SEARCH · PubMed Health

Results for “QTL mapping”

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

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

At least 469 records · Page 26Linked to original sources

PubMed2004

Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits.

From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given.

Chromosome Mapping↗

PubMed2003

Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana.

Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a quantitative trait loci (QTL) mapping approach to identify loci affecting the after-ripening requirement measured as the number of days of seed dry storage required to reach 50% germination. Thus, seven QTL were identified and named delay of germination (DOG) 1-7. To confirm and characterize these loci, we developed 12 near-isogenic lines carrying single and double Cvi introgression fragments in a Ler genetic background. The analysis of these lines for germination in water confirmed four QTL (DOG1, DOG2, DOG3, and DOG6) as showing large additive effects in Ler background. In addition, it was found that DOG1 and DOG3 genetically interact, the strong dormancy determined by DOG1-Cvi alleles depending on DOG3-Ler alleles. These genotypes were further characterized for seed dormancy/germination behavior in five other test conditions, including seed coat removal, gibberellins, and an abscisic acid biosynthesis inhibitor. The role of the Ler/Cvi allelic variation in affecting dormancy is discussed in the context of current knowledge of Arabidopsis germination.

Abscisic Acid↗

PubMed1998

Localization of genes mediating acute and sensitized locomotor responses to cocaine in BXD/Ty recombinant inbred mice.

Sensitization to the psychostimulant effects of cocaine has received widespread attention because concomitant changes occur in neurochemical pathways that are part of the brain reward pathway. The current study was undertaken with the purpose of mapping genes determining sensitivity to the acute stimulant and sensitizing effects of cocaine. Sensitivity and sensitization to cocaine (5, 10, and 40 mg/kg) were measured in 25 BXD/Ty recombinant inbred (BXD RI) strains and the progenitor C57BL/6J (B6) and DBA/2J (D2) strains. Quantitative trait locus (QTL) mapping provisionally localized cocaine sensitivity genes to regions on all chromosomes except 6, 11, 17, and X; sensitization QTLs were localized to chromosomes 1-10, 13, 15, 18, 19, and X. Provisional QTLs for locomotion after saline injection in a novel setting were mapped to chromosomes 1, 3-6, 9, 12, 13, 18, and 19 and in a familiar setting to chromosomes 4-7, 9, 13, and 19. There were both common and unique QTL regions across the phenotypes. Evidence for a genetic association between magnitude of acute cocaine response and sensitization was obtained for only the 10 mg/kg dose. Some common QTL regions for cocaine, ethanol, and methamphetamine responses suggest the possibility that these drugs induce stimulant effects or sensitization through some common mechanisms. However, independent mechanisms were also indicated. Many candidate genes reside near the provisional QTLs mapped for cocaine responses, including genes coding a variety of neurotransmitter and hormone receptors. These data, once confirmed, should prove useful for directing investigations of acute and chronic cocaine effects down already suspected and novel avenues.

Animals↗

PubMed2003

Quantitative trait loci for susceptibility to tapeworm infection in the red flour beetle.

Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

Animals↗

PubMed2006

Characterization of the PGK2 associated microsatellite S0719 on SSC7 suitable for parentage and QTL diagnosis.

We isolated and characterized the highly polymorphic tetra-nucleotide microsatellite S0719 on SSC7q14-q15 adjacent to the porcine testis-specific phosphoglycerate kinase 2 (PGK2) gene and assigned it to the USDA-MARC linkage map on SSC7 position 77.5 cM closely linked to markers SW859 (76.3 cM) and SWR2036 (79.0 cM). In a panel of 344 individuals representing 11 pig breeds (European, Chinese, and North American), a total of 32 alleles were observed, and the overall breeds' calculated PIC (polymorphism information content), HE (heterozygosity), and NE (effective allele number) were 0.94, 0.94, and 16.41. Breed-specific PIC and HE ranged from 0.66 to 0.87, whereas NE was as low as 2.95 and as high as 7.96. Considering the high allelic variation of S0719 within and among pig breeds (79% of the genotyped animals were heterozygous), the marker is useful for individual animal identification and parentage determination. Finally, S0719 is also a valuable STS marker for fine-mapping QTL on SSC7 as position 77.5 cM is located in 25 QTL intervals.

Alleles↗

PubMed2000

[QTLs and epistasis underlying rice (Oryza sativa L.) panicle length in different genetic background and environments].

A double haploid (DH) population and a recombinant inbred (RI) population derived from a cross between a japonica male parent Azucena and indica female parents, IR64 and IR1552 respectively, were used in both field and pot experiments for detecting QTLs and epistasis for rice panicle length in different genetic background and different environments. Panicle length (PL) was measured at maturity. QTLs for PL were detected using single marker analysis and interval mapping. Epistasis effects on the trait were also analyzed. Nine QTLs were detected in DH population, including 5 QTLs detected from field experiment and 4 from pot experiment, among them 3 QTLs mapped on chromosomes 1 and 4 were identified in both field and pot experiments. No significant epistasis effect was detected for PL. Four QTLs were detected in RI population, among them 2 from field condition and 2 from pot experiment. 6 pairs of epistasis loci were detected in RI population. One QTL mapped on chromosome 4 and two pairs of epistatic loci were detected in both field and pot experiments. One QTL on chromosome four was identified in both populations, and one marker locus RG323 on chromosome one was involved in additive effect in DH population, but epistasis effects in RI population.

Chromosome Mapping↗

PubMed2002

Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions.

Drought stress during the reproductive stage is one of the most important environmental factors reducing the grain yield and yield stability of pearl millet. A QTL mapping approach has been used in this study to understand the genetic and physiological basis of drought tolerance in pearl millet and to provide a more-targeted approach to improving the drought tolerance and yield of this crop in water-limited environments. The aim was to identify specific genomic regions associated with the enhanced tolerance of pearl millet to drought stress during the flowering and grain-filling stages. Testcrosses of a set of mapping-population progenies, derived from a cross of two inbred pollinators that differed in their response to drought, were evaluated in a range of managed terminal drought-stress environments. A number of genomic regions were associated with drought tolerance in terms of both grain yield and its components. For example, a QTL associated with grain yield per se and for the drought tolerance of grain yield mapped on linkage group 2 and explained up to 23% of the phenotypic variation. Some of these QTLs were common across stress environments whereas others were specific to only a particular stress environment. All the QTLs that contributed to increased drought tolerance did so either through better than average maintenance (compared to non-stress environments) of harvest index, or harvest index and biomass productivity. It is concluded that there is considerable potential for marker-assisted backcross transfer of selected QTLs to the elite parent of the mapping population and for their general use in the improvement of pearl millet productivity in water-limited environments.

Journal Article↗

PubMed2004

The genetics of inviability and male sterility in hybrids between Anopheles gambiae and An. arabiensis.

Male hybrids between Anopheles gambiae and An. arabiensis suffer from hybrid sterility, and inviability effects are sometimes present as well. We examined the genetic basis of these reproductive barriers between the two species, using 21 microsatellite markers. Generally, recessive inviability effects were found on the X chromosome of gambiae that are incompatible with at least one factor on each arabiensis autosome. Inviability is complete when the gambiae and arabiensis inviability factors are hemi- or homozygous. Using a QTL mapping approach, regions that contribute to male hybrid sterility were also identified. The X chromosome has a disproportionately large effect on male hybrid sterility. Additionally, several moderate-to-large autosomal QTL were found in both species. The effect of these autosomal QTL is contingent upon the presence of an X chromosome from the other species. Substantial regions of the autosomes do not contribute markedly to male hybrid sterility. Finally, no evidence for epistatic interactions between conspecific sterility loci was found.

Animals↗

PubMed1999

Quantitative trait linkage mapping in anthropology.

Recent years have seen rapid progress in several areas of both biomedical and anthropological genetics. While genetic analyses have come to play a significant role in biological anthropology, there has been little use of modern methods for linkage mapping of quantitative trait loci (QTLs). It is now feasible to design research studies to investigate the quantitative genetics of complex phenotypes that are of primary importance to traditional questions in biological anthropology. Complex traits such as functionally significant morphological features, physiological characteristics or aspects of behavior can be examined to estimate the influence of genetic variation on within-species phenotypic variation. In addition, new methods for mapping quantitative trait loci provide opportunities to identify the regions within chromosomes that contain the functional genes of interest. This review summarizes molecular genetic and statistical genetic approaches to QTL mapping, and presents examples of how this approach can expand the scope of anthropological genetics to include mapping and identifying individual genes that influence complex phenotypic traits relevant to fundamental questions in biological anthropology.

Animals↗

PubMed2005

Back to the future: genetic correlations, adaptation and speciation.

Genetic correlations can affect the course of phenotypic evolution. Although genetic correlations among traits are a common feature of quantitative genetic analyses, they have played a very minor role in recent linkage-map based analyses of the genetic architecture of quantitative traits. Here, we use our work on host-associated races in pea aphids to illustrate how quantitative trait locus (QTL) mapping can be used to test specific hypotheses about how genetic correlations may facilitate ecological specialization and speciation.

Adaptation, Biological↗

PubMed2002

Extremely elongated tomato fruit controlled by four quantitative trait loci with epistatic interactions.

Cultivated tomato ( Lycopersicon esculentum) encompass a wide range of fruit shape and size variants. This variation can be used to genetically dissect the molecular basis of ovary and fruit morphology. The cultivar Long John displays an extremely elongated fruit phenotype, while the wild relative Lycopersicon pimpinellifolium LA1589 produces fruit that are nearly perfect spheres, typical of wild tomatoes. Quantitative trait mapping of an F2 population between Long John and LA1589 revealed four fruit shape QTLs, located on chromosomes 2, 3, 7 and 11. The primary role of the fruit shape QTL located on chromosome 7, ljfs7, is to control pericarp elongation. The primary role of the fruit shape QTLs on chromosome 2, 3 and 11 ( ljfs2, ljfs3 and ljfs11, respectively) is to control pear shape, measured as the eccentricity index. QTL map position and the effect of the loci on fruit shape suggested that ljfs2 and ljfs7 are allelic to the well-studied fruit shape loci ovate and sun, respectively. ljfs3 and ljfs11 map near the previously identified, but less characterized, fruit shape loci fs3.2 and fs11.1, respectively. This result suggests that most of the variation in tomato fruit shape is controlled by a few major QTLs. Although eccentricity and pericarp elongation were largely controlled by independent growth processes, significant interactions were detected between all four fruit shape loci in the control of eccentricity. This indicates that the three eccentricity loci, ljfs2, ljfs3 and ljfs11, epistatically control the same developmental process, while ljfs7 had a pleiotropic effect on eccentricity.

Journal Article↗

PubMed2002

Lifespan, QTLs, age-specificity, and pleiotropy in Drosophila.

We have constructed a set of 120 recombinant inbred lines for use in studies of the genetics of lifespan in Drosophila. The lines are derived from Luckinbill and Clare's (Heredity 55 (1985) 9) artificial selection experiment for increased lifespan. Inbred lines retain the relative lifespan characteristics of the experimental and control stocks from which they are derived. Mapping experiments suggest that a small number of QTLs accounts for much of the selection response. The age-specificity of genetic effects is best visualized in three-dimensional QTL maps of age-specific mortality. QTLs are shared by males and females, and have effects on age-specific mortality that are positively correlated across ages, with different times of onset. There is evidence for positively correlated pleiotropic effects of lifespan QTLs on mid-life fertility and resistance to an oxidizing chemical, and a striking lack of evidence for negative pleiotropy.

Animals↗

PubMed1995

Interval mapping of quantitative trait loci employing correlated trait complexes.

An approach to increase the resolution power of interval mapping of quantitative trait (QT) loci is proposed, based on analysis of correlated trait complexes. For a given set of QTs, the broad sense heritability attributed to a QT locus (QTL) (say, A/a) is an increasing function of the number of traits. Thus, for some traits x and y, H(xy)2(A/a) > or = H(x)2(A/a). The last inequality holds even if y does not depend on A/a at all, but x and y are correlated within the groups AA, Aa and aa due to nongenetic factors and segregation of genes from other chromosomes. A simple relationship connects H2 (both in single trait and two-trait analysis) with the expected LOD value, ELOD = -1/2N log(1-H2). Thus, situations could exist that from the inequality H(xy)2(A/a) > or = H(x)2(A/a) a higher resolution is provided by the two-trait analysis as compared to the single-trait analysis, in spite of the increased number of parameters. Employing LOD-score procedure to simulated backcross data, we showed that the resolution power of the QTL mapping model can be elevated if correlation between QTs is taken into account. The method allows us to test numerous biologically important hypotheses concerning manifold effects of genomic segments on the defined trait complex (means, variances and correlations).

Analysis of Variance↗

PubMed2004

Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas.

We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70-75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping.

Animals↗

PubMed2005

Fine mapping of a QTL for intramuscular fat on porcine chromosome 6 using combined linkage and linkage disequilibrium mapping.

In this study data from a commercial Norwegian slaughter pig cross was analysed to confirm a previous reported quantitative trait locus (QTL) affecting intramuscular fat (IMF) on porcine chromosome 6. The data consisted of an old experiment, in which the QTL was previously detected, and new experimental data from the Norwegian slaughter pig cross. The old and new experimental data were analysed separately and together. A previously described method combining linkage and linkage disequilibrium analysis (LDLA) was used for the analysis, but this method assumes that all animals are descendants from a common base population, which is not realistic in a cross between different breeds. An adjusted version of the method, able to distinguish between different breeds in the cross, is presented here. Using the LDLA method, we were not able to confirm the QTL in the old experimental data, because the genetic variance could be explained by the polygenic effect. Analysis from the new experimental data did however detect the QTL, and analysing the data from both experiments together gave highly significant results for a QTL (p < 0.001) between markers SW1355 and SW1823. The main conclusion is therefore that the previously reported QTL for IMF on porcine chromosome 6 was confirmed within a 8.7-cM confidence interval.

Adipose Tissue↗

PubMed2001

Two tightly linked QTLs modify tomato sugar content via different physiological pathways.

Congenic lines that differ in a single defined chromosome segment are useful for the study of complex phenotypes, as they allow isolation of the effect of a particular quantitative trait locus (QTL) from those of the entire genome. We conducted high-resolution QTL mapping of a 9-cM introgression, originating from the wild tomato species Lycopersicon pennellii, in two extremely different genetic and physiological backgrounds. In the "indeterminate" glasshouse background we identified only a single QTL ( Brix9-2-5) that affects the total soluble solids of the fruit [mainly sugars, measured in Brix units (B)]. This QTL was previously delimited within the gene for an apoplastic invertase, Lin5, that modulates sugar partitioning to the fruit. Analysis of the effects of the same chromosome segment in "determinate", open-field tomatoes, revealed two QTLs, 0.3 cM apart: the fruit-specific Brix9-2-5 that affects B only, and the shoot-specific PW9-2-5, which accounts for an altered growth habit resulting in increases in plant weight, yield, and B. This study highlights the power of the congenic approach for dissecting developmental pathways leading to complex phenotypes.

Base Sequence↗

PubMed2006

QTL methodology for response curves on the basis of non-linear mixed models, with an illustration to senescence in potato.

The improvement of quantitative traits in plant breeding will in general benefit from a better understanding of the genetic basis underlying their development. In this paper, a QTL mapping strategy is presented for modelling the development of phenotypic traits over time. Traditionally, crop growth models are used to study development. We propose an integration of crop growth models and QTL models within the framework of non-linear mixed models. We illustrate our approach with a QTL model for leaf senescence in a diploid potato cross. Assuming a logistic progression of senescence in time, two curve parameters are modelled, slope and inflection point, as a function of QTLs. The final QTL model for our example data contained four QTLs, of which two affected the position of the inflection point, one the senescence progression-rate, and a final one both inflection point and rate.

Nonlinear Dynamics↗

PubMed2002

Two QTLs located on chromosomes 1 and 5 modulate different aspects of the performance of mice of the B x D Ty RI strain series in the Morris navigation task.

The Morris navigation task is widely used to study spatial abilities in rodents; namely, to analyze the effects of mutations in genetically engineered mice. Although quantitative and Mendelian genetic studies have shown that the variation of these abilities is partly under genetic control, little is known about these genetic factors. In order to analyze the genetic architecture of spatial navigation in mice, a wide genome scan was performed to map the QTLs that control various aspects of the performance, using the RI strain methodology. Latencies to locate the submerged platform across learning sessions and performance to the spatial probe test were analyzed in the 26 strains of the B x D RI series. Both cluster analysis of behavioral measurements and QTL mapping confirmed previous data showing that the escape latencies and the spatial bias rely on two distinct components of the task, controlled by different loci. A QTL on chromosome 1 influenced escape latencies during the four training sessions, whereas another QTL, located on chromosome 5, was shown to control spatial performance at the probe trial and also exhibited epistatic interactions with two other QTLs on chromosomes 2 and 13. The function of these QTLs is examined in the broader context of hippocampal-dependent learning processes and in relation to QTLs already found in similar positions in other behavioral traits.

Animals↗