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At least 505 records · Page 28Linked to original sources
PubMed2005

Mapping quantitative trait loci in multiple populations of Arabidopsis thaliana identifies natural allelic variation for trichome density.

The majority of biological traits are genetically complex. Mapping the quantitative trait loci (QTL) that determine these phenotypes is a powerful means for estimating many parameters of the genetic architecture for a trait and potentially identifying the genes responsible for natural variation. Typically, such experiments are conducted in a single mapping population and, therefore, have only the potential to reveal genomic regions that are polymorphic between the progenitors of the population. What remains unclear is how well the QTL identified in any one mapping experiment characterize the genetics that underlie natural variation in traits. Here we provide QTL mapping data for trichome density from four recombinant inbred mapping populations of Arabidopsis thaliana. By aligning the linkage maps for these four populations onto a common physical map, the results from each experiment were directly compared. Seven of the nine QTL identified are population specific while two were mapped in all four populations. Our results show that many lineage-specific alleles that either increase or decrease trichome density persist in natural populations and that most of this genetic variation is additive. More generally, these findings suggest that the use of multiple populations holds great promise for better understanding the genetic architecture of natural variation.

Arabidopsis↗
PubMed2000

Optimal marker density for interval mapping in a backcross population.

An important question in QTL mapping is the optimal choice of marker density. Using analytical results, it is shown for the case of interval mapping in a backcross population, that the power of QTL detection and the standard errors of genetic effect estimates are little affected by an increase of marker density beyond 10 cM. This finding confirms published simulation results by other authors.

Analysis of Variance↗
PubMed1992

Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland.

Linkage disequilibrium mapping in isolated populations provides a powerful tool for fine structure localization of disease genes. Here, Luria and Delbrück's classical methods for analysing bacterial cultures are adapted to the study of human isolated founder populations in order to estimate (i) the recombination fraction between a disease locus and a marker; (ii) the expected degree of allelic homogeneity in a population; and (iii) the mutation rate of marker loci. Using these methods, we report striking linkage disequilibrium for diastrophic dysplasia (DTD) in Finland indicating that the DTD gene should lie within 0.06 centimorgans (or about 60 kilobases) of the CSF1R gene. Predictions about allelic homogeneity in Finland and mutation rates in simple sequence repeats are confirmed by independent observations.

Base Sequence↗
PubMed2004

Linkage disequilibrium mapping in trisomic populations: analytical approaches and an application to congenital heart defects in Down syndrome.

Many of the birth defects associated with trisomy exhibit both variable expressivity and incomplete penetrance. This variability suggests that it is allelic variation and not simply the presence of an additional chromosome that leads to the development of certain trisomy-associated birth defects. With the proper tools, one may use trisomic populations to identify genes involved in the development of specific birth defects. A trisomic population may be advantageous over a normal population if the defect is over-represented in the trisomic population. Alternatively, one can view the trisomic populations as a "model system" to offer insight into aspects of both normal and abnormal embryonic development. Standard disomic linkage disequilibrium mapping approaches need to be adjusted to account for the presence of the additional genetic material in the trisomic individuals. We present an approach for linkage disequilibrium mapping of variable phenotypes in a trisomic population that adequately accounts for the additional alleles and the pattern of non-independent inheritance. We establish the laboratory methods and statistical tools necessary to conduct an association study in a trisomic population. As an example, we have applied these tools to a pilot study of Down syndrome-associated congenital heart defects.

Alleles↗
PubMed2003

On the applicability of a haplotype map to un-assayed populations.

The rationale for mapping all common haplotypes in our species relies on reports of the conservation of haplotype blocks across human populations. Recent findings indicate that these blocks may, at least in part, be a random artifact of genetic drift. This raises the concern that the latter process may challenge the general applicability of a human haplotype map to case-by-case population-specific association studies. We develop arguments indicating that even stochastic drift-originated blocks will, under many conditions, be shared across populations, supporting the utilization of a panhuman haplotype map.

Alleles↗
PubMed2003

Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping.

Efforts to build a comprehensive genetic linkage map for the turkey (Meleagris gallopavo) have focused on development of genetic markers and experimental resource families. In this study, PCR amplification was attempted for 772 microsatellite markers that had been previously developed for three avian species (chicken, quail and turkey). Allelic polymorphism at 410 markers (53.1% of total examined) was determined by genotyping ten individuals (six F1 parents and four grandparents) in a new resource population specifically developed for genetic linkage mapping. Of these 410 markers, 109 (26.6%) were polymorphic in the tested individuals, with an average of 2.3 alleles per marker. Higher levels of polymorphism were found for the turkey-specific markers (61.1%) than for the chicken (22.7%) or quail-specific markers (33.3%). To test the fidelity of the matings, demonstrate the power of these families for linkage analysis, and determine genetic linkage relationships, 86 polymorphic markers were genotyped for up to 224 birds including founder grandparents, parents and F2 progeny. Linkage relationships for many of the chicken markers elucidated in the turkey were comparable to those observed in the chicken. These data demonstrate that the new UMN/NTBF resource population will provide a solid foundation for constructing a comparative genetic map of the turkey.

Alleles↗
PubMed2005

The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population.

Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.

Allium↗
PubMed2000

Cocaine-induced seizure thresholds: quantitative trait loci detection and mapping in two populations derived from the C57BL/6 and DBA/2 mouse strains.

Seizures are a well known consequence of human cocaine abuse, and in rodent models, sensitivity to cocaine seizures has been shown to be strongly influenced by genotype. For example, several studies have reported significant differences between the C57BL/6 (B6) and DBA/2 (D2) inbred mouse strains in their sensitivity to cocaine-induced seizures. This prompted our use of the BXD recombinant inbred (RI) strain set and an F(2) population derived from the B6 and D2 progenitor strains for further genetic analyses and for gene mapping efforts in this study. Cocaine was infused into the lateral tail vein, and the doses needed to induce a running bouncing clonic seizure and a tonic hindlimb extensor seizure were recorded for each mouse. In the BXD RI set, a genome-wide search was carried out for QTLs (quantitative trait loci), which are sites on a chromosome containing genes that influence seizure susceptibility. An F(2) population (B6D2F2, n = 408) was subsequently used as a second, confirmation step. Based on both RI and F(2) results, three QTLs emerged as significant (P <.00005): one for clonic seizures on chromosome 9 (distal), and two for tonic seizures on chromosomes 14 (proximal to mid) and 15 (distal). Two additional QTLs emerged as suggestive (P <.0015), both associated with clonic seizures on chromosomes 9 (proximal) and 15 (distal). Both QTLs on chromosome 9 were sex-specific, with much larger effects on the phenotype seen in females than in males.

Animals↗
PubMed2006

Comparison of linkage maps from F2 and three times intermated generations in two populations of European flint maize (Zea mays L.).

Intermated mapping populations are expected to result in high mapping resolution for tightly linked loci. The objectives of our study were to (1) investigate the consequences of constructing linkage maps from intermated populations using mapping methods developed for F(2) populations, (2) compare linkage maps constructed from intermated populations (F(2)Syn3) with maps generated from corresponding F(2) and F(3) base populations, and (3) investigate the advantages of intermated mapping populations for applications in plant breeding programs. We constructed linkage maps for two European flint maize populations (A x B, C x D) by mapping 105 SSR markers in generations F(2) and F(2)Syn3 of population A x B, and 102 SSR markers in generations F(3) and F(2)Syn3 of population C x D. Maps for F(2)Syn3 were constructed with mapping methods for F(2) populations (Map A) as well as with those specifically developed for intermated populations (Map B). Both methods relate map distances to recombination frequencies in a single meiosis and, therefore, did not show a map expansion in F(2)Syn3 compared with maps constructed from the respective F(2) or F(3) base populations. Map A and B differed considerably, presumably because of theoretical shortcomings of Map A. Since loosely linked markers could not unambiguously be mapped in the F(2)Syn3 populations, they may hamper the construction of linkage maps from intermated populations.

Chromosome Mapping↗
PubMed2001

Linkage disequilibrium mapping: the role of population history, size, and structure.

Linkage disequilibrium mapping attempts to infer the location of a disease gene from observed associations between marker alleles and disease phenotype. This approach can be quite powerful when disease chromosomes are descended from a single founder mutation and the markers considered are tightly linked to the disease locus. The success of linkage disequilibrium map ping in fine-scale localization has led to the suggestion that genome-wide association testing might be useful in the detection of susceptibility genes for complex traits. Such studies would likely be performed in small, relatively isolated founder populations, where heterogeneity of the disease is less likely. To interpret the patterns of association observed in such populations, we need to understand the effect of population size, history, and structure on linkage disequilibrium. In this chapter, we first review measures of allelic association at a single locus. Measures of association between two loci are described, and some theoretical results are reviewed. We then consider some methods for inferring linkage between a marker and a rare disease, focusing on those that model the ancestry of the disease chromosomes. Next we discuss factors whose effect on disequilibrium are understood, and finally we describe the characteristics of some human populations that may be useful for disequilibrium mapping of complex traits.

Analysis of Variance↗
PubMed2005

Place cells, spatial maps and the population code for memory.

The study of population dynamics in hippocampal place cells has emerged as one of the most powerful tools for understanding the encoding, storage and retrieval of declarative memory. Recent work has laid out the contours of an attractor-based hippocampal population code for memory in recurrent circuits of the hippocampus. The code is based on inputs from a topographically organized, path-integration-dependent spatial map that lies upstream in the medial entorhinal cortex. The recurrent networks of the hippocampal formation enable these spatial inputs to be synthesized with nonspatial event-related information.

Animals↗
PubMed2002

Multiple QTL mapping in related plant populations via a pedigree-analysis approach.

QTL mapping experiments in plant breeding may involve multiple populations or pedigrees that are related through their ancestors. These known relationships have often been ignored for the sake of statistical analysis, despite their potential increase in power of mapping. We describe here a Bayesian method for QTL mapping in complex plant populations and reported the results from its application to a (previously analysed) potato data set. This Bayesian method was originally developed for human genetics data, and we have proved that it is useful for complex plant populations as well, based on a sensitivity analysis that was performed here. The method accommodates robustness to complex structures in pedigree data, full flexibility in the estimation of the number of QTL across multiple chromosomes, thereby accounting for uncertainties in the transmission of QTL and marker alleles due to incomplete marker information, and the simultaneous inclusion of non-genetic factors affecting the quantitative trait.

Journal Article↗
PubMed2002

Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations.

Several plant genetic maps presented in the literature are longer than expected from cytogenetic data. Here we compare F(2) and RI maps derived from a cross between the same two parental lines and show that excess heterozygosity contributes to map inflation. These maps have been constructed using a common set of dominant markers. Although not generally regarded as informative for F(2) mapping, these allowed rapid map construction, and the resulting data analysis has provided information not otherwise obvious when examining a population from only one generation. Segregation distortion, a common feature of most populations and marker systems, found in the F(2) but not the RI, has identified excess heterozygosity. A few markers with a deficiency of heterozygotes were found to map to linkage group V (chromosome 3), which is known to form rod bivalents in this cross. Although the final map length was longer for the F(2) population, the mapped order of markers was generally the same in the F(2) and RI maps. The data presented in this analysis reconcile much of the inconsistency between map length estimates from chiasma counts and genetic data.

Chromosome Mapping↗
PubMed1995

Perspectives of identity by descent (IBD) mapping in founder populations.

In a founder population patients with a genetic disease are likely to share predisposing genes from a common ancestor. We show that, depending on the distance of the relationship, patients are expected to share extended segments of DNA around the disease gene. Because of the size of the shared segment, a genomic search with DNA markers for such shared segments, identity by descent (IBD) mapping, can efficiently find the map position of genes, particularly due to genetic drift leading to reduction of heterogeneity and the large number of meioses that is implicitly observed. The statistical power of this method and the approximate cost are given as a function of the density of the map of tested markers and the number of generations since a common ancestor. Initial marker spacings between 5 and 15 centiMorgans are shown to be optimal. IBD mapping is applicable to many genetic diseases, because it does not presuppose a specific genetic model.

Alleles↗
PubMed2001

Joint linkage and linkage disequilibrium mapping in natural populations.

A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the information about the linkage of the markers (as measured by recombination fraction) and the degree of their linkage disequilibrium created at a historic time. Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and positional cloning of the genes underlying both simple and complex traits.

Alleles↗
PubMed2002

Development of "normal" dermatomes and somatotopic maps by "abnormal" populations of cutaneous neurons.

During development, motor and sensory axons grow to peripheral targets with remarkable precision. Whereas much has been learned about the development of motoneuron connectivity, less is known about the regulation of cutaneous innervation. In adults, dorsal root ganglia (DRG) innervate characteristic skin regions, termed dermatomes, and their axons project somatotopically in the dorsal horn. Here, we have investigated whether cutaneous neurons are selectively matched with specific skin regions, and whether peripheral target skin influences the central connections of cutaneous neurons. To address these questions, we shifted limb buds rostrally in chick embryos prior to axon outgrowth, causing DRGs to innervate novel skin regions, and mapped the resulting dermatomes and central projections. Following limb shifts, cutaneous innervation arose from more rostral and from fewer DRGs than normal, but the overall dermatome pattern was preserved. Thus, DRGs parcel out innervation of skin in a consistent manner, with no indication of matching between skin and DRGs. Similarly, cutaneous nerves established a "normal" somatotopic map in the dorsal horn, but in more rostral segments than usual. Thus, the peripheral target skin may influence the pattern of CNS projections, but does not direct cutaneous axons to specific populations of neurons in the dorsal horn.

Afferent Pathways↗
PubMed1996

Haplotype identity between individuals who share a CFTR mutation allele "identical by descent": demonstration of the usefulness of the haplotype-sharing concept for gene mapping in real populations.

Cystic fibrosis (CF) patients with the A455E mutation, in both the French Canadian and the Dutch population, share a common haplotype over distances of up to 25 cM. French Canadian patients with the 621+1G-->T mutation share a common haplotype of more than 14 cM. In contrast, haplotypes containing the delta F508 mutation show haplotype identity over a much shorter genomic distance within and between populations, probably because of the multiple introduction of this most common mutation. Haplotype analysis for specific mutations in CF or in other recessive diseases can be used as a model for studying the occurrence of genetic drift conditional on gene frequencies. Moreover, from our results, it can be inferred that analysis of shared haplotypes is a suitable method for genetic mapping in general.

Base Sequence↗
PubMed2003

Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population.

Admixture mapping is a potentially powerful tool for mapping complex genetic diseases. For application of this method, admixed individuals must have genomes composed of large segments derived intact from each founding population. Such segments are thought to be present in African Americans (AA) and should be demonstrable by examination of linkage disequilibrium (LD). Previous studies using a variety of polymorphic markers have variably reported long-range LD or rapid decay of LD. To further define the extent and characteristics of LD caused by admixture in the AA population, the current study utilized a set of 52 diallelic markers that were selected for large standard variances between putative representatives of the founder populations. LD was examined in over 250 marker-pairs, including linked markers from four different chromosomal regions and an equal number of matched unlinked comparisons. In the representative founder populations, strong LD was not observed for markers separated by more than 10 kb. In contrast, results indicated significant LD ( P<0.001, D'>0.3) in AA over large genomic segments exceeding 10 centiMorgans (cM) and 15 megabases (Mb). Only marginally significant LD was present between unlinked markers in this population, suggesting that choosing appropriate levels of significance for admixture mapping can minimize false positive results. The ability to detect LD for extended chromosomal segments in AA decayed not only as a function of the distance between markers, but also as a function of the standard variance of the markers. This examination of several genomic segments provides strong evidence that appropriate selection of informative markers is a crucial prerequisite for the application of admixture mapping to the AA population.

Black or African American↗