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PubMed2002

Similar genetic susceptibility to form-deprivation myopia in three strains of chicken.

Myopia development in humans depends on a complex interplay between genetic and environmental factors. Many of those who become myopic when exposed to a myopigenic environment are likely to do so because of a genetic susceptibility, whereas others somehow remain immune. In the most intensively studied model of environmentally induced myopia, form-deprivation myopia in the chick, there is convincing evidence of differential genetic susceptibility to myopia development, both within-strains and between-strains. To date, however, these have involved relatively small differential responses. The aim of this investigation was to examine genetic susceptibility to a highly uniform regimen of form-deprivation in three strains of chick (white leghorn, brown leghorn and broiler) expected to differ greatly in genetic background and in normal eye size, and to gauge the potential for mapping the quantitative trait loci (QTL) underlying this differential susceptibility. Despite striking differences in normal eye size, all three strains studied developed a similar degree of induced myopia. Whilst the degree of induced vitreous chamber elongation differed significantly between-strains, it was concluded that the high within-strain variation in the response to form-deprivation would prevent the effective application of QTL mapping approaches to identify genes conferring this susceptibility. In contrast, the strains used here would be ideal for use in mapping QTL controlling normal ocular component dimensions.

Analysis of Variance↗
PubMed2005

Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice.

We have mapped epistatic quantitative trait loci (QTL) in an F2 cross between DU6i x DBA/2 mice. By including these epistatic QTL and their interaction parameters in the genetic model, we were able to increase the genetic variance explained substantially (8.8%-128.3%) for several growth and body composition traits. We used an analysis method based on a simultaneous search for epistatic QTL pairs without assuming that the QTL had any effect individually. We were able to detect several QTL that could not be detected in a search for marginal QTL effects because the epistasis cancelled out the individual effects of the QTL. In total, 23 genomic regions were found to contain QTL affecting one or several of the traits and eight of these QTL did not have significant individual effects. We identified 44 QTL pairs with significant effects on the traits, and, for 28 of the pairs, an epistatic QTL model fit the data significantly better than a model without interactions. The epistatic pairs were classified by the significance of the epistatic parameters in the genetic model, and visual inspection of the two-locus genotype means identified six types of related genotype-phenotype patterns among the pairs. Five of these patterns resembled previously published patterns of QTL interactions.

Animals↗
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↗
PubMed2002

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

BACKGROUND: The identification of genes underlying complex traits has been aided by quantitative trait locus (QTL) mapping approaches, which in turn have benefited from advances in mammalian genome research. Most recently, whole-genome draft sequences and assemblies have been generated for mouse strains that have been used for a large fraction of QTL mapping studies. Here we show how such strain-specific mouse genome sequence databases can be used as part of a high-throughput pipeline for the in silico discovery of gene-coding variations within murine QTLs. As a test of this approach we focused on two QTLs on mouse chromosomes 1 and 13 that are involved in physical dependence on alcohol. RESULTS: Interstrain alignment of sequences derived from the relevant mouse strain genome sequence databases for 199 QTL-localized genes spanning 210,020 base-pairs of coding sequence identified 21 genes with different coding sequences for the progenitor strains. Several of these genes, including four that exhibit strong phenotypic links to chronic alcohol withdrawal, are promising candidates to underlie these QTLs. CONCLUSIONS: This approach has wide general utility, and should be applicable to any of the several hundred mouse QTLs, encompassing over 60 different complex traits, that have been identified using strains for which relatively complete genome sequences are available.

Alcohol Withdrawal Seizures↗
PubMed2005

Quantitative trait loci and interaction effects responsible for variation in female postmating mortality in Drosophila simulans and D. sechellia introgression lines.

Mating appears to inflict a cost to Drosophila females, resulting in a reduction of their lifespan shortly after mating. Males from different chromosome extracted lines differ significantly in their detrimental effects on postmating female survival, and seminal fluid proteins produced in the male accessory glands are at least partially responsible for the effect. This suggests that there is a genetic basis underlying the male inflicted effect on female's postmating mortality. However, the genes responsible for this effect remain elusive. Using males from introgression lines between D. simulans and D. sechellia genomes and a quantitative trait locus (QTL) mapping approach, we identified chromosomal regions that affect postmating mortality of females. We found a second chromosome QTL with an effect on average female lifespan after mating and a third chromosome QTL with an effect on postmating female mortality rate. Under the general observation of a faster divergence of sex-related genes among closely related species, it is predicted that genes for reproductive traits other than hybrid sterility will show evidence of epistatic effects when brought into a heterospecific background. We detected a significant epistatic genetic effect on postmating female mortality rate that supports this prediction.

Animals↗
PubMed2006

Isolation, characterization, and linkage analyses of 74 novel microsatellites in Barramundi (Lates calcarifer).

Barramundi (Lates calcarifer) is an important marine food fish species in Southeast Asia and Australia. Seventy-four novel microsatellites were isolated from a genomic DNA library enriched for CA repeats and were characterized in 24 unrelated individuals. Among the 74 microsatellites, 71 were polymorphic, with an average allele number of 7.0 +/- 3.6/locus. The average expected heterozygosity of these polymorphic markers was 0.66. Sixty-three of the 71 polymorphic microsatellites conformed to Hardy-Weinberg equilibrium. Linkage analyses were conducted in a reference family, leading to the assignment of 34 novel microsatellites and 16 published markers in 16 linkage groups. The novel microsatellites developed in this study will contribute significantly to the construction of a first-generation linkage map for mapping of quantitative trait loci in Barramundi, and supply a large choice of markers for studies on population genetics, stock management, and pedigree reconstruction.

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 mechanisms of floral trait correlations in a natural population.

Genetic correlations among traits are important in evolution, as they can constrain evolutionary change or reflect past selection for combinations of traits. Constraints and integration depend on whether the correlations are caused by pleiotropy or linkage disequilibrium, but these genetic mechanisms underlying correlations remain largely unknown in natural populations. Quantitative trait locus (QTL) mapping studies do not adequately address the mechanisms of within-population genetic correlations because they rely on crosses between distinct species, inbred lines or selected lines (see ref. 5), and they cannot distinguish moderate linkage disequilibrium from pleiotropy because they commonly rely on only one or two episodes of recombination. Here I report that after nine generations of enforced random mating (nine episodes of recombination), correlations between six floral traits in wild radish plants are unchanged, showing that pleiotropy generates the correlations. There is no evidence for linkage disequilibrium despite previous correlational selection acting on one functionally integrated pair of traits. This study provides direct evidence of the genetic mechanisms underlying correlations between quantitative traits in a natural population and suggests that there may be constraints on the independent evolution of pairs of highly correlated traits.

Biological Evolution↗
PubMed1996

Less-than-additive epistatic interactions of quantitative trait loci in tomato.

Epistasis plays a role in determining the phenotype yet quantitative trait loci (QTL) mapping has uncovered little evidence for it. To address this apparent contradiction, we analyzed interactions between individual Lycopersicon pennellii chromosome segments introgressed into an otherwise homogeneous genetic background of L. esculentum (cv. M82). Ten different homozygous introgression lines, each containing from 4 to 58 cM of introgressed DNA, were crossed in a half diallele scheme. The 45 derived double heterozygotes were evaluated in the field for four yield-associated traits, along with the 10 single heterozygotes and M82. Of 180 (45 x 4) tested interactions, 28% were epistatic (P < 0.05) on both linear and geometric scales. The detected epistasis was predominantly less-than-additive, i.e., the effect of the double heterozygotes was smaller than the sum of the effects of the corresponding single heterozygotes. Epistasis was also found for homozygous linked QTL affecting fruit mass and total soluble solids. Although the frequency of epistasis was high, additivity was the major component in the interaction of pairs of QTL. We propose that the diminishing additivity of QTL effects is amplified when more loci are involved; this mode of epistasis may be an important factor in phenotype canalization and in breeding.

Epistasis, Genetic↗
PubMed1998

Genetic determinants of autoimmune disease and coronary vasculitis in the MRL-lpr/lpr mouse model of systemic lupus erythematosus.

MRL-lpr/lpr (MRL/lpr) mice are a model of human autoimmune disease. They exhibit a number of characteristics of systemic lupus erythematosus, including anti-DNA Abs, anti-cardiolipin Abs, immune complex-mediated vasculitis, lymphadenopathy, and severe glomerulonephritis. Although the autoimmune disorder is mediated primarily by mutation of the Fas gene (lpr), which interferes with lymphocyte apoptosis, MRL/lpr mice also have other predisposing genetic factors. In an effort to identify these additional factors, we have applied quantitative trait locus (QTL) mapping using an intercross between MRL/lpr mice and the nonautoimmune inbred strain BALB/cJ. A complete linkage map spanning the entire genome was constructed for 189 intercross progeny, and genetic loci contributing to features of the autoimmunity were identified using statistical analytic procedures. As expected, the primary genetic determinant of autoimmune disease in this cross was the Fas gene on mouse chromosome 19, exhibiting a lod score of 60. In addition, two novel loci, one on chromosome 2 (lod score, 4.3) and one on chromosome 11 (lod score, 3.1), were found to contribute to levels of anti-DNA Abs. Interestingly, the chromosome 19 and chromosome 11 QTLs, but not the chromosome 2 QTL, also exhibited associations with anti-cardiolipin Abs (lod scores, 38.4 and 2.6). We further examined the effects of these QTLs on the development of coronary vasculitis in the F2 mice. Our results indicate that the QTLs on chromosomes 11 and 19 also control the development of vasculitis, demonstrating common genetic determinants of autoantibody levels and vasculitis.

Animals↗
PubMed2003

[Localization of genes, determining quantitative traits in wheat: amendment to the "catalog of chromosomal mapping of genes in domestic cultivars of wheat"].

An amendment to the catalog of chromosome location of genes in Russian wheat cultivars was constructed with the published data of the recent decade. The results of chromosomal localization were summarized and analyzed by methods of multivariate statistics. Chromosomes critical for 40 quantitative traits under study proved to cluster according to their homeology, i.e., by homeological groups. The hypotheses providing an explanation for this finding are considered. It is suggested that quantitative traits are similarly controlled by genes located on homeological chromosomes in common wheat, making it possible to isolate a limited number of major genes for each particular quantitative trait.

Chromosome Mapping↗
PubMed1999

Rapid and precise genotyping of porcine microsatellites.

Microsatellites are useful markers for genetic mapping and linkage analysis because they are highly polymorphic, abundant in genomes and relatively easily scored with polymerase chain reaction (PCR). A rapid genotyping system for microsatellites was developed, which included multiplex PCRs, multiple use of Hydrolink gels, automated fluorescent detection of fragments on an A.L.F. DNA sequencer, automatic assignment of alleles to each locus and verification of genotypes with a self-developed computer program "Fragtest". Eight multiplex PCRs have been developed to genotype 29 microsatellites for genetic and quantitative trait loci (QTL) mapping on pig chromosomes 6, 7, 12 and 13. Three to six microsatellites could be amplified in one multiplex PCR. Each multiplex reaction required only different concentrations of each pair of primers and a low concentration of dNTP (100 microM). A dNTP concentration of 100 microM proved to be optimal for the coamplification of microsatellites under the concentration of 1.5 mM MgCl2. Using four internal size standards added in each sample, the 5% Hydrolink gel could subsequently be used up to five times (total running time of 500 min) on the A.L.F. automated sequencer without significant loss of resolution and precision of fragment length analysis. Automatic assignment of alleles on each locus using "Fragtest" significantly increased the efficiency and precision of the genotyping. This system is thus a rapid, cheap, and highly discriminating genotyping system.

Animals↗
PubMedDate not supplied

A male linkage map of the cattle (Bos taurus) genome.

A male linkage map of the cattle (Bos taurus) genome was constructed using nine large half-sib families. The map consists of 269 loci, of which 249 are microsatellites and 20 are structural genes. Among the 249 microsatellites, 140 are markers selected from other maps and 98 are new assignments. Chromosome assignment were established for 35 new markers by somatic cell hybrid analysis, of which 26 were confirmed by linkage analysis. Genome coverage is 1975 cM contained within terminal markers on all 29 autosomes. The average distance between adjacent loci is 9.7 cM, with 72.1% of the map intervals < or = 15 cM and 4.9% of the intervals > or = 25 cM. The inclusion of mapped markers permitted integration and comparisons with other maps, facilitating the identification of discrepancies in chromosome assignment, gene order, and map distance. The inclusion of Type I and blood group markers in the map was useful for comparative mapping, revealing possible blood group orthologies between humans and cattle. The map generated will serve as a useful tool for comparative mapping, mapping of quantitative trait loci and marker assisted selection.

Animals↗
PubMed2005

[Mapping QTLs controlling vascular bundle and panicle-related traits from Yuanjiang common wild rice (Oryza rufipogon Griff.)].

An advanced backcross population (BC3F2), derived from the cross between Yuanjiang common wild rice as the donor parent and Teqing as recurrent parent, was used to map QTLs controlling the number of vascular bundle and panicle-related traits from Yuanjiang common wild rice. Seven QTLs controlling the number of large vascular bundles in peduncle were detected on chromosome 1, 2, 3, 4, 7 and 10. Five QTLs for the number of small vascular bundles in peduncle were mapped on chromosome 1, 2, 3, 4 and 8. A total of 15 QTLs for the number of primary and secondary rachis branches and spikelets per panicle were identified on all chromosomes except chromosome 11 and 12. Most of alleles derived from O. rufipogon Griff. showed negative effect that reduced significantly vascular bundle, rachis branches and spikelets per panicle, suggesting that during the evolution from common wild rice to cultivated rice, favorable alleles were retained while removed undesirable ones. Most of QTLs controlling vascular bundle, rachis branches and spikelets per panicle showed cluster form or close linkage on chromosomes. The directions of their additive effects were consistent, which explained the genetic basis of significant correlation of their phenotypic characters. All the information suggested parallel evolution relationship among these traits.

Chromosomes, Plant↗
PubMed2004

The genetic architecture of the behavioral ontogeny of foraging in honeybee workers.

The initiation of foraging during the life course of honeybee workers is of central interest to understanding the division of labor in social insects, a central theme in sociobiology and behavioral research. It also provides one of the most complex phenotypic traits in biological systems because of the interaction of various external, social, and individual factors. This study reports on a comprehensive investigation of the genetic architecture of the age of foraging initiation in honeybees. It comprises an estimation of genetic variation, the study of candidate loci, and two complementary quantitative trait loci (QTL) maps using two selected, continually bred lines of honeybees. We conclude that considerable genetic variation exists between the selected lines for this central life history component. The study reveals direct pleiotropic and epistatic effects of candidate loci (including previously identified QTL for foraging behavior). Furthermore, two maps of the honeybee genome were constructed from over 400 AFLP markers. Both maps confirm the extraordinary recombinational size of the honeybee genome. On the basis of these maps, we report four new significant QTL and two more suggestive QTL that influence the initiation of foraging.

Aging↗
PubMed1998

A Huntington disease-like neurodegenerative disorder maps to chromosome 20p.

Huntington disease (HD) is an autosomal dominant neurodegenerative disorder characterized by motor disturbance, cognitive loss, and psychiatric manifestations. The disease is associated with a CAG trinucleotide-repeat expansion in the Huntington gene (IT15) on chromosome 4p16.3. One family with a history of HD was referred to us initially for predictive testing using linkage analysis. However, the chromosome 4p region was completely excluded by polymorphic markers, and later no CAG-repeat expansion in the HD gene was detected. To map the disease trait segregating in this family, whole-genome screening with highly polymorphic dinucleotide-, trinucleotide-, and tetranucleotide-repeat DNA markers was performed. A positive LOD score of 3.01 was obtained for the marker D20S482 on chromosome 20p, by two-point LOD-score analysis with the MLINK program. Haplotype analysis indicated that the gene responsible for the disease is likely located in a 2.7-cM region between the markers D20S193 and D20S895. Candidate genes from the mapping region were screened for mutations.

Adult↗
PubMed2002

The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

Genetic Linkage↗
PubMed1997

Assessment of learning by the Morris water task and fear conditioning in inbred mouse strains and F1 hybrids: implications of genetic background for single gene mutations and quantitative trait loci analyses.

Genetic methods including the creation of transgenic or null mutant models and mapping studies using quantitative trait loci strategies can be used to identify candidate genes in mice that regulate learning processes. Interpretations as to the impact of single gene mutations for polygenic behaviours like learning will depend in part on the genetic background of the animals used for these manipulations. To address the issue of genetic variability, 12 inbred strains and seven different F1 hybrids were tested on multiple behavioural tasks, including two complex learning paradigms: the Morris water task and fear conditioning. Strain differences were found for all variables measured. In the hidden platform version of the Morris task, the albino animals performed poorly while overall the F1 hybrids showed the best selectivity for the trained quadrant as measured in a probe trial. In contrast, almost all genotypes performed well on the contextual fear conditioning task and learned to associate the test context with the pairing of a foot shock and auditory stimulus as demonstrated 24 h after training by increased freezing in the test environment compared to an altered context. Significant genetic correlations were obtained for behavioural measures suggesting that the same genes regulate various aspects of performance on behavioural tasks. Scores from these multiple inbred strains and F1 hybrids provide a baseline level of learning ability for fear conditioning and the Morris water task. The results of the present study confirm the importance of genetic background in the performance of various learning tasks. This variability should be considered when developing new transgenic or null mutant animal models.

Acoustic Stimulation↗