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Results for “quantitative trait locus”

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PubMed2003

Fine mapping a quantitative trait locus affecting ovulation rate in swine on chromosome 8.

Ovulation rate is an integral component of litter size in swine, but is difficult to directly select for in commercial swine production. Because a QTL has been detected for ovulation rate at the terminal end of chromosome 8p, genetic markers for this QTL would enable direct selection for ovulation rate in both males and females. Eleven genes from human chromosome 4p16-p15, as well as one physiological candidate gene, were genetically mapped in the pig. Large insert swine genomic libraries were screened, clones were isolated and then screened for microsatellite repeats, and informative microsatellite markers were developed for seven genes (GNRHR, IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C, and RGS12). Three genes (LRPAP1, GPRK2L, and FLJ20425) were mapped using genotyping assays developed from single nucleotide polymorphisms. Two genes were assigned since they were present in clones that contained mapped markers (HGFAC and HMX1). The resulting linkage map of pig chromosome 8 contains markers associated with 14 genes in the first 27 cM. One inversion spanning at least 3 Mb in the human genome was detected; all other differences could be explained by resolution of mapping techniques used. Fourteen of the most informative microsatellite markers in the first 27 cM of the map were genotyped across the entire MARC swine resource population, increasing the number of markers typed from 2 to 14 and more than doubling the number ofgenotyped animals with ovulation rate data (295 to 600). Results from the revised data set for the QTL analysis, assuming breed specific QTL alleles, indicated that the most likely position of the QTL resided at 4.85 cM on the new linkage map (F1,592 = 20.5150, genome-wide probability less than 0.015). The updated estimate of the effect of an allele substitution was -1.65 ova for the Meishan allele. The F-ratio peak was closest to markers for MAN2B2 (4.80 cM) and was flanked on the other side by markers for PPP2R2C. Two positional candidate genes included in this study are MAN2B2 and RGS12. These results validate the presence of a QTL affecting ovulation rate on chromosome 8 and facilitate selection of positional candidate genes to be evaluated.

Animals↗
PubMed2001

Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking.

The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.

Chromosome Walking↗
PubMed2001

Putative quantitative trait locus affecting birth weight on bovine chromosome 2.

A genome scan for chromosomal regions influencing birth weight was performed using 151 progeny of a single Hereford x composite bull and 170 microsatellite markers spanning 2.497 morgans on 29 bovine autosomes. A QTL was identified at the telomeric end of bovine chromosome 2 (maximum effect at 114 cM) accounting for approximately 2.8 kg of birth weight or 0.64 residual standard deviations (after adjustment for sex of calf, age of dam, and breed of dam). No significant effect on growth from birth to weaning was detected in this region. The presence of this QTL within a resource herd composed of breeds common to the Northern Great Plains provides an opportunity to initiate marker-assisted selection to reduce birth weight with minimal effect on postnatal growth. Thus, potentially the amount and degree of dystocia can be reduced and the economic loss associated with calving difficulty lessened without compromise of subsequent growth performance. In addition, this finding indicates that significant genetic variation for birth weight (and presumably other production-related traits) exists within herds composed of commercially adapted Bos taurus germplasm.

Animals↗
PubMed2003

Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide.

The ability to taste the substance phenylthiocarbamide (PTC) has been widely used for genetic and anthropological studies, but genetic studies have produced conflicting results and demonstrated complex inheritance for this trait. We have identified a small region on chromosome 7q that shows strong linkage disequilibrium between single-nucleotide polymorphism (SNP) markers and PTC taste sensitivity in unrelated subjects. This region contains a single gene that encodes a member of the TAS2R bitter taste receptor family. We identified three coding SNPs giving rise to five haplotypes in this gene worldwide. These haplotypes completely explain the bimodal distribution of PTC taste sensitivity, thus accounting for the inheritance of the classically defined taste insensitivity and for 55 to 85% of the variance in PTC sensitivity. Distinct phenotypes were associated with specific haplotypes, which demonstrates that this gene has a direct influence on PTC taste sensitivity and that sequence variants at different sites interact with each other within the encoded gene product.

Alleles↗
PubMed2004

Effects of a quantitative trait locus for muscle hypertrophy from Belgian Texel sheep on carcass conformation and muscularity.

A QTL for muscle hypertrophy has been identified in the Belgian Texel breed. A population of F2 and backcross lambs created from crosses of Belgian Texel rams with Romanov ewes was studied. Effects on carcass traits and muscle development of the Belgian Texel breed polygenes and Belgian Texel single QTL were compared. In both cases, carcass conformation and muscularity were improved. The Texel polygenic environment improved conformation mainly through changes in skeletal frame shape. Segments were shorter and bone weight lower. Muscles were more compact, shorter, and thicker. The single QTL affected muscle development. Thickness and weight of muscles were increased. Composition in myosin changed toward an increase of fast contractile type. The relative contribution of hind limb joint to carcass weight was increased. Differences in skeletal frame morphology among the three genotypes of the single QTL were small. Conformation scoring was mainly influenced by leg muscularity. Back and shoulder muscle development, which largely contributed to variability of muscularity, were less involved in the conformation scoring. Lastly, the QTL explains a small part of differences between these Belgian Texel and Romanov breeds for conformation or muscle development. A large part of genetic variability remains to be explored.

Animals↗
PubMed2025

From aerial drone to quantitative trait locus: leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa.

In recent years, accurate and low-cost variant calling has enabled the genotyping of large diversity panels for genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. This has created a strong need for high-throughput, accurate, and low-cost in-field phenotyping. Here, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera. Our high-throughput phenotyping approach integrates an RGB- and MSP camera to measure the color and height of lettuce in this large-scale field experiment. We used the mean and other summary statistics, such as median, quantiles, skewness, kurtosis, minimum, and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using these summary statistics as traits for GWAS, we confirm several previously described genetic associations, now under field conditions, and identify additional novel associations for color and height traits in lettuce.

Lactuca↗
PubMed2006

Bayesian reanalysis of a quantitative trait locus accounting for multiple environments by scaling in broilers.

A Bayesian method was developed to handle QTL analyses of multiple experimental data of outbred populations with heterogeneity of variance between sexes for all random effects. The method employed a scaled reduced animal model with random polygenic and QTL allelic effects. A parsimonious model specification was applied by choosing assumptions regarding the covariance structure to limit the number of parameters to estimate. Markov chain Monte Carlo algorithms were applied to obtain marginal posterior densities. Simulation demonstrated that joint analysis of multiple environments is more powerful than separate single trait analyses of each environment. Measurements on broiler BW obtained from 2 experiments concerning growth efficiency and carcass traits were used to illustrate the method. The population consisted of 10 full-sib families from a cross between 2 broiler lines. Microsatellite genotypes were determined on generations 1 and 2, and phenotypes were collected on groups of generation 3 animals. The model included a polygenic correlation, which had a posterior mean of 0.70 in the analyses. The reanalysis agreed on the presence of a QTL in marker bracket MCW0058-LEI0071 accounting for 34% of the genetic variation in males and 24% in females in the growth efficiency experiment. In the carcass experiment, this QTL accounted for 19% of the genetic variation in males and 6% in females.

Animal Husbandry↗
PubMed2003

Quantitative trait locus detection in commercial broiler lines using candidate regions.

A QTL that explained a large proportion of the phenotypic difference between broiler and layer chickens in an experimental cross was evaluated in a commercial broiler line. A three-generation design, consisting of 15 grandsires, 608 half-sib hens, and more than 50,000 third-generation offspring, was implemented within the existing breeding scheme of a broiler breeding company. Four markers from a candidate region on chicken chromosome 4 were selected for their informativeness in the grandsires and used to genotype the first two generations. Using half-sib analyses, linkage was studied between these markers and 13 growth and carcass traits. The QTL analyses confirmed the presence of significant QTL for body weight (P < 0.01) and residual feed intake (P < 0.05) on chicken chromosome 4. Furthermore, evidence was found for QTL affecting the relative weight of bone and muscle in the thigh. Four more markers were added to increase resolution of the QTL positions. This increased the significance of the QTL for body weight (P < 0.001) and residual feed intake (P < 0.01) and showed evidence (P < 0.05) for additional QTL affecting carcass weight and conformation score. This study showed for the first time that a QTL that explains differences between broilers and layers was segregating in lines that have been selected for body weight over 50 generations. A possible explanation could be a pleiotropic or closely linked effect on fitness-related traits that are not part of the present study. The results demonstrate the feasibility of QTL detection and the potential for marker-assisted selection within a commercial broiler line without altering the existing breeding scheme.

Animals↗
PubMed2001

Potential gain from optimizing multigeneration selection on an identified quantitative trait locus.

The potential extra response that can be obtained from the optimal use of a known QTL in selection by optimizing weights in an index of breeding value for the QTL and polygenic EBV was investigated for a range of parameters. Optimal strategies were derived for a deterministic model of simultaneous selection on a QTL and polygenic effects using optimal control theory. Responses over 10 generations to the following selection strategies were compared: 1) standard QTL selection, with QTL weights equal to 1, 2) optimal QTL selection, 3) stepwise single-generation optimal QTL selection, and 4) non-QTL selection based on phenotype. Cumulative discounted response with discount rates of 10 or 30% per generation were evaluated and used as objective for optimal selection strategies. Optimal selection balanced the conflict between short- and long-term responses and gave greater cumulative discounted response than standard QTL selection of up to 20%, but less than 5% for most cases. Discount rate had limited impact. For a QTL with an additive effect of one polygenic standard deviation, cumulative discounted response from optimal QTL selection was less than 5% greater than response for non-QTL selection for most cases. Exceptions were traits with low heritability and recessive QTL at low frequency, for which extra response was up to 55% greater. Stepwise optimal selection resulted in less cumulative discounted response than standard QTL selection for QTL with negative dominance. The benefit of optimal over stepwise optimal selection was limited (less than 4%) for most cases, except for overdominant QTL. These results indicate that optimizing selection on an identified QTL can result in greater responses to selection but that extra responses tend to be limited for the situations studied here of single-stage purebred selection on a single QTL for a trait observed on both sexes.

Animals↗
PubMed1995

Congenic strains reveal effects of the epilepsy quantitative trait locus, El2, separate from other El loci.

Congenic mouse strains made by transferring epilepsy predisposing alleles El1, El2, and El3 from the EL/Suz strain to the ABP/Le recipient were tested for seizure frequency following gentle rhythmic stimulation. Mice homozygous for El2, but not El1 or El3, experienced seizures much more frequently than ABP controls, while respective El1 homozygotes and El2 heterozygotes had only a modest increase over ABP, and El3 homozygotes showed no increase. Association between marker genotypes and seizure frequency in small intra-strain crosses showed that the phenotypic effects of El2 map to the selected interval, and that segregation of El2 accounts for virtually all genetic effects. However, in separating El2 from other EL susceptibility alleles, the seizure frequency phenotype was weaker and less heritable than in crosses between parental strains. These results confirm El2 as an important QTL and show that it has significant phenotypic effects in the absence of other EL-derived alleles, including El1. In addition, the present localization of El2 on Chr 2 suggests several potential candidate genes for El2, including the beta subunit of phospholipase-C. The approach to dissecting complex traits by making congenic strains for individual QTL is discussed.

Animals↗
PubMed2004

A quantitative trait locus influences coordinated variation in measures of ApoB-containing lipoproteins.

Lipoprotein phenotypes are known to be strongly intercorrelated. These intercorrelations are due to genetic and environmental effects on common metabolic pathways. The purpose of this study was to determine if we could localize genes that exert pleiotropic effects on multiple related lipoprotein traits in humans. Using data from the San Antonio Family Heart Study, we extracted principal components from a set of 12 intercorrelated lipoprotein traits that included phenotypes reflecting lipid and protein concentrations and size distributions for LDLs and HDLs. Five principal components were extracted from the data and all were significantly heritable (h(2) = 0.41-0.57). When subjected to linkage analyses, only one, Component 5, returned a LOD score > or = 3 (LOD score was 3.0 at 38cM on chromosome 15; genome-wide P-value = 0.039). LDL median diameter (-0.529), non-HDLC (-0.422), and ApoB (-0.403) concentrations were the only traits with loadings (absolute value) >0.4, suggesting Component 5 is related to LDL size or perhaps more generally to beta-lipoprotein metabolism. Surprisingly, none of the 12 original lipoprotein traits had a LOD >1 in this region of chromosome 15. These data provide evidence for a novel gene, influencing beta-lipoprotein phenotypes, whose effect(s) is detected only when several lipoprotein traits are considered together.

Adult↗
PubMed1996

A major quantitative trait locus influences hyperactivity in the WKHA rat.

The syndrome of hyperactivity describes behavioural disorders existing mainly in children and characterized by increased levels of motor activity, inattention and impulsivity. Overall the aetiology is poorly understood due to the heterogeneity of the pathology although psychological, biological and social factors acting singly or in concert are generally thought to be involved. In animal studies the observed hyperactivity phenotype results from relative participation of exploration, emotionality and general activity. Studies using brain lesions, neuropharmacology and gene knock-out strategies have shown that specific elements of the brain dopaminergic system can subserve hyperactivity. Evidence of a genetic contribution comes from family and twin studies but also from the ability to select divergent animal lines on the basis of their differential activity. The Wistar-Kyoto (WKY) and Wistar-Kyoto hyperactive (WKHA) rats are such strains--distinct for their low and high activity scores in a novel environment, respectively. Here, we report the detection of a major hyperactivity-related QTL on chromosome 8, explaining 29% of the variance of an intercross between these strains. This study represents the first behavioural QTL analysis in rat and provides a new starting point for biologically categorizing different forms of hyper-activity.

Animals↗
PubMed1995

Quantitative trait locus for reading disability: correction.

In the news article "Can risky mergers save hospital-based research?" by Wade Roush (19 May, p. 968), the statement that University Hospitals of Cleveland rose from 20th in the rankings of teaching hospitals funded by the National Institutes of Health (NIH) in 1991 to 12th at present was incorrect. In fact, it was Case Western Reserve University (CWRU), with which University Hospitals of Cleveland is affiliated, that received $69 million in NIH grants in 1993, making it the 20th largest recipient of such grants among medical centers; the university then received $97 million in 1994, raising its rank to 12th. About $15 million of the increase, or 53%, was attributable to CWRU's 1992 affiliation with Henry Ford Hospital in Detroit. Other hospitals affiliated with Case Western include MetroHealth Medical Center, Mount Sinai Medical Center, St. Luke's Medical Center, and Cleveland Veterans' Affairs Medical Center.

Chromosome Mapping↗
PubMed1995

Genetic linkage of the ACE gene to plasma angiotensin-converting enzyme activity but not to blood pressure. A quantitative trait locus confers identical complex phenotypes in human and rat hypertension.

BACKGROUND: An allelic variant of the ACE gene has been found to be linked to plasma angiotensin-converting enzyme (ACE) activity in humans and has been implicated in the etiology of some common cardiovascular disorders. Previously, we have shown significant genetic linkage of blood pressure to a region on rat chromosome 10 that contains ACE in an experimental F2-intercross between the stroke-prone spontaneously hypertensive rat (SHRSPHD) and the normotensive Wistar-Kyoto (WKYHD-0) reference strain. Subsequent investigations revealed marked differences in plasma ACE activity among the SHRSPHD and WKYHD-0 strains. Nonetheless, the physiological relevance of these findings remained obscure. We therefore investigated the genetic determination of plasma ACE activity and its relation to blood pressure and dietary NaCl exposure in a model of experimental genetic hypertension, the SHRSPHD. METHODS AND RESULTS: We conducted a further crossbreeding experiment between SHRSPHD and a congenic reference strain, WKYHD-1, that carries a 6-centimorgan (cM) long, SHRSP-homologous segment introgressed in chromosome 10, 26 cM remote from ACE. This allowed us to contrast effects on blood pressure and ACE activity conferred by the ACE locus with other more remote loci within the congenic chromosomal region. Genetic analysis in this F2 (WKYHD-1 x SHRSPHD) cross revealed that plasma ACE activity was determined almost entirely by genetic effects of the ACE gene locus (lod score = 43). However, neither plasma ACE nor the ACE locus showed any cosegregation with blood pressure before or after dietary NaCl exposure. CONCLUSIONS: These results demonstrate that a molecular variant of the ACE gene determines plasma ACE activity but exhibits no direct effect on blood pressure. Moreover, the findings also exclude the possibility that plasma ACE is secondarily affected by blood pressure or excess dietary NaCl exposure. Our results reconcile the previous discrepancy between findings in human and experimental hypertension.

Animals↗
PubMed2005

Model selection in binary trait locus mapping.

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.

Animals↗
PubMed2001

Distribution of lod scores in oligogenic linkage analysis.

In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

Chromosome Mapping↗