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Results for “quantitative trait locus”

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At least 631 records · Page 35Linked to original sources
PubMed2006

Mapping the R10 and R11 genes for resistance to late blight (Phytophthora infestans) present in the potato (Solanum tuberosum) R-gene differentials of black.

The R10 and R11 late blight differentials of Black (tetraploid clones 3681ad1 and 5008ab6) were crossed with the susceptible potato (Solanum tuberosum) cultivar Maris Piper and the progeny were assessed for blight resistance in a whole plant glasshouse test using race 1,2,3,4,6,7 of Phytophthora infestans. The disease scores for the R10 population displayed a continuous distribution whereas the progeny in the R11 population could be categorised as resistant or susceptible. A bulk segregant analysis using amplified fragment length polymorphism assays was done on the ten most resistant and ten most susceptible progeny in each population and two closely linked markers were found to be associated with resistance. R11 mapped to 8.5 cM from marker PAG/MAAG_172.3 and R10 mapped as a quantitative trait locus in which marker PAC/MATC_264.1 explained 56.9% of the variation in disease scores. The results were consistent with R10 and R11 being allelic versions of genes at the R3 locus on chromosome 11. The implications are discussed for mapping R-genes which fail to give complete immunity to a pathogen.

Alleles↗
PubMed1998

Mapping of murine diabetogenic gene mody on chromosome 7 at D7Mit258 and its involvement in pancreatic islet and beta cell development during the perinatal period.

Mutation of the murine maturity-onset diabetes mellitus of the young (Mody) locus induces diabetes, but the effects of its homozygosity on the pancreas remain unknown. F2 mice were obtained by F1 (diabetic C57BL6 x normal Mus musculus castaneus) crosses. About 20% of the F2 progeny developed diabetes by 2 wk of age, 50% of the progeny were normal at 2 wk and developed diabetes between 5 and 8 wk of age, and the remaining 30% did not develop diabetes. Quantitative trait locus analysis using blood glucose levels of 118 F2 mice at 2 wk of age and 5-8 wk of age located Mody within 3 cM of D7Mit258. Histopathological investigation revealed hypoplastic islets (approximately 33% of that of wild-type mice) and a lower density of beta cells (approximately 20% of wild-type) with a reciprocal dominance of alpha cells (four times that of wild-type) in Mody homozygotes. Electron microscopic observations revealed a specific decrease in the number of insulin secretory granules and a lower density of beta cells. Ratios of insulin to glucagon contents confirmed specific decreases in insulin content: 0.01 for homozygotes, 0.54 for heterozygotes, and 1.11 for wild-type mice on day 14. These results suggest that Mody is involved in both islet growth and beta cell function.

Animals↗
PubMed2026

Genome-wide association study combined with multi-assay phenotyping identifies a novel anthracnose resistance locus in apple.

BACKGROUND: Apple anthracnose, a disease complex that includes Glomerella leaf spot (GLS) and bitter rot caused by Colletotrichum species, is a major disease affecting apple production worldwide. In this study, we combined multi-year field evaluations with controlled inoculation assays to identify genomic regions associated with anthracnose resistance in apple. RESULTS: A total of 440 apple genotypes, including 411 F₁ progenies derived from six parental crosses and 29 cultivars, were evaluated under natural orchard conditions and through artificial fruit and leaf inoculation assays using wound and non-wound methods. Disease severity varied substantially between years, particularly under contrasting environmental conditions, indicating strong genotype-by-environment interactions. Genome-wide association analysis (GWAS) using field-derived disease severity scores from 2019 identified a significant quantitative trait locus (QTL) on chromosome 15 (~ 31.8 Mb) associated with reduced anthracnose severity. This locus was distinct from the previously reported Rgls/MdTNL1 region on chromosome 15 (~ 2-5 Mb), suggesting the presence of a novel resistance-associated locus. In contrast, no genome-wide significant associations were detected from artificial inoculation datasets. CONCLUSIONS: These findings demonstrate the importance of field-based, multi-environment phenotyping for detecting field-relevant resistance loci and improving understanding of the genetic architecture underlying anthracnose resistance in apple.

Malus↗
PubMed2002

Microsatellite markers associated with quantitative trait loci controlling antibody response to Escherichia coli and Salmonella enteritidis in young broilers.

A unique resource population was produced to facilitate detection of microsatellite markers associated with quantitative trait loci controlling antibody (Ab) response in broiler chickens. Three F1 males were produced by mating two lines divergently selected on Ab response to Escherichia coli vaccination. Each F1 male was mated with females from four genetic backgrounds: F1, high-Ab line (HH), low-Ab line and commercial line, producing three resource families, each with four progeny types. About 1700 chicks were immunized with E. coli and Salmonella enteritidis vaccines. Selective genotyping was conducted on the individuals with highest or lowest average Ab to E. coli and S. enteritidis within each progeny type in each sire family. Twelve markers were significantly associated with Ab to E. coli and six of them were also associated with Ab to S. enteritidis, mostly exhibiting a similar low effect (approximately 0.35 phenotypic SD) in all progeny types. Four markers exhibited a highly significant and much larger effect (approximately 1.7 SD), but only in progeny of females from the HH, suggesting that a backcross to the high parental line should be preferred over the commonly used F2 population. Results from two markers suggested a quantitative trait locus on chromosome 2 around 400 cM. The marker MCW0083, significant in two sire families, is closely linked to the bone morphogenetic protein 2 (BMP2) gene, known to be associated with the control of T-cell transformation in humans.

Animals↗
PubMed2002

Identification of quantitative trait loci controlling acute virulence in Toxoplasma gondii.

Strains of Toxoplasma gondii can be grouped into three predominant clonal lineages with members of the type I group being uniformly lethal in mice. To elucidate the basis of this extreme virulence, a genetic cross was performed between a highly virulent type I strain (GT-1) and a less-virulent type III strain (CTG), and the phenotypes of resulting progeny were analyzed by genetic linkage mapping. Analysis of independent recombinant progeny identified several quantitative trait loci that contributed to acute virulence. A major quantitative trait locus located on chromosome VII accounted for approximately 50% of the virulence phenotype, whereas a minor locus on chromosome IV, linked to the ROP1 gene, accounted for approximately 10%. These loci are conserved in other type I strains, indicating that acute virulence is controlled by discrete genes common to the type I lineage.

Animals↗
PubMed2002

Genetic analysis of inferior nurturing ability in RR mice.

Females of the inbred mouse RR strain have a limited ability to nurture their offspring, and frequently the young die during rearing. Quantitative trait locus analysis was carried out on the F2 progeny produced from a genetic cross between RR and KK, a strain of normal nurturing ability, to elucidate the putative genetic basis governing certain aspects of the inferior nurturing ability in the RR strain. One hundred and ninety-two F2 female mice were mated with C57BL/6J males. After the number of newborns was adjusted to six per dam, nurturing ability was evaluated on the basis of litter weight at days 7, 12 and 21 after parturition. The results showed that 147 of the 192 F2 dams were able to rear all six pups, although the litter weight varied considerably among litters. Significant evidence for linkage was identified on chromosome 5 near the microsatellite marker of D5Mit161 for litter weight at 12 days after parturition. The R allele (RR strain) at this locus was recessive to the K allele (KK strain), and reduced the litter weight. It is suggested that this locus is one of the heritable components that determine the inferior nurturing ability of RR mice.

Animals↗
PubMed2006

Prediction of IBD based on population history for fine gene mapping.

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBDL are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Alleles↗
PubMed1998

Quantitative trait loci for compensatory renal hypertrophy in the mouse.

Reduction in numbers of nephrons or decrease in kidney function due to a variety of diseases results in compensatory renal hypertrophy (CRH). Recently, it has been proposed that CRH may be a prerequisite for progression of renal injury; genetic dissection of CRH may be therefore helpful in understanding the process whereby people with partial renal insufficiency progress to end-stage renal disease. Since genetic analysis of CRH in humans is quite limited, we searched for genetic determinants of CRH after unilateral nephrectomy using a total genome scan of the mouse BXD recombinant inbred strains. We demonstrated that CRH is a highly heritable trait and we identified a quantitative trait locus on mouse chromosome 11 near the D11Mit14 marker that exerts a major effect on CRH (lod score = 3.4) and is responsible for approximately 52% of genetic variation in CRH. This marker maps near Ace, Gh, and Ngfr positional candidate genes.

Animals↗
PubMed2004

Solanum mochiquense chromosome IX carries a novel late blight resistance gene Rpi-moc1.

Screening of a large number of different diploid Solanum accessions with endosperm balance number (EBN) 1 revealed segregation for strong resistance and sensitivity to Phytophthora infestans in accessions of Solanum mochiquense. Genetic analysis showed that resistance in S. mochiquense accession CGN18263 resides at the distal end of the long arm of chromosome IX, is linked to restriction fragment length polymorphism marker TG328 and is in the neighbourhood of the quantitative trait locus (QTL) Ph-3 conferring resistance to P. infestans in tomato. This is the first genetic study of S. mochiquense, a wild diploid species originating from fog oases in the Peruvian coastal desert.

Chromosome Mapping↗
PubMed2001

The MHC locus controls size variations in the CD4 compartment of the mouse thymus.

The genetic factors that determine the size of lymphocyte populations are largely unknown. We studied the genetic control of variations in the size of the CD4 thymic compartment in unmanipulated mouse strains. A time-course experiment showed that the C57BL/6 mouse strain has a consistently reduced proportion of thymic CD4 cells compared to the BALB/c strain. This difference denotes a decrease in the efficiency of the transition from CD4(+)CD8(+) to CD4(+) thymocytes in the C57BL/6 mouse. Genome-wide genetic mapping identified a major quantitative trait locus in the MHC region that controlled the variations in the proportion of CD4 thymocytes in an F2 intercrossed progeny from C57BL/6 and BALB/c mice (LOD score=21.7). The linkage was maximal at the MHC class II molecule Ea locus, which explained 59% of the observed phenotypic variance. As the C57BL/6 mouse does not express Ea, we hypothesize that the decreased size of the CD4 compartment in the C57BL/6 thymus is due to a reduction in the number of functional MHC class II genes. This study suggests that, at the level of the thymus, the MHC molecules in addition to conferring functional restriction and self-tolerance on the T-cell repertoire, also play a role in determining the homeostasis of the thymic compartments.

Age Factors↗
PubMed1996

Sensitivity to dietary obesity linked to a locus on chromosome 15 in a CAST/Ei x C57BL/6J F2 intercross.

Details of a new model of diet-dependent polygenic obesity are presented. CAST/Ei (Mus m. castaneus) mice remain lean after 12 weeks on a high-fat (32 kcal% fat) diet, while C57BL/6J mice become obese. The genes responsible for the obesity segregate in an F2 population derived from an intercross between CAST/Ei and C57BL/6J mice. Quantitative trait analysis, with simple sequence length polymorphisms (SSLPs) at loci previously linked to rodent obesities, identified a quantitative trait locus (QTL) on Chromosome (Chr) 15, accounting for approximately 9% of the variance in adiposity and 14% of the variance in mesenteric depot size. This locus appears to be at the same location as the dietary obesity-3 (Do3) locus controlling body fat content, which was previously identified in an F2 population derived from an SWR/J x AKR/J cross. This is also at the same location as the multigenic obesity-4 (Mob4) locus found in BSB mice, which display spontaneous polygenic obesity. Suggestive linkage also was found at loci close to the single gene mutations Ay on Chr 2 and tub on Chr 7.

Adipose Tissue↗
PubMed2004

Quantitative trait loci associated with elevated thyroid-stimulating hormone in the Wistar-Kyoto rat.

Thyroid hormones are essential for the regulation of developmental and physiological processes. The genetic factors underlying naturally occurring variability in mammalian thyroid function are, however, only partially understood. Genetic control of thyroid function can be studied with animal models such as the inbred Wistar-Kyoto (WKY) rat strain. Previous studies established that WKY rats have elevated TSH, slightly elevated total T3, and normal total T4 levels compared with Wistar controls. The present study confirmed a persistent 24-h elevation of TSH in WKY rats compared with the Fisher 344 (F344) rat, another inbred strain. Acute T3 challenge (25 microg/100 g body weight ip) suppressed serum TSH and T4 levels in both strains. Quantitative trait locus analysis of elevated TSH in a reciprocally bred WKY x F344 F2 population identified one highly significant locus on chromosome 6 (LOD=11.7, TSH-1) and one suggestive locus on chromosome 5 (LOD=2.3, TSH-2). The confidence interval of TSH-1 contains the TSH receptor and type 2 deiodinase genes, and TSH-2 contains the type 1 deiodinase gene. The WKY alleles of each gene contain sequence alterations, but additional studies are indicated to identify the specific gene or genes responsible for altered regulation of the thyroid axis. These findings suggest that one or more genetic alterations within the TSH-1 locus significantly contribute to the altered thyroid function tests of the WKY rat.

3' Untranslated Regions↗
PubMed1999

The effect of phenotype variation on detection of linkage in the COGA data.

Error in phenotypic measurement can significantly compromise ability to detect linkage. We assessed the impact of introducing phenotypic measurement error on our ability to detect a quantitative trait locus in the Collaborative Study on the Genetics of Alcoholism (COGA) data. The impact of introducing three different types of errors was evaluated: 1) errors generated by sampling from a normal distribution; 2) errors generated by permuting phenotype values between subjects; and 3) errors generated by sampling from a uniform error distribution.

Alcoholism↗
PubMed2006

Genetic analysis of NHLH2 and its putative role in bovine body weight control.

The control of energy balance is fundamental to adult animals and is necessary for weight gain/loss, reproductive capacity and general health. In mice, targeted deletion of the neuronal transcription factor Nhlh2 results in adult-onset obesity because of reduced exercise and infertility because of reduced sexual behaviour. Nhlh2 (NHLH2 for humans) is expressed in the hypothalamus, particularly in neurons that have been shown to regulate energy balance. We have cloned the bovine Nhlh2 gene (bNHLH2) and we have shown that bNHLH2 is also expressed in the hypothalamus. Phylogenetic analysis of Nhlh2 reveals that it is very highly conserved in humans, mice, chimps and cattle, and found in organisms with simpler nervous systems, including Caenorhabditis elegans and Drosophila. Using a cattle-human comparative map and online databases, we have evidence that bNHLH2 is located near a quantitative trait locus for marbling on bovine chromosome 3 between microsatellite markers BM723 and BMS963. Cloning of the bNHLH2 gene from Holstein cattle and a mixed breed individual and comparison with Hereford sequences shows that the gene is highly conserved among bovine breeds.

Amino Acid Sequence↗
PubMed1996

QTL mapping and quantitative disease resistance in plants.

Quantitative trait locus (QTL) mapping is a highly effective approach for studying genetically complex forms of plant disease resistance. With QTL mapping, the roles of specific resistance loci can be described, race-specificity of partial resistance genes can be assessed, and interactions between resistance genes, plant development, and the environment can be analyzed. Outstanding examples include: quantitative resistance to the rice blast fungus, late blight of potato, gray leaf spot of maize, bacterial wilt of tomato, and the soybean cyst nematode. These studies provide insights into the number of quantitative resistance loci involved in complex disease resistance, epistatic and environmental interactions, race-specificity of partial resistance loci, interactions between pathogen biology, plant development and biochemistry, and the relationship between qualitative and quantitative loci. QTL mapping also provides a framework for marker-assisted selection of complex disease resistance characters and the positional cloning of partial resistance genes.

Journal Article↗
PubMed2001

Multigenic control of Listeria monocytogenes susceptibility in mice.

We have used a novel quantitative trait locus model to study the genetics of survival of F2 progeny of susceptible BALB/cByJ and resistant C57BL/6ByJ mice that have been infected with Listeria monocytogenes. This allowed us to map modifiers of L. monocytogenes susceptibility to chromosomes 5 and 13.

Animals↗
PubMed2005

Fine mapping of the hyperglycemic and obesity QTL by congenic strains suggests multiple loci on rat chromosome 14.

Linkage analysis previously identified a hyperglycemic quantitative trait locus (QTL), Nidd 2/of, on rat Chromosome 14 in crosses utilizing OLETF (Otsuka Long Evans Tokushima Fatty) rat, a model for type 2 diabetes. A separate QTL study mapped an obesity QTL, Obs5, to the same chromosomal region. A congenic strain placing ca. 38 cM OLETF-derived segments containing both Nidd2/of and Obs5 on the F344 background was shown to possess mild diabetic and obese phenotypes, suggesting the presence of mutations affecting the glucose metabolism and fat accumulation. In order to localize the loci more precisely, we generated a series of deletion-subcongenic strains in which OLETF-segments were shortened from either ends. We found that there are at least two hyperglycemic QTLs within the Nidd2/of locus. We predict that they are localized towards both ends of the Nidd2/of region. In contrast, Obs5 QTL was further narrowed down to a single region of ca. 10 cM fragment.

Animals↗
PubMed2002

Evidence for linkage and association with reading disability on 6p21.3-22.

Reading disability (RD), or dyslexia, is a common heterogeneous syndrome with a large genetic component. Several studies have consistently found evidence for a quantitative-trait locus (QTL) within the 17 Mb (14.9 cM) that span D6S109 and D6S291 on chromosome 6p21.3-22. To characterize further linkage to the QTL, to define more accurately the location and the effect size, and to identify a peak of association, we performed Haseman-Elston and DeFries-Fulker linkage analyses, as well as transmission/disequilibrium, total-association, and variance-components analyses, on 11 quantitative reading and language phenotypes. One hundred four families with RD were genotyped with a new panel of 29 markers that spans 9 Mb of this region. Linkage results varied widely in degree of statistical significance for the different linkage tests, but multipoint analysis suggested a peak near D6S461. The average 6p QTL heritability for the 11 reading and language phenotypes was 0.27, with a maximum of 0.66 for orthographic choice. Consistent with the region of linkage described by these studies and others, there was a peak of transmission disequilibrium with a QTL centered at JA04 (chi2=9.48; empirical P=.0033; orthographic choice), and there was strong evidence for total association at this same marker (chi2=11.49; P=.0007; orthographic choice). Although the boundaries of the peak could not be precisely defined, the most likely location of the QTL is within a 4-Mb region surrounding JA04.

Adolescent↗