a role for genes of the major histocompatibility complex (MHC), the interleukin-1 cluster and chromosome 21 in the pathogenesis. The strongest association is with HLA class II alleles, although whether this indicates a direct contribution to the pathogenesis or results merely from linkage disequilibrium with nearby disease genes is unknown. Notch4 is a recently defined gene in the HLA class III region. Notch signalling is a direct determinant of keratinocyte growth arrest and entry into differentiation. A possible role for Notch in hair growth has been indicated by transgenic mouse findings that activation of the Notch pathway in the hair cortex leads to aberrant differentiation of adjacent hair-shaft layers. Notch4 is therefore a plausible candidate gene for AA. We have examined two polymorphisms in the coding sequence of the Notch4 gene at positions +1297 and +3063 in a case-control study of 116 AA patients and 142 ethnically matched, healthy control subjects. The initial analysis showed a significant association of AA in the overall data set with the Notch4(T+1297C) polymorphism (P<0.001) but not with Notch4(A+3063G). To confirm this association, we genotyped an additional 62 patients and found that the risk for disease was higher in Notch4(+1297C) homozygotes [odds ratio (OR) 3.43 (1.63, 7.19)] than in heterozygotes [OR 2.58 (1.57, 4.24)]. On classifying the patients by severity of disease, the association appeared to be confined to the severest form (alopecia universalis) [OR 4.02 (1.64, 9.88), P=0.0014]. These results support previous findings showing that different HLA susceptibility alleles are associated with mild and severe AA.

Alleles↗
PubMed2002

Genetics of multiple sclerosis: determinants of autoimmunity and neurodegeneration.

Since the first description of multiple sclerosis (MS) as an inheritable disease by Eichhorst [1] accumulating epidemiological observations support a genetic hypothesis. Population, family and twin studies have revealed that Mendelian transmission of a single susceptibility gene would not be compatible with the observed patterns of inheritance. Like most other common diseases, MS is a complex trait, defined by several genes, each probably exerting a relatively small effect. Complex interactions among susceptibility genes and the environment are believed to contribute to a predisposition to dysregulation of inflammatory pathways, demyelination and tissue degeneration in the central nervous system (CNS). Natural history and pathological studies, however, define that MS represents a spectrum rather than a single entity of inflammatory demyelination. Despite a growing need for identifying molecular markers of biological subtypes of MS, only limited information is available for genotype-phenotype correlations. Four full genome scans using polymorphic microsatellite markers in nuclear and multiplex MS families indicated several chromosomal regions of susceptibility. With the recently discovered, highly abundant single nucleotide polymorphisms (SNPs) and family-based association methods, the means are now available to confine these relatively large regions of interest to candidate genes and susceptibility alleles. The currently available SNP maps favor indirect association studies based on linkage disequilibrium between marker and disease alleles. Here, we review available genetic data in MS, and introduce an additional strategy which correlate genetic markers with major biological components of the disease such as autoimmunity and neurodegeneration. This approach may yield important insights with utility in clinical practice.

Autoimmunity↗
PubMed2006

Dissecting the regulation of fructan metabolism in perennial ryegrass (Lolium perenne) with quantitative trait locus mapping.

Quantitative trait locus (QTL) mapping, which can be a useful tool for dissecting complex traits, has been used here to study the regulation of fructan metabolism in temperate forage grasses. An F2 mapping family, derived from a high water-soluble carbohydrate (WSC) x low WSC cross, was used to map fructans and the other components of WSC (sucrose, glucose and fructose) in leaves and tiller bases of perennial ryegrass (Lolium perenne) in spring and autumn. To characterize regions of the genome that control basic carbohydrate metabolism, a strategy to minimize the impact of genotype (G) x environment (E), and E-effects on the characterization of G-effects, was adopted. Most traits were highly variable within the family. There was also considerable year-to-year environmental variation. However, significant genetic effects were detected, and several traits had high broad-sense heritability. QTL were identified on chromosomes 1, 2, 5 and 6. Leaf and tiller base QTL did not coincide. Individual QTL explained between 8 and 59% of the total phenotypic variation in the traits. Fructan turnover, metabolism and their genetic control, and the effect of environment, are discussed in the context of the results.

Biomarkers↗
PubMed2006

[Methodology of QTL's linkage analysis for discrete traits controlled by polygenes].

Many characters of biological interest and economical importance that are not inherited in a simple Mendelian fashion vary in a discrete form. These traits are called complex discrete traits. A complex discrete trait is presumably controlled by several genes, and characteristic of the trait is modified by environmental effects. Although methods of mapping QTL for continuous quantitative characters have been well developed, such methods for discrete characters are not available yet. So many non-linear methods were developed under the framework of the generalized linear model. In this paper, we reviewed the recent progress and improvement of the methods for QTL mapping in this field.

Animals↗
PubMed2004

Triallelic inheritance: a bridge between Mendelian and multifactorial traits.

The increasing identification of disease genes is revealing a growing number of traits that fail to conform to traditional Mendelian paradigms, thereby creating new challenges to both genetic investigators and clinicians. Bardet-Biedl syndrome (BBS) is one such disorder that has helped to define 'oligogenic' inheritance, a term that implies that some diseases are not inherited as simple single-gene Mendelian disorders and yet are not classic complex traits, but rather fit a model in which mutations in a small number of genes may interact genetically to manifest the phenotype. BBS is a pleiotropic disorder characterized by postnatal obesity, post-axial polydactyly, and progressive retinal dystrophy. Eight BBS loci have been identified to date and six of these genes have been cloned. Mutation analysis of these BBS genes in a cohort of patients has led to the description of the novel phenomenon of 'triallelic inheritance', wherein families were identified in which three mutations from genes at two different BBS loci segregate with expression of the disease. Modeling the cooperative ability of alleles of different genes at distinct loci to give rise to a particular phenotype will facilitate the understanding of complex multifactorial and polygenic traits.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Heritability of blood pressure in Nigerian families.

OBJECTIVES: There are few studies of familial aggregation of blood pressure in African populations. This study was undertaken to provide estimates of heritability for four blood pressure phenotypes: systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP) and pulse pressure. METHODS: A population-based sample of 528 pedigrees or extended families, comprising 1825 measured individuals, was studied in a poor urban community in Ibadan, Nigeria. RESULTS: The mean SBP was 121.7 (SD 22.6) mmHg for men and 120.7 (SD 26.8) mmHg for women, while the mean DBP was 74.6 (SD 14.1) mmHg for men and 75.5 (SD 15.2) mm Hg for women. The study sample was lean [mean body mass index (BMI) approximately 21 kg/m2]. Maximum-likelihood heritability estimates were obtained under a polygenic model with simultaneous estimation of household effects using a variance components method, as implemented in the SOLAR software package. Heritability estimates of the traits were 34% for SBP, 29% for DBP, 36% for MAP and 13% for pulse pressure. Household effects were statistically significant for DBP (7.1%) and MAP (4.5%). Measured covariates (age, sex and BMI) accounted for 25, 24, 26 and 16% of the total variance, respectively, for SBP, DBP, MAP and pulse pressure. CONCLUSIONS: These figures suggest that, similar to that reported in other populations, blood pressure is a heritable trait. Studies similar to this are needed to describe the familial aggregation of other complex traits in sub-Saharan African populations and to serve as a prelude to the identification of susceptibility genes involved in the pathophysiology of common complex diseases, including blood pressure and hypertension.

Adolescent↗
PubMed2006

Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci.

Obesity is a highly heritable and genetically complex trait with hundreds of potential loci identified. An intercross of 513 F2 progeny between the SM/J x NZB/BINJ inbred mouse strains was generated to identify quantitative trait loci (QTL) that are involved in the weight of four fat pads: mesenteric, inguinal, gonadal, and retroperitoneal. Sex and lean body weight were treated as covariates in the analysis of these fat pads. This analysis uncoupled genetic effects related to overall body size from those influencing the adiposity of a mouse. We identified multiple significant QTL. QTL alleles associated with increased lean body weight and individual fat pad weights are contributed by the NZB background. Adiposity loci are distinct from these body size QTLs and high-adiposity alleles are contributed by the SM background. An extended network of epistatic QTL is also observed. A QTL on Chr 19 is the center of a network of eight interacting QTL, Chr 4 is the center of six, and Chr 17 the center of four interacting QTL. We conclude that interacting networks of multiple genes characterize the regulation of fat pad depots and body weight. Haplotype patterns and a literature-driven approach were used to generate hypotheses regarding the identity of the genes and pathways underlying the QTL.

Animals↗
PubMed2006

High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila species.

Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a and QTL3b. QTL3a shows sign epistasis: it has opposite effects in two different genetic backgrounds, the presence vs. the absence of the QTL3b D. sechellia allele. This property of QTL3a allows us to reconstruct the probable order of fixation of the QTL alleles during evolution.

Animals↗
PubMed2006

SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values.

BACKGROUND: With the recent advances in high-throughput genotyping technologies that allow for large-scale association mapping of human complex traits, promising statistical designs and methods have been emerging. Efficient simulation software are key elements for the evaluation of the properties of new statistical tests. SLINK is a flexible simulation tool that has been widely used to generate the segregation and recombination processes of markers linked to, and possibly associated with, a trait locus, conditional on trait values in arbitrary pedigrees. In practice, its most serious limitation is the small number of loci that can be simulated, since the complexity of the algorithm scales exponentially with this number. RESULTS: I describe the implementation of a two-step algorithm to be used in conjunction with SLINK to enable the simulation of a large number of marker loci linked to a trait locus and conditional on trait values in families, with the possibility for the loci to be in linkage disequilibrium. SLINK is used in the first step to simulate genotypes at the trait locus conditional on the observed trait values, and also to generate an indicator of the descent path of the simulated alleles. In the second step, marker alleles or haplotypes are generated in the founders, conditional on the trait locus genotypes simulated in the first step. Then the recombination process between the marker loci takes place conditionally on the descent path and on the trait locus genotypes. This two-step implementation is often computationally faster than other software that are designed to generate marker data linked to, and possibly associated with, a trait locus. CONCLUSION: Because the proposed method uses SLINK to simulate the segregation process, it benefits from its flexibility: the trait may be qualitative with the possibility of defining different liability classes (which allows for the simulation of gene-environment interactions or even the simulation of multi-locus effects between unlinked susceptibility regions) or it may be quantitative and normally distributed. In particular, this implementation is the only one available that can generate a large number of marker loci conditional on the set of observed quantitative trait values in pedigrees.

Algorithms↗
PubMed2001

Score tests for association between traits and haplotypes when linkage phase is ambiguous.

A key step toward the discovery of a gene related to a trait is the finding of an association between the trait and one or more haplotypes. Haplotype analyses can also provide critical information regarding the function of a gene; however, when unrelated subjects are sampled, haplotypes are often ambiguous because of unknown linkage phase of the measured sites along a chromosome. A popular method of accounting for this ambiguity in case-control studies uses a likelihood that depends on haplotype frequencies, so that the haplotype frequencies can be compared between the cases and controls; however, this traditional method is limited to a binary trait (case vs. control), and it does not provide a method of testing the statistical significance of specific haplotypes. To address these limitations, we developed new methods of testing the statistical association between haplotypes and a wide variety of traits, including binary, ordinal, and quantitative traits. Our methods allow adjustment for nongenetic covariates, which may be critical when analyzing genetically complex traits. Furthermore, our methods provide several different global tests for association, as well as haplotype-specific tests, which give a meaningful advantage in attempts to understand the roles of many different haplotypes. The statistics can be computed rapidly, making it feasible to evaluate the associations between many haplotypes and a trait. To illustrate the use of our new methods, they are applied to a study of the association of haplotypes (composed of genes from the human-leukocyte-antigen complex) with humoral immune response to measles vaccination. Limited simulations are also presented to demonstrate the validity of our methods, as well as to provide guidelines on how our methods could be used.

Algorithms↗
PubMed2006

A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture.

Although quantitative trait locus (QTL) mapping has been successful in describing the genetic architecture of complex traits, the molecular basis of quantitative variation is less well understood, especially in plants such as maize that have large genome sizes. Regulatory changes at the teosinte branched1 (tb1) gene have been proposed to underlie QTLs of large effect for morphological differences that distinguish maize (Zea mays ssp. mays) from its wild ancestors, the teosintes (Z. mays ssp. parviglumis and mexicana). We used a fine mapping approach to show that intergenic sequences approximately 58-69 kb 5' to the tb1 cDNA confer pleiotropic effects on Z. mays morphology. Moreover, using an allele-specific expression assay, we found that sequences >41 kb upstream of tb1 act in cis to alter tb1 transcription. Our findings show that the large stretches of noncoding DNA that comprise the majority of many plant genomes can be a source of variation affecting gene expression and quantitative phenotypes.

Genes, Plant↗