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PubMedDate not supplied

Quantitative trait loci influencing honeybee alarm pheromone levels.

Quantitative trait loci (QTL) mapping procedures were used to identify loci that influence the levels of alarm pheromones found in the stinging apparatus of worker honeybees. An F1 queen was produced from a cross between a queen of European origin and a drone descended from an African subspecies. Haploid drones from the hybrid queen were individually backcrossed to European queens to produce 172 colonies. Samples of stings were taken from backcross workers of these colonies. Alarm pheromone levels were determined by gas chromatography. RAPD markers were scored from the haploid drone fathers of these colonies. The multiple-QTL model (MQM) of MapQTL was used to identify QTLs that influence the levels of four alarm pheromone components. Seven independent, potential QTLs were identified with LOD scores greater than two, and one at LOD 1.88. We identified one QTL for n-decyl acetate, three for n-octanol, four for isopentyl acetate, and one for hexyl acetate. One region of linkage group XI shows a strong influence on body size and the levels of three alarm pheromone components. This locus explained 40% of the variance for the amount of n-decyl acetate (LOD 6.57). In general, the QTLs influencing alarm pheromone levels were independent of previously identified loci that influenced the stinging behavior of these colonies. The only exception was a potential locus influencing levels of n-octanol, which was inversely correlated with stinging behavior.

1-Octanol↗
PubMed2005

Single and interacting QTLs for cholesterol gallstones revealed in an intercross between mouse strains NZB and SM.

Quantitative trait locus (QTL) mapping was employed to investigate the genetic determinants of cholesterol gallstone formation in a large intercross between mouse strains SM/J (resistant) and NZB/B1NJ (susceptible). Animals consumed a gallstone-promoting diet for 18 weeks. QTL analyses were performed using gallstone weight and gallstone absence/presence as phenotypes; various models were explored for genome scans. We detected seven single QTLs: three new, significant QTLs were named Lith17 [chromosome (Chr) 5, peak=60 cM, LOD=5.4], Lith18 (Chr 5, 76 cM, LOD=4.3), and Lith19 (Chr 8, 0 cM, LOD=5.3); two confirmed QTLs identified previously and were named Lith20 (Chr 9, 44 cM, LOD=2.7) and Lith21 (Chr 10, 24 cM, LOD=2.9); one new, suggestive QTL (Chr 17) remains unnamed. Upon searching for epistatic interactions that contributed to gallstone susceptibility, the final suggestive QTL on Chr 7 was determined to interact significantly with Lith18 and, therefore, was named Lith22 (65 cM). A second interaction was identified between Lith19 and a locus on Chr 11; this QTL was named Lith23 (13 cM). mRNA expression analyses and amino acid haplotype analyses likely eliminated Slc10a2 as a candidate gene for Lith19. The QTLs identified herein largely contributed to gallstone formation rather than gallstone severity. Cloning the genes underlying these murine QTLs should facilitate prediction and cloning of the orthologous human genes.

Animals↗
PubMed2007

Separation of base allele and sampling term effects gives new insights in variance component QTL analysis.

BACKGROUND: Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix). RESULTS: We present an alternative notation of the variance component model, where the elements of the random effect are independent base generation allele effects and sampling term effects. The relationship between the phenotypic vales and the random effect is given by an incidence matrix, which results in a novel, but statistically equivalent, version of the traditional VC model. A general algorithm to estimate this incidence matrix is presented. Since the model is given in terms of base generation allele effects and sampling term effects, these effects can be estimated separately using best linear unbiased prediction (BLUP). From simulated data, we showed that biallelic QTL effects could be accurately clustered using the BLUP obtained from our model notation when markers are fully informative, and that the accuracy increased with the size of the QTL effect. We also developed a measure indicating whether a base generation marker homozygote is a QTL heterozygote or not, by comparing the variances of the sampling term BLUP and the base generation allele BLUP. A ratio greater than one gives strong support for a QTL heterozygote. CONCLUSION: We developed a simple presentation of the VC QTL model for identification of base generation allele effects in QTL linkage analysis. The base generation allele effects and sampling term effects were separated in our model notation. This clarifies the assumptions of the model and should also enhance the development of genome scan methods.

Alleles↗
PubMed1996

Molecular dissection of a major gene effect on a quantitative trait: the level of alcohol dehydrogenase expression in Drosophila melanogaster.

A molecular mapping experiment shows that a major gene effect on a quantitative trait, the level of alcohol dehydrogenase expression in Drosophila melanogaster, is due to multiple polymorphisms within the Adh gene. These polymorphisms are located in an intron, the coding sequence, and the 3' untranslated region. Because of nonrandom associations among polymorphisms at different sites, the individual effects combine (in some cases epistatically) to produce "superalleles" with large effect. These results have implications for the interpretation of major gene effects detected by quantitative trait locus mapping methods. They show that large effects due to a single locus may be due to multiple associated polymorphisms (or sequential fixations in isolated populations) rather than individual mutations of large effect.

Alcohol Dehydrogenase↗
PubMed2004

Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice.

Norin-PL8 is a cold-tolerant variety of rice (Oryza sativa L.) that was developed by introgressing chromosomal segments from a cold-tolerant tropical japonica variety, Silewah, into a template japonica variety, Hokkai241. We previously identified two closely linked quantitative trait loci, Ctb1 and Ctb2, for cold tolerance at the booting stage of Norin-PL8 in the long arm of chromosome 4. We report here the physical mapping of Ctb1 and the identification of the candidate genes. A total of 2,008 segregating individuals were screened for recombination in the Ctb1 region by a PCR-based screening, and a series of near-isogenic lines (NILs) were developed from progenies of recombinants. A comparison of the degrees of cold tolerance of the NILs indicated that Ctb1 is located in the 56-kb region covered by a bacterial artificial chromosome clone, OSJNBa0058 K23, that had been sequenced by the International Rice Genome Sequence Project. We found seven open reading frames (ORFs) in the 56-kb region. Two ORFs encoded receptor-like protein kinases that are possibly involved in signal transduction pathways. Proteins that may be associated with a ubiquitin-proteasome pathway were encoded by three ORFs, two of which encoded F-box proteins and one of which encoded a protein with a BAG domain. The other two ORFs encoded a protein with an OTU domain and an unknown protein. We were also able to show that Ctb1 is likely to be associated with anther length, which is one of major factors in cold tolerance at the booting stage.

Blotting, Southern↗
PubMed2006

The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat.

High grain protein content (GPC) is a frequent target of wheat breeding programmes because of its positive effect on bread and pasta quality. A wild wheat allele at the Gpc-B1 locus with a significant impact on this trait was identified previously. The precise mapping of several senescence-related traits in a set of tetraploid recombinant substitution lines (RSLs) segregating for Gpc-B1 is reported here. Flag leaf chlorophyll degradation, change in peduncle colour, and spike water content were completely linked to the Gpc-B1 locus and to the differences in GPC within a 0.3 cM interval corresponding to a physical distance of only 250 kb. The effect of Gpc-B1 was also examined in different environments and genetic backgrounds using a set of tetraploid and hexaploid pairs of isogenic lines. The results were consistent with those observed in the RSLs. The high GPC allele conferred a shorter duration of grain fill due to earlier flag leaf senescence and increased GPC in all four genetic backgrounds. The effect on grain size was more variable, depending on the genotype-environment combinations. These results are consistent with a model in which the wild-type allele of Gpc-B1 accelerates senescence in flag leaves producing pleiotropic effects on nitrogen remobilization, total GPC, and grain size.

Alleles↗
PubMedDate not supplied

A transmission disequilibrium test for quantitative trait loci.

The transmission disequilibrium test uses association between marker alleles and dichotomous traits for precise genetic mapping while avoiding confounding due to population admixture. Here, the methodology is generalized from dichotomous traits to quantitative traits. The generalization is computationally straightforward and may be used with multiple alleles and with siblings. Parametric assumptions on the distribution of the quantitative traits are not needed. Environmental and demographic covariates may be incorporated into the analysis. The results of simulation studies that provide information about the power of the approach are reported.

Alleles↗
PubMed2001

Map Manager QTX, cross-platform software for genetic mapping.

Map Manager QTX (QTX) is software for analysis of genetic mapping experiments in experimental plants and animals. It includes functions for mapping both Mendelian and quantitative trait loci. QTX is an enhanced version of Map Manager QT, rewritten with the aid of cross-platform libraries (XVT, Boulder Software Foundry, Inc.), which allow it to be compiled for multiple computer platforms. It currently is distributed for Microsoft Windows and Mac OS and is available at http://mapmgr.roswellpark.org/mmQTX.html.

Animal Population Groups↗
PubMed1996

High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato.

A high-resolution physical and genetic map of a major fruit weight quantitative trait locus (QTL), fw2.2, has been constructed for a region of tomato chromosome 2. Using an F(2) nearly isogenic line mapping population (3472 individuals) derived from Lycopersicon esculentum (domesticated tomato) x Lycopersicon pennellii (wild tomato), fw2.2 has been placed near TG91 and TG167, which have an interval distance of 0.13 +/- 0.03 centimorgan. The physical distance between TG91 and TG167 was estimated to be </= 150 kb by pulsed-field gel electrophoresis of tomato DNA. A physical contig composed of six yeast artificial chromosomes (YACs) and encompassing fw2.2 was isolated. No rearrangements or chimerisms were detected within the YAC contig based on restriction fragment length polymorphism analysis using YAC-end sequences and anchored molecular markers from the high-resolution map. Based on genetic recombination events, fw2.2 could be narrowed down to a region less than 150 kb between molecular markers TG91 and HSF24 and included within two YACs: YAC264 (210 kb) and YAC355 (300 kb). This marks the first time, to our knowledge, that a QTL has been mapped with such precision and delimited to a segment of cloned DNA. The fact that the phenotypic effect of the fw2.2 QTL can be mapped to a small interval suggests that the action of this QTL is likely due to a single gene. The development of the high-resolution genetic map, in combination with the physical YAC contig, suggests that the gene responsible for this QTL and other QTLs in plants can be isolated using a positional cloning strategy. The cloning of fw2.2 will likely lead to a better understanding of the molecular biology of fruit development and to the genetic engineering of fruit size characteristics.

Journal Article↗
PubMed2003

Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits.

The bovine CSN1S1 5' flanking region (CSN1S1-5') was screened for polymorphisms in different cattle breeds. Single-strand conformation polymorphisms (SSCP) and sequence analyses revealed four alleles (1-4), two of them being new allelic forms (3 and 4). Sequences were deposited in GenBank with accession numbers AF549499-502. In alleles 1 and 4, potential transcription factor binding sites are altered by the mutations. Using SSCP analysis, all four alleles were identified in German Holsteins. Six intragenic haplo-types comprising CSN1S1-5' (alleles 1, 2, 3, 4) and exon 17 (CSN1S1*B and C) genotypes were found. Linkage mapping using half-sib families from the German QTL project positioned CSN1S1 between the markers FBN14 and CSN3, with 5.6 cM distance between CSN1S1 and CSN3. Variance analysis, using family and CSN1S1 promoter genotypes as fixed effects, of breeding values and deregressed proofs for milk production traits (milk, fat, and protein yield and also fat and protein percentage) revealed significant effects on protein percentage when all families and genotypes were considered. Contrast calculations assigned a highly significant effect to genotype 24, which was associated with highest LS-means for protein percentage breeding values. As CSN1S1 is one of the main caseins in milk, this could be an effect of mutations in regulatory elements in the promoter region. An effect on milk yield breeding values was indicated for genotype 12, but is probably caused by a linked locus.

Alleles↗
PubMed1990

Sensorimotor gating and schizophrenia. Human and animal model studies.

Human and animal model studies of sensorimotor gating allow us to understand the functional significance of attentional abnormalities and monoaminergic alterations in patients with schizophrenic disorders. Clinically, schizophrenic patients report oversensitivity to sensory stimulation that theoretically correlates with stimulus overload and leads to cognitive fragmentation. Paradigms using cortical event-related potentials and the prepulse inhibition of startle responses show that schizophrenic patients also have impaired central nervous system inhibition (sensorimotor gating). Animal model studies demonstrate that increased systemic aminergic activity and increased nucleus accumbens dopamine tone causes sensorimotor gating failure, similar to that seen in schizophrenic patients. The time course of the observed schizophrenic and animal model deficits is compatible with the "temporal map" of monoaminergic neuron functions (le, several hundred milliseconds). Studies of sensorimotor gating allow investigators to comment on the spatial and temporal mapping of neurons, trait and state deficits, and vulnerability factors in the schizophrenic spectrum of disorders. By translating attentional theories into testable hypotheses, the neurobiology of schizophrenic disorders becomes clearer.

Animals↗
PubMed2004

Affected-sib-pair test for linkage based on constraints for identical-by-descent distributions corresponding to disease models with imprinting.

Holmans' possible triangle test for affected sib pairs has proven to be a powerful tool for linkage analysis. This test is a likelihood-ratio test for which maximization is restricted to the set of possible sharing probabilities. Here, we extend the possible triangle test to take into account genomic imprinting, which is also known as parent-of-origin effect. While the classical test without imprinting looks at whether affected sib pairs share 0, 1, or 2 alleles identical-by-descent, the likelihood-ratio test allowing for imprinting further distinguishes whether the sharing of exactly one allele is through the father or mother. Thus, if the disease gene is indeed subject to imprinting, the extended test presented here can take into account that affecteds will have inherited the mutant allele preferentially from one particular parent. We calculate the sharing probabilities at a marker locus linked to a disease susceptibility locus. Using our formulation, the constraints on these probabilities given by Dudoit and Speed ([1999] Statistics in Genetics; New York: Springer) can easily be verified. Next, we derive the asymptotic distribution of the restricted likelihood-ratio test statistic under the null hypothesis of no linkage, and give LOD-score criteria for various test sizes. We show, for various disease models, that the test allowing for imprinting has significantly higher power to detect linkage if imprinting is indeed present, at the cost of only a small reduction in power in case of no imprinting. Altogether, unlike many methods currently available, our novel model-free sib-pair test adequately models the epigenetic parent-of-origin effect, and will hopefully prove to be a useful tool for the genetic mapping of complex traits.

Alleles↗
PubMed1999

Sex-based linkage analysis of alcoholism.

A high degree of locus heterogeneity is likely in alcoholism, and linkage heterogeneity analysis may be helpful in mapping susceptibility loci. The genetic contribution to alcoholism in females may be higher than in males, and therefore sex of affected individuals was used in linkage analysis. Families with female alcoholics demonstrated evidence for linkage to chromosomes 10p11-p15 and 21q22.1-q22.2 while those with male alcoholics did not provide evidence for linkage to these regions. Sharing of maternal and paternal alleles was also investigated separately, and evidence for linkage of maternal alleles on chromosomes 1 and 8, and paternal alleles on chromosome 2 was observed, suggesting parental origin effects. Mapping of complex traits may benefit from tests of linkage heterogeneity based on sex, and parental origin.

Alcoholism↗
PubMed2003

Tnfa and Il-10 deficiencies have contrasting effects on lung tumor susceptibility: gender-dependent modulation of IL-10 haploinsufficiency.

Epidemiologic evidence suggests that pulmonary diseases with a prominent chronic inflammatory component elevate lung cancer risk. Genetic manipulations of mouse models of lung inflammation and tumorigenesis can be used to investigate this association. The genes encoding pro-inflammatory tumor necrosis factor-alpha (TNFalpha) and antiinflammatory IL-10 cytokines map within quantitative trait loci that regulate susceptibility to lung tumor development in mice; sensitive A/J and resistant C57BL/6J (B6) mice have different Tnfa and Il-10 alleles. Genetic ablation studies were performed to examine whether these genes would qualify as candidate tumor modifiers. Tnfa null (-/-) mice on a B6 background and B6.129 Il-10(-/-) mice were intercrossed with A/J mice and subjected to urethane carcinogenesis; lung tumor multiplicity was determined 20 weeks later. In the absence of one copy of Tnfa, tumor number. Male Il-10(+/+) mice developed more tumors than did female mice (P < 0.001), absence of one copy of Il-10 raised tumor number in female mice to that observed in +/+ males, but no change in multiplicity occurred in Il-10 hemizygous males. Thus, a deficit of pro-inflammatory TNFalpha decreased the number of tumors, whereas diminished gene copy number of anti-inflammatory IL-10 increased tumorigenesis; manifestation of an effect of Il-10 haploinsufficiency is gender dependent. These studies support a role for inflammation in lung cancer susceptibility.

Alleles↗
PubMed1995

Aedes aegypti: a quantitative trait locus (QTL) influencing filarial worm intensity is linked to QTL for susceptibility to other mosquito-borne pathogens.

Because intensity of infection was significantly increased in a substrain of Aedes aegypti selected for susceptibility to the filarial worm, Brugia malayi, experiments were designed to assess numbers of microfilariae (mf) ingested and midgut penetration by mf in this susceptible substrain as compared to a refractory substrain selected from the same parental stock. Refractory mosquitoes ingested significantly fewer mf than susceptible mosquitoes and significantly fewer numbers of mf penetrated through refractory midguts as compared to susceptible midguts. In 16.7% of the refractory midguts, no mf were able to penetrate the midgut and in three refractory mosquitoes over 250 mf were ingested, but no mf penetrated the midgut. These results indicate that permissiveness of the midgut for penetration by microfilariae can determine not only parasite intensity, but also prevalence of infection. The genetic basis for ingestion of mf and midgut penetration was assessed using restriction fragment length polymorphism markers and quantitative trait loci (QTL) mapping. This mapping identified a QTL on chromosome 2, idb[2,LF181] (idb, intensity determinant for Brugia), that seems to influence ingestion ability. This QTL is linked to a previously identified QTL for susceptibility to B. malayi, fsb[2,LF98], as well as to loci for susceptibility to the malaria parasite, Plasmodium gallinaceum, and yellow fever virus. These results suggest that this region of chromosome 2 contains one or more genes that influence susceptibility of A. aegypti to several mosquito-transmitted pathogens.

Aedes↗
PubMed2001

Case-control studies of association in structured or admixed populations.

Case-control tests for association are an important tool for mapping complex-trait genes. But population structure can invalidate this approach, leading to apparent associations at markers that are unlinked to disease loci. Family-based tests of association can avoid this problem, but such studies are often more expensive and in some cases--particularly for late-onset diseases--are impractical. In this review article we describe a series of approaches published over the past 2 years which use multilocus genotype data to enable valid case-control tests of association, even in the presence of population structure. These tests can be classified into two categories. "Genomic control" methods use the independent marker loci to adjust the distribution of a standard test statistic, while "structured association" methods infer the details of population structure en route to testing for association. We discuss the statistical issues involved in the different approaches and present results from simulations comparing the relative performance of the methods under a range of models.

Alleles↗
PubMed2004

Physiological roles of angiotensin-converting enzyme 2.

Angiotensin-converting enzyme 2 (ACE2) is a recently discovered homologue of the key enzyme of the renin-angiotensin system, the angiotensin-converting enzyme. The ACE2 enzyme is mainly expressed in cardiac blood vessels and tubular epithelia of the kidneys. Together with ACE2's unique metallocarboxypeptidase activity, the restricted tissue distribution suggests a distinctive physiological function in blood pressure, blood flow and fluid regulation. The ace2 gene was mapped to quantitative trait loci affecting susceptibility to hypertension in rats. Furthermore, ACE2 appears to be a negative regulator of ACE in the heart. ACE2 messenger RNA and protein levels are substantially regulated in the kidney of diabetic and pregnant rats. The mechanism of ACE2 function and its physiologic significance are not yet fully understood; however, as ACE2 differs in its specificity and physiological role from ACE, this opens a new potential venue for drug discovery aimed at cardiovascular disease, hypertension and diabetic complications.

Angiotensin-Converting Enzyme 2↗
PubMed2002

Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis thaliana.

Nitrogen absorption and assimilation is variable among plants as a result of two factors: the source of nitrogen available and the genetic variation among species within the resulting nitrogen pathways. Several genes involved in nitrogen cycling have been identified, yet little is known about the genes that control quantitative responses to different nitrogen sources. With quantitative trait loci (QTL) mapping in Arabidopsis thaliana recombinant inbred lines (Columbia x Landsberg erecta) we have identified chromosomal regions controlling aerial mass, root mass, and root length when plants are grown in nitrate, ammonium, ammonium nitrate, or low nitrogen treatments. A total of 16 QTL ( P < 0.01) were identified among the nitrogen treatments. Most of the QTL were specific to a single treatment. The percentage additive genetic effects of significant QTL were as high as 17%. Five significant QTL corresponded to the locations of candidate genes associated with nitrogen assimilation, while a few QTL corresponded with candidate genes in the developmental pathways. Most QTL were not shared across treatments, suggesting that there is no optimal genotype for all nitrogen sources.

Journal Article↗