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PubMed2001

High-resolution quantitative trait locus mapping for body weight in mice by recombinant progeny testing.

A major obstacle to the positional cloning of quantitative trait loci (QTLs) lies in resolving genetic factors whose allelic effects are blurred by environmental and background genetic variation. We investigate a fine-mapping approach that combines the use of an interval-specific congenic strain with progeny testing of recombinants for markers flanking a QTL. We apply the approach to map a murine QTL with an approximately 20% effect on growth rate by progeny testing 39 recombinants in a 12 cM region of the X chromosome. We use a likelihood analysis in an attempt to maximize the information on QTL map location and effect. The major X-linked effect is mapped to an approximately 2 cM region flanked by markers about 5 cM apart, outside which LOD support for the QTL drops extremely steeply by about 80. Nearly unambiguous assignment of the QTL genotypic state is obtained for each recombinant. The resolution of individual recombinants in the region is therefore sufficiently high to facilitate the positional cloning of the locus, although progress has been hampered because the genomic region containing the QTL shows an exceptionally low level of polymorphism in comparison with recent studies.

Alleles↗
PubMed2005

A genome scan for fasting insulin and fasting glucose identifies a quantitative trait locus on chromosome 17p: the insulin resistance atherosclerosis study (IRAS) family study.

Plasma insulin and glucose concentrations are important quantitative phenotypes related to diabetes and the metabolic syndrome. Reports purporting to identify quantitative trait loci (QTLs) that contribute to the variation in fasting insulin and glucose concentrations are discrepant. As part of the Insulin Resistance Atherosclerosis Study (IRAS) Family Study, a genome scan was performed in African-American (n = 42) and Hispanic (n = 90) extended families to identify regions that may contain positional candidate genes for fasting insulin and fasting glucose (n = 1,604 subjects). There was significant evidence for linkage of fasting insulin to the short arm of chromosome 17 (logarithm of odds [LOD] = 3.30; 54 cM between D17S1294 and D17S1299, P = 1.0 x 10(-4)). The strongest evidence for linkage over all pedigrees for fasting glucose was also observed in this region (LOD = 1.44; 58 cM, P = 9.9 x 10(-3)). The results of this study provide impetus for future positional cloning of QTLs regulating insulin and glucose levels. Identifying genes in these regions should provide insight into the nature of genetic factors regulating plasma glucose and insulin concentrations.

Black or African American↗
PubMed1999

Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle.

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval.

Animals↗
PubMed2001

Quantitative trait loci affecting growth in high growth (hg) mice.

A genome-wide scan was performed in order to identify Quantitative Trait Loci (QTL) associated with growth in a population segregating high growth (hg), a partially recessive mutation that enhances growth rate and body size in the mouse. A sample of 262 hg/hg mice was selected from a C57BL/6J-hg/hg x CAST/EiJ F2 cross and typed with 79 SSLP markers distributed across the genome. Eight significant loci were identified through interval mapping. Loci on Chromosomes (Chrs) 2 and 8 affected the growth rate of F2 mice. Loci on Chr 2 and 11 affected growth rate and carcass lean mass (protein and ash). A locus on Chr 9 modified femur length and another one in Chr 17 affected both carcass lean mass and femur length, but none of these had significant effects on growth rate. Loci on Chrs 5 and 9 modified carcass fat content. Additive effects were positive for C57BL/6J alleles, except for the two loci affecting carcass fatness. Typing of selected markers in 274 +/+ F2 mice revealed significant interactions between hg and other growth QTL, which were detected as changes in gene action (additive or dominant) and in allele substitution effects. Knowledge about interactions between loci, especially when major genes are involved, will help in the identification of positional candidate genes and in the understanding of the complex genetic regulation of growth rate and body size in mammals.

Animals↗
PubMed2006

Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato.

The efficiency of marker-assisted backcross for the introgression of a quantitative trait locus (QTL) from a donor line into a recipient line depends on the stability of QTL expression. QTLs for six quality traits in tomato (fruit weight, firmness, locule number, soluble solid content, sugar content and titratable acidity) were studied in order to investigate their individual effect and their stability over years, generations and genetic backgrounds. Five chromosome regions carrying fruit quality QTLs were transferred following a marker-assisted backcross scheme from a cherry tomato line into three modern lines with larger fruits. Three sets of genotypes corresponding to three generations were compared: (1) an RIL population, which contained 50% of each parental genome, (2) three BC3S1 populations which segregated simultaneously for the five regions of interest but were almost fully homozygous for the recipient genome on the eight chromosomes carrying no QTL and (3) three sets of QTL-NILs (BC3S3 lines) which differed from the recipient line only in one of the five regions. QTL detection was performed in each generation, in each genetic background and during 2 successive years for QTL-NILs. About half of the QTLs detected in QTL-NILs were detected in both years. Eight of the ten QTLs detected in RILs were recovered in the QTL-NILs with the genetic background used for the initial QTL mapping experiment, with the exception of two QTLs for fruit firmness. Several new QTLs were detected. In the two other genetic backgrounds, the number of QTLs in common with the RILs was lower, but several new QTLs were also detected in advanced generations.

Fruit↗
PubMed2004

Quantitative trait loci with parent-of-origin effects in chicken.

We investigated potential effects of parent-of-origin specific quantitative trait loci (QTL) in chicken. Two divergent egg-layer lines differing in egg quality were reciprocally crossed to produce 305 F2 hens. Searching the genome using models with uni-parental expression, we identified four genome-wide significant QTL with parent-of-origin effects and three highly suggestive QTL affecting age at first egg, egg weight, number of eggs, body weight, feed intake, and egg white quality. None of these QTL had been detected previously using Mendelian models. Two genome-wide significant and one highly suggestive QTL show exclusive paternal expression while the others show exclusive maternal expression. Each of the parent-of-origin specific QTL explained 3-5 % of the total phenotypic variance, with the effects ranging from 0.18 to 0.4 phenotypic SD in the F2. Using simulations and further detailed analyses, it was shown that departure from fixation in the founder lines, grand-maternal effects (i.e. mitochondrial or W-linked) and Z-linked QTL were unlikely to give rise to any spurious parent-of-origin effects. The present results suggest that QTL with parent-of-origin specific expression are a plausible explanation for some reciprocal effects in poultry and deserve more attention. An intriguing hypothesis is whether these effects could be the result of genomic imprinting, which is often assumed to be unique to eutherian mammals.

Age Factors↗
PubMed2005

Locating a blood pressure quantitative trait locus within 117 kb on the rat genome: substitution mapping and renal expression analysis.

Previously, a blood pressure (BP) quantitative trait locus (QTL) on rat chromosome 9 (RNO9) was localized to a <2.4 cM interval using congenic strains generated by introgressing segments of RNO9 from the Dahl salt-resistant (R) rat into the background of the Dahl salt-sensitive (S) rat. Renal gene expression using Affymetrix gene chips was profiled on S and a congenic strain spanning the 2.4-cM BP QTL interval. This analysis identified 20 differentially expressed genes/expressed sequence tags. Of these, the locus with the greatest differential expression (30- to 35-fold) was regulated endocrine-specific protein 18 (Resp18), which also mapped in the 2.4-cM BP QTL interval. Additional substitution mapping located the QTL to <0.4 cM or approximately 493 kb. This newly defined QTL region still included Resp18. Nucleotide variants were identified between S and R genomic DNA of Resp18 in the coding, 5' regulatory and 3' untranslated regions. The coding sequence variation (T/C) occurs in exon 2 and predicts an amino acid change (Ile/Val) in the protein product. Resp18 was considered a differentially expressed positional candidate for the QTL. To fine-map the BP QTL, we constructed a congenic strain with a smaller introgressed region. Compared with the S rat, this strain (1) had significantly lower BP, (2) did not contain the R form of Resp18, and (3) did not retain the rather spectacular differential expression of Resp18. Together, these results demonstrate that a BP QTL independent of Resp18 exists within the newly defined 117-kb QTL region on RNO9.

Animals↗
PubMed1999

An empirical test of the significance of an observed quantitative trait locus effect that preserves additive genetic variation.

We propose a constrained permutation test that assesses the significance of an observed quantitative trait locus effect against a background of genetic and environmental variation. Permutations of phenotypes are not selected at random, but rather are chosen in a manner that attempts to maintain the additive genetic variability in phenotypes. Such a constraint maintains the nonindependence among observations under the null hypothesis of no linkage. The empirical distribution of the lod scores calculated using permuted phenotypes is compared to that obtained using phenotypes simulated from the assumed underlying multivariate normal model. We make comparisons of univariate analyses for both a quantitative phenotype that appears consistent with a multivariate normal model and a quantitative phenotype containing pronounced outliers. An example of a bivariate analysis is also presented.

Alcoholism↗
PubMed1998

Mapping quantitative trait loci for binary traits using a heterogeneous residual variance model: an application to Marek's disease susceptibility in chickens.

A typical problem in mapping quantitative trait loci (QTLs) comes from missing QTL genotype. A routine method for parameter estimation involving missing data is the mixture model maximum likelihood method. We developed an alternative QTL mapping method that describes a mixture of several distributions by a single model with a heterogeneous residual variance. The two methods produce similar results, but the heterogeneous residual variance method is computationally much faster than the mixture model approach. In addition, the new method can automatically generate sampling variances of the estimated parameters. We derive the new method in the context of QTL mapping for binary traits in a F2 population. Using the heterogeneous residual variance model, we identified a QTL on chromosome IV that controls Marek's disease susceptibility in chickens. The QTL alone explains 7.2% of the total disease variation.

Algorithms↗
PubMed1999

A quantitative trait locus for live weight maps to bovine chromosome 23.

A multiple-marker mapping approach was used to search for quantitative trait loci (QTLs) affecting production, health, and fertility traits in Finnish Ayrshire dairy cattle. As part of a whole-genome scan, altogether 469 bulls were genotyped for six microsatellite loci in 12 families on Chromosome (Chr) 23. Both multiple-marker interval mapping with regression and maximum-likelihood methods were applied with a granddaughter design. Eighteen traits, belonging to 11 trait groups, were included in the analysis. One QTL exceeded experiment level and one QTL genome level significance thresholds. Across-families analysis provided strong evidence (P(experiment) = 0.0314) for a QTL affecting live weight. The QTL for live weight maps between markers BM1258 and BoLA DRBP1. A QTL significant at genome level (P(genome) = 0.0087) was mapped for veterinary treatment, and the putative QTL probably affects susceptibility to milk fever or ketosis. In addition, three traits exceeded the chromosome 5% significance threshold: protein percentage of milk, calf mortality (sire), and milking speed. In within-family analyses, protein percentage was associated with markers in one family (LOD score = 4.5).

Alleles↗
PubMed2002

Variation and inter-relationships of quantitative traits in tef (Eragrostis tef (Zucc.) Trotter) germplasm from western and southern Ethiopia.

Three thousand tef (Eragrostis tef (Zucc.) Trotter) lines representing 60 germplasm populations from western and southern Ethiopia were sown on pellic Vertisols at Debre Zeit Agricultural Research Center during the 1999/2000 main season. The objectives were to assess the variation with respect to regions and altitude zones of origin and to study the inter-relationships of 17 pheno-morphic and agronomic traits. The populations showed significant (p < or = 0.05) regional variation in 10 (59%) of the quantitative traits, but clinal variation among altitude zones was significant (p < or = 0.05) only for six (35%) of the traits. On the other hand, the populations revealed consistent variation (p < or = 0.05) within both regions and altitude zones in all the traits evaluated. Likewise, the variation among lines within populations of both regions and altitude zones was significant (p < or = 0.05) in most of the traits. The number of characters showing substantial correlation depicted regional and clinal variation mainly depending on the number of populations. Based on the mean of the populations, grain yield panicle and shoot phytomass plant showed negative correlation with harvest index, and positive correlation with most of the remaining traits. Individual plant grain yield was positively correlated with all the other traits except harvest index, days to maturity, grain filling period and number of primary panicle branches. Overall, the tef germplasm populations showed substantial phenotypic variation which can be utilized in the genetic improvement of the crop.

Edible Grain↗
PubMed2005

Sex-linked quantitative trait loci for thermotolerance and length in the rainbow trout.

We hypothesized that correlation between growth traits and upper thermal tolerance (UTT) in rainbow trout (Oncorhynchus mykiss) might be explained by quantitative trait loci (QTL) localized to the same linkage groups. Microsatellites on three autosomal linkage groups carrying UTT QTL in rainbow trout were tested for associations with fork length (FL) and condition factor (K) in half-sib families of outbred rainbow trout and in backcrosses of trout lines selected on UTT. Additionally, we used a sex-linked microsatellite (OmyFGT19TUF) to test for marker-trait associations at the sex chromosomes. The sex-linked marker OmyFGT19TUF was significantly associated with FL and UTT, accounting for up to 9.6% and 9.7% of variance in these traits, respectively. Male advantages in FL (and, to a lesser extent, UTT) relative to their female sibs were dependent on the origin of the Y chromosome and thus varied among grandsire lines. However, males had higher K in a manner unrelated to Y chromosomal origin, suggesting a partially sex-limited expression of this trait. Omy325UoG was significantly associated with K in one of the outbred half-sib families, but no other significant autosomal marker-trait associations were detected. Our findings illustrate minor evidence that correlation between UTT and FL is partially determined by one or more sex-chromosomal QTL.

Acclimatization↗
PubMed2004

Ecologically relevant stress resistance: from microarrays and quantitative trait loci to candidate genes - a research plan and preliminary results using Drosophila as a model organism and climatic and genetic stress as model stresses.

We aim at studying adaptation to genetic and environmental stress and its evolutionary implications at different levels of biological organization. Stress influences cellular processes, individual physiology, genetic variation at the population level, and the process of natural selection. To investigate these highly connected levels of stress effects, it is advisable - if not critical - to integrate approaches from ecology, evolution, physiology, molecular biology and genetics. To investigate the mechanisms of stress resistance, how resistance evolves, and what factors contribute to and constrain its evolution, we use the well-defined model systems of Drosophila species, representing both cosmopolitan species such as D. melanogaster with a known genome map, and more specialized and ecologically well described species such as the cactophilic D. buzzatii. Various climate-related stresses are used as model stresses including desiccation, starvation, cold and heat. Genetic stress or genetic load is modelled by studying the consequences of inbreeding, the accumulation of (slightly) deleterious mutations, hybridization or the loss of genetic variability. We present here a research plan and preliminary results combining various approaches: molecular techniques such as microarrays, quantitative trait loci (QTL) analyses, quantitative PCR, ELISA or Western blotting are combined with population studies of resistance to climatic and genetic stress in natural populations collected across climatic gradients as well as in selection lines maintained in the laboratory.

Adaptation, Physiological↗
PubMed1998

Test of candidate gene--quantitative trait locus association applied to fatness in mice.

We test for the contribution of five strong candidate genes for obesity to quantitative variation for fatness in mice. The candidate loci are known through their major mutant phenotypes. We propose a randomization test for overall contribution of candidate genes, based on the empirical distribution of LOD scores from a quantitative trait locus (QTL) genome scan. The test is applied to data on body fat content and male gonadal fatpad weight from a QTL genome scan with an F2 population of C57BL/6J and DBA/2J inbred mice. The test is nonsignificant in this experiment for overall body fat content. QTLs detected at an experiment-wide significance level on chromosome 4, 6, 13 and 15 have effects on mean fatness of up to 19% between the homozygotes, but map to locations where there is no strong candidate gene. The test is significant for gonadal fat pad weight in males, and gives weak support for an association with the diabetes gene.

Adipose Tissue↗
PubMed2000

Testing the robustness of the new Haseman-Elston quantitative-trait loci-mapping procedure.

Variance components (VC) techniques have emerged as among the more powerful methods for detection of quantitative-trait loci (QTL) in linkage analysis. Allison et al. found that, with particularly marked leptokurtosis in the phenotypic distribution and moderate-to-high residual sibling correlation, maximum likelihood (ML) VC methods may produce a severe excess of type I errors. The new Haseman-Elston (NHE) method is a least-squares-based VC method for mapping of QTL in sib pairs (Elston et al.). Using simulation, we investigate the robustness of the NHE to marked nonnormality, by means of the same distributions and worst-case conditions identified by Allison et al. for the ML approach (i.e., 100 pairs; high residual sibling correlation). Results showed that, when marked nonnormality is present, the NHE can be used without severe type I error-rate inflation, even at very small alpha levels.

Chromosome Mapping↗
PubMed2006

Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross.

A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%.

Animals↗
PubMedDate not supplied

Quantitative trait loci mapping in dairy cattle: review and meta-analysis.

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).

Alleles↗
PubMed2002

Detection of quantitative trait loci for carcass traits in the pig by using AFLP.

For evaluation of the suitability of Amplified Fragment Length Polymorphism (AFLP) for detection of quantitative trait loci in farm animals, a combination of AFLP and selective genotyping has been applied as a rapid screening method for marker-QTL associations. Focusing on loci affecting eye muscle area, six extreme discordant sib pairs were selected from a Duroc x Berlin Miniature Pig F2 experimental cross and examined by using 48 AFLP primer combinations. Two prominent AFLP markers were converted into simple codominant PCR markers ( STS-Bo1 and STS-Bo3) and assigned to Sscr4 by physical and linkage mapping. Single marker analysis indicated association of the STS markers with a putative QTL influencing eye muscle area. Interval mapping confirmed the presence of a significant QTL for eye muscle area (Pgenomewide < 0.01) on the Sscr4, with STS-Bo1 being the closer marker. At the same location, significant effects (Pgenomewide < 0.01) on carcass length and backfat thickness were also detected. Our results demonstrate the capability of the combination of AFLP analysis and selective genotyping as a method for detection of genome regions containing QTL in livestock.

Animals↗