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PubMed2003

Quantitative trait loci mapping for fatty acid contents in the backfat on porcine chromosomes 1, 13, and 18.

A partial genome scan using microsatellite markers was conducted in order to detect quantitative trait loci (QTLs) for 10 fatty acid contents of the backfat in a pig reference population. Two QTLs were found by studying SSC1, SSC13, and SSC18, where QTLs had already been identified for backfat thickness. A QTL was located between marker loci S0113 and SW974 on chromosome 1; this QTL was only significantly detected (P < 0.05) for linoleic acid. The other QTL was discovered between markers S0062 and S0120 on chromosome 18, and its significance only showed (P < 0.05) for myristic acid. The two QTLs mapped to the same location as the backfat thickness QTL. A third of the phenotypic variation was explained for linoleic acid by the QTL on chromosome 1, and a quarter for myristic acid by the QTL on chromosome 18. Further studies on fine mapping and positional comparative candidate gene analyses will be the next step toward a better understanding of the genetic architecture of fatty acid contents.

Adipose Tissue↗
PubMed2006

Multilocus linkage disequilibrium mapping of epistatic quantitative trait loci that regulate HIV dynamics: a simulation approach.

The time-dependent change of HIV particle load, i.e. HIV dynamics, is likely to be controlled by a multitude of quantitative trait loci (QTL) that interact with each other as well as with various developmental and environmental factors in a coordinated manner. In this article, we have derived a new statistical model for mapping the epistatic QTL responsible for HIV dynamics in a natural human population. This model, constructed on the integrated theme of functional mapping and linkage disequilibrium (LD) mapping, can make use of information from multiple markers genotyped from the human genome. It allows for the test and estimation of genetic actions and interactions involved in the control of HIV progression and provides a general platform to identify the detailed genetic architecture of resistance or susceptibility of humans to HIV on a dynamic scale. We have generalized this model to accommodate various complicated clincal designs for AIDS studies. Simulation studies with different scenarios are performed to examine the statistical behaviour of the model. The genetic and statistical extensions of this mapping model to HIV/AIDS genomic research are discussed.

Computer Simulation↗
PubMed2000

A transmission/disequilibrium test approach to screen for quantitative trait loci in two selected lines of large white pigs.

Pedigree and marker data from a multiple-generation pig selection experiment have been analysed to screen for loci affecting quantitative traits (QTL). Pigs from a base population were selected either for low backfat thickness at fixed live weight (L-line) or high live weight at fixed age (F-line). Selection was based on single-trait own performance and DNA was available on selected individuals only. Genotypes for three marker loci with known positions on chromosome 4 were available. The transmission/disequilibrium test (TDT) was originally described in human genetics to test for linkage between a genetic marker and a disease-susceptibility locus, in the presence of association. Here, we adapt the TDT to test for linkage between a marker and QTL favoured by selection, and for linkage disequilibrium between them in the base population. The a priori unknown distribution of the test statistic under the null hypothesis, no linkage, was obtained via Monte Carlo simulation. Significant TDT statistics were found for markers AFABP and SW818 in the F-line, indicating the presence of a closely linked QTL affecting growth performance. In the L-line, none of the markers studied showed significance. This study emphasizes the potential of the TDT as a quick and simple approach to screen for QTL in situations where marker genotypes are available on selected individuals. The results suggest that previously identified QTL in crosses of genetically diverse breeds may also segregate in commercial selection lines.

Animals↗
PubMed2002

A genome scan for quantitative trait loci affecting resistance to Trichostrongylus colubriformis in sheep.

A genome linkage scan was carried out using a resource flock of 1029 sheep in six half-sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematode Trichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome-wide significance for QTL influencing either of the traits. However, one region attained chromosome-wide significance and five other regions attained point-wise significance for the presence of QTL affecting parasite resistance.

Analysis of Variance↗
PubMed2006

Identification of a quantitative trait locus on rat chromosome 4 that is strongly linked to femoral neck structure and strength.

Risk factors for osteoporotic hip fracture include reduced bone mineral density and poor structure of the femoral neck, both of which are heritable traits. Previously, we showed that despite similar body size, Fischer 344 (F344) rats have significantly different skeletal traits compared with Lewis (LEW) rats. To identify a gene or genes regulating fracture risk at the femoral neck, we mapped quantitative trait loci (QTL) for femoral neck density and structure phenotypes using a 595 F2 progeny derived from the inbred F344 and LEW strains of rats. Femoral neck phenotypes included volumetric bone mineral density (vBMD), neck width, femoral neck cross-sectional area and polar moment of inertia (Ip). A 20-cM genome-wide scan was performed using 118 microsatellite markers and linkage analysis was conducted to identify chromosomal regions harbor QTL for femoral neck phenotypes. Strong evidence of linkage (P<0.01) to femoral neck vBMD was observed on chromosomes (Chrs) 1, 2, 4, 5, 7, 10 and 15. QTL affecting femoral neck structure and biomechanical properties were detected only on Chr 4 where the F344 alleles were shown to improve femoral neck structure, whereas these alleles had no effect on bone measurements at the lumbar spine and only modest effects at the femoral midshaft. In contrast, QTL on Chrs 1, 2 and 10 affected multiple skeletal sites. Several QTL regions in this study are homologous to human chromosomal regions, where linkage to femoral neck and related phenotypes has been reported previously. These findings represent an important first step in localizing and identifying genes that influence hip fragility.

Animals↗
PubMed2002

Genetic dissection of quantitative trait loci specifying sedative/hypnotic sensitivity to ethanol: mapping with interval-specific congenic recombinant lines.

BACKGROUND: Linkage studies alone do not produce sufficient resolution to narrow the location of a quantitative trait locus (QTL) to a small-enough chromosomal region for gene identification. One solution to this problem is to use interval-specific congenic recombinant (ISCR) lines to narrow the chromosomal interval known to contain the QTL. In previous work, we mapped four QTLs for differential ethanol sensitivity in the inbred long-sleep (ILS) and inbred short-sleep (ISS) strains and generated reciprocal congenic strains in which each full QTL interval from ILS was bred onto the ISS background and vice versa. METHODS: ISCR lines were derived by identifying mice carrying recombination events in the congenic interval during backcrossing of the ISS.ILS.Lore congenics to ISS. Recombinant mice were backcrossed to ISS, and progeny carrying the ISCR chromosome were identified and tested to determine whether the ISCR region carried the donor Lore QTL. RESULTS: We developed multiple ISCR lines for each Lore QTL, in which the QTL interval was broken into a number of smaller intervals. For all four QTLs, we reduced the size of the interval, in one case to 3.7 cM. CONCLUSIONS: Use of ISCR lines can narrow each Lore candidate region to a few centimorgans. Such an interval size is conducive to brute-force approaches to identify candidate genes, entailing bioinformatics, gene expression, and DNA sequencing strategies.

Alcohol Drinking↗
PubMed2006

A genomewide scan for quantitative trait loci underlying areal bone size variation in 451 Caucasian families.

BACKGROUND: Bone size is an important determinant of bone strength and is under strong genetic control. OBJECTIVE: To identify quantitative trait loci (QTL) for areal bone size variation, a large-scale genomewide linkage scan was carried out in 451 Caucasian families. PARTICIPANTS AND METHODS: Of 4124 people with phenotypes, 3899 were genotyped with 410 microsatellite markers. Multipoint linkage analyses were carried out in the entire sample, as well as in men and women separately. Potential epistatic interactions between identified genomic regions were also assessed. RESULTS: Several potentially important genomic regions were identified, such as 8q24 for hip bone size (logarithm of the ratio of the odds that two loci are linked (LOD) 3.27) and 2p24 (LOD 2.04) for spine bone size. 8q24 may also interact with 19p13 to affect hip bone size. Several sex-specific QTL were also detected, such as 14q21 (LOD 2.94) for wrist bone size in women and 16q12 (LOD 2.19) for hip bone size in men. CONCLUSIONS: Together with previous findings, this study has further delineated the genetic basis of bone size and laid a foundation for future studies to eventually elucidate the mechanisms of bone size regulation and associated fracture risks.

Adult↗
PubMed2003

Confirmation of quantitative trait loci for cocaine-induced activation in the AcB/BcA series of recombinant congenic strains.

Individual differences in the psychomotor stimulant effects of cocaine are influenced by genetic factors. Several quantitative trait loci (QTL) have been identified for cocaine-induced locomotor activation using the AXB/BXA recombinant inbred series of strains derived from the A/J (A) and C57BL/6J (B6). The aim of the present study was to conduct an independent analysis of cocaine-induced activation in the AcB/BcA recombinant congenic strains. The AcB/BcA RC series consists of 37 inbred strains derived from reciprocal backcrosses between the A and B6, followed by systematic inbreeding. Locomotor activity was measured in a computerized open-field apparatus following intraperitoneal administration of saline and cocaine (20 mg/kg). Linkage maps constructed with 625 informative microsatellite markers were used to identify chromosomal regions associated with cocaine difference scores. Significant (P < 0.00001) regions were identified on chromosomes 1 (13-25.7 and 36.9-58.5 cM), 5 (1-28 and 84-86 cM), 6 (7-26.35 cM), 7 (9.4-27.8 cM), 9 (9-28 cM), 13 (21-37 cM), 16 (36-66 cM), 17 (22.5-24.5 cM) and 18 (45-48 cM). Multiple regression analysis demonstrated that a subset of four markers, including D5Mit182 (24 cM), D5Mit409 (84 cM), D7Mit83 (26.5 cM) and D13Mit54 (35 cM), accounted for 90% of the genetic variance in cocaine difference scores. The results of the present study provide confirmation for a number of QTL on chromosomes 1, 5, 6, 9, 16 and 17 which were previously identified in the recombinant inbred AXB/BXA and BXD strains that share a common B6 ancestor.

Animals↗
PubMed2006

Sensitivity to the locomotor-stimulant effects of ethanol and allopregnanolone: a quantitative trait locus study of common genetic influence.

Previous studies have suggested that common genetic mechanisms influence sensitivity to the locomotor-stimulant effects of ethanol and allopregnanolone. We conducted two quantitative trait locus (QTL) studies to identify chromosomal regions that harbor genes that influence locomotor response to ethanol (2 g/kg) and allopregnanolone (17 mg/kg) using F2 crosses between C57BL/6J and DBA/2J mice. Because our previous data from the BXD recombinant inbred strains had indicated that chromosome 2 contained QTL for sensitivity to the locomotor-stimulant effects of both ethanol and allopregnanolone, we also tested reciprocal chromosome 2 congenic strains for sensitivity to the locomotor-stimulant effects of both drugs. The F2 analysis for ethanol sensitivity identified significant QTL on chromosomes 1 and 2 and suggestive QTL on chromosomes 5 and 9. The analysis of the allopregnanolone F2 study identified suggestive QTL on chromosomes 3, 5 and 12. Suggestive evidence for a female-specific QTL on chromosome 2 was also found. The studies of congenic mouse strains indicated that both the congenic strains captured one or more QTL for sensitivity to the locomotor-stimulant effects of both ethanol (2 g/kg) and allopregnanolone (17 mg/kg). When Fisher's method was used to combine the P values for the RI, F2 and congenic studies of the chromosome 2 QTL, cumulative probability scores of 9.6 x 10(-15) for ethanol and 7.7 x 10(-7) for allopregnanolone were obtained. These results confirm the presence of QTL for ethanol and allopregnanolone sensitivity in a common region of chromosome 2 and suggest possible pleiotropic genetic influence on sensitivity to these drugs.

Animals↗
PubMed2006

Mapping quantitative trait loci associated with selenate tolerance in Arabidopsis thaliana.

Selenium is essential for many organisms, but is toxic at higher levels. To investigate the genetic basis of selenate tolerance in Arabidopsis thaliana, quantitative trait loci (QTL) associated with selenate tolerance in accessions Landsberg erecta and Columbia were mapped using recombinant inbred lines (RILs). The selenate tolerance index (TI(D10) = root growth + 30 microm selenate/root growth control x 100%) was fourfold higher for parental line Col-4 (59%) than for parent Ler-0 (15%). Among the 96 F8 RILs, TI(D10) ranged from 11 to 75% (mean 37%). Using composite interval mapping, three QTL were found on chromosomes 1, 3 and 5, which together explained 24% of variation in TI(D10) and 32% of the phenotypic variation for the difference in root length +/- Se (RL(D10)). Highly significant epistatic interactions between the QTL and markers on chromosome 2 explained additional variation for both traits. Potential candidate genes for Se tolerance in each of the QTL regions are discussed. These results offer insight into the genetic basis of selenate tolerance, and may be useful for identification of selenate-tolerance genes.

Arabidopsis↗
PubMed2000

Model selection for quantitative trait locus analysis in polyploids.

Over the years, substantial gains have been made in locating regions of agricultural genomes associated with characteristics, diseases, and agroeconomic traits. These gains have relied heavily on the ability to statistically estimate the association between DNA markers and regions of a genome (quantitative trait loci or QTL) related to a particular trait. The majority of these advances have focused on diploid species, even though many important agricultural crops are, in fact, polyploid. The purpose of our work is to initiate an algorithmic approach for model selection and QTL detection in polyploid species. This approach involves the construction of all possible chromosomal configurations (models) that may result in a gamete, model reduction based on estimation of marker dosage from progeny data, and lastly model selection. While simplified for initial explanation, our approach has demonstrated itself to be extendible to many breeding schemes and less restricted settings.

Agriculture↗
PubMed2005

Novel quantitative trait loci (QTL) for Fusarium head blight resistance in wheat cultivar Chokwang.

Fusarium head blight (FHB) is one of the most destructive diseases in wheat. This study was to identify new quantitative trait loci (QTL) for FHB resistance and the molecular markers closely linked to the QTL in wheat cultivar Chokwang. The primers of 612 simple sequence repeats (SSRs) and 12 target-region-amplified polymorphism (TRAP) marker were analyzed between resistant (Chokwang) and susceptible (Clark) parents. One hundred and seventy-two polymorphic markers were used to screen a population of 79 recombinant inbred lines (RILs) derived from the cross of Chokwang and Clark. One major QTL, Qfhb.ksu-5DL1, was identified on chromosome 5DL. The SSR marker Xbarc 239 was mapped in the QTL region, and also physically located to the bin of 5DL1-0.60-0.74 by using Chinese Spring deletion lines. Another QTL Qfhb.ksu-4BL1was linked to SSR Xbarc 1096 and tentatively mapped on 4BL. A QTL on 3BS, Qfhb.ksu-3BS1, was also detected with marginal significance in this population. Different marker alleles for these QTL were detected between Chokwang and Sumai 3 and its derivatives. These results suggested that Chokwang contains new QTL for FHB resistance that are different from those in Sumai 3. Pyramiding resistance QTL from various sources may enhance FHB resistance in wheat cultivars.

Crosses, Genetic↗
PubMed2003

Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon.

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC(2)F(2 )families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.

Crosses, Genetic↗
PubMed2002

Power and sample sizes for linkage with extreme sampling under an oligogenic model for quantitative traits.

Extreme sampling of sibling pairs has been shown to be efficient in terms of statistical power and sample sizes (in number of sibling pairs needed to genotype) to detect a quantitative trait locus (QTL) when the residual distribution is normal. In the present study, the efficiency of extreme sampling strategies to detect each locus under an oligogenic model is analytically explored with a test statistic based on identical-by-descent (IBD) statuses of independent sibling pairs. In the oligogenic model, the joint effect of oligogenes is the sum of the effects of each locus. Under this model, detecting each single locus will depend, in part, on the allele frequencies and magnitudes of effect of the other loci. Effects of two QTLs with different magnitudes of displacement and acting nonepistatically are considered. Three types of extreme sampling-that is, extreme concordant high (ECH), extreme concordant low (ECL), and extreme discordant (ED)-are primarily considered herein. Among these, ED sampling under the oligogenic model is shown to be most efficient in most situations considered here in terms of allele frequency and mode of inheritance. Differences in results between ECH and ECL sampling are purely arbitrary, brought up mostly by the directions of displacement effects. However, power to detect a locus with the lesser (in magnitude) displacement effect does not necessarily increase with extremity of sampling. Combinations of extreme discordant and extreme concordant sibling pairs are briefly discussed.

Alleles↗
PubMed2003

A quantitative trait locus on 7q31 for the changes in plasma insulin in response to exercise training: the HERITAGE Family Study.

Several genome-wide linkage scans have been carried out to identify quantitative trait loci for type 2 diabetes and related metabolic phenotypes. However, no previous linkage scans have focused on the response to exercise training of relevant metabolic traits. We performed a genome-wide linkage scan for baseline fasting glucose, insulin, and C-peptide and their responses to a 20-week exercise training program in nondiabetic white and black men and women from the HERITAGE Family Study. In SIBPAL linkage analyses, the maximum number of sibpairs available was 344 and 93 for baseline phenotypes and 300 and 72 for exercise training response phenotypes in whites and blacks, respectively. A total of 509 markers with an average spacing of 6.0 Mb were used. The strongest linkage was found for the changes in fasting insulin in response to exercise training with a marker in the leptin gene on 7q31 (empirical multipoint P = 0.0004) in whites. In blacks, the strongest linkage was observed for baseline fasting glucose on 12q13-q14 (empirical multipoint P = 0.0006). These regions harbor several potential candidate genes. The present findings may be important in identifying individuals at increased risk of developing type 2 diabetes and who are most likely to benefit from a physically active lifestyle.

Black People↗
PubMed2002

Gene expression between a congenic strain that contains a quantitative trait locus of high bone density from CAST/EiJ and its wild-type strain C57BL/6J.

Peak bone density is an important determining factor of future osteoporosis risk. We previously identified a quantitative trait locus (QTL) that contributes significantly to high bone density on mouse chromosome 1 from a cross between C57BL/6J (B6) and CAST/EiJ (CAST) mouse strains. We then generated a congenic strain, B6.CAST-1T, in which the chromosomal fragment containing this QTL had been transferred from CAST to the B6 background. The congenic mice have a significantly higher bone density than the B6 mice. In this study we performed cDNA microarray analysis to evaluate the gene expression profile that might yield insights into the mechanisms controlling the high bone density by this QTL. This study led to several interesting observations. First, approximately 60% of 8,734 gene accessions on GEM I chips were expressed in the femur of B6 mice. The expression and function of two-thirds of these expressed genes and ESTs have not been documented previously. Second, expression levels of genes related to bone formation were lower in congenic than in B6 mice. These data are consistent with a low bone formation in the congenic mice, a possibility that is confirmed by reduced skeletal alkaline phosphatase activity in serum compared with B6 mice. Third, expression levels of genes that might have negative regulatory action on bone resorption were higher in congenic than in B6 mice. Together these findings suggest that the congenic mice might have a lower bone turnover rate than B6 mice and raise the possibility that the high bone density in the congenic mice could be due to reduced bone resorption rather than increased bone formation.

Animals↗
PubMed2001

Improved radiation hybrid map of rat chromosome 2: colocalization of the genes encoding corticotropin-releasing hormone and IL6-receptor with quantitative trait loci regulating the inflammatory response.

We established a radiation hybrid (RH) map of several genes and anonymous markers in the lower half of rat chromosome 2, a chromosome region that contains quantitative trait loci (QTLs) for blood pressure, diabetes and inflammatory response. Two of the newly localized genes (Crh and Il6r) encode proteins involved in the regulation of inflammatory and immune events. Our data show that they reside within regions that were genetically defined as QTLs controlling the inflammatory response. These genes are thus both functional and positional candidates.

Animals↗
PubMed1996

Type I and type II error rates for quantitative trait loci (QTL) mapping studies using recombinant inbred mouse strains.

Effective mapping strategies for quantitative trains must allow for the detection of the more important quantitative trait loci (QTLs) while minimizing false positives. Type I (false-positive) and Type II (false-negative) error rates were estimated from a computer simulation of QTL mapping in the BXD recombinant inbred (RI) set compromising 26 strains of mice, and comparisons made with theoretical predictions. The results are generally applicable to other RI sets when corrections are made for differing strain numbers and marker densities. Regardless of the number or magnitude of simulated QTLs contributing to the trait variance, the p value necessary to provide adequate protection against both Type I (alpha=.0001) and Type II (beta=.2) errors, a QTL would have to account for more than half of the between-strain (genetic) variance if the BXD or similar set was used alone. In contrast, a two-step mapping strategy was also considered, where RI strains are used as a preliminary screen for QTLs to be specifically tested (confirmed) in an F2 (or other) population. In this case, QTLs accounting for approximately 16% of the between-strain variance could be detected with an 80% probability in the BXD set when alpha = 0.2. To balance the competing goals of minimizing Type I and II errors, an economical strategy is to adopt a more stringent alpha initially for the RI screen, since this requires only a limited genome search in the F2 of the RI-implicated regions (approximately 10% of the F2 genome when p < .01 in the RIs). If confirmed QTLs do not account in the aggregate for a sufficient proportion of the genetic variance, then a more relaxed alpha value can be used in the RI screen to increase the statistical power. This flexibility in setting RI alpha values is appropriate only when adequate protection against Type I errors comes from the F2 (or other) confirmation test(s).

Animals↗