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PubMed2006

Mapping of quantitative trait loci for carcass traits in a Japanese Black (Wagyu) cattle population.

To detect quantitative trait loci (QTL) that influence economically important traits in a purebred Japanese Black cattle population, we performed a preliminary genome-wide scan using 187 microsatellite markers across a paternal half-sib family composed of 258 offspring. We located six QTL at the 1% chromosome-wise level on bovine chromosomes (BTA) 4, 6, 13, 14 and 21. A second screen of these six QTL regions using 138 additional paternal offspring half-sib from the same sire, provided further support for five QTL: carcass weight on BTA14 (22-39 cM), one for rib thickness on BTA6 (27-58 cM) and three for beef marbling score (BMS) on BTA4 (59-67 cM), BTA6 (68-89 cM) and BTA21 (75-84 cM). The location of QTL for subcutaneous fat thickness on BTA13 was not supported by the second screen (P > 0.05). We determined that the combined contribution of the three QTLs for BMS was 10.1% of the total variance. The combined phenotypic average of these three Q was significantly different (P < 0.001) from those of other allele combinations. Analysis of additional half-sib families will be necessary to confirm these QTL.

Animals↗
PubMed2002

Mapping of quantitative trait loci for body weight at three, six, and nine weeks of age in a broiler layer cross.

An F2 chicken population was established from a cross of a broiler sire-line and an egg laying (White Leghorn) line. There were two males and two females from both lines in the base population. The F1 progeny consisted of 8 males and 32 females. Over 500 F2 offspring from five hatches were reared to slaughter at a live weight of 2 kg at 9 wk of age. Body weights at 3, 6, and 9 wk were recorded. The DNA was extracted from blood samples, and genotypes for 101 microsatellite markers were determined. Data of 466 individuals from 30 families were available for analysis. Interval mapping QTL analyses were carried out. The QTL significant at the genome wide level that affected body weight at two ages were identified on chromosomes 1, 2, 4, 7, and 8 and a QTL on Chromosome 13 influenced body weight at all three ages. Genetic effects were generally additive, and the broiler allele increased body weight in all cases. The effects for significant individual QTL accounted for between 0.2 and 1.0 phenotypic standard deviations and the sum of the additive effects accounted for approximately 0.75 of the line difference in body weight at 6 wk of age. The largest single additive effect was on chromosome 4, and the effect of substituting one copy of the gene was an increase in weight of 249 g. Interactions of the QTL with sex or family were unimportant. There was no evidence for imprinting or of two or more QTL at the same location for any of the traits.

Aging↗
PubMed2002

A penalized likelihood method for mapping epistatic quantitative trait Loci with one-dimensional genome searches.

Epistasis is a common and important phenomenon, as indicated by results from a number of recent experiments. Unfortunately, the discovery of epistatic quantitative trait loci (QTL) is difficult since one must search for multiple QTL simultaneously in two or more dimensions. Such a multidimensional search necessitates many statistical tests, and a high statistical threshold must be adopted to avoid false positives. Furthermore, the large number of (interaction) parameters in comparison with the number of observations results in a serious danger of overfitting and overinterpretation of the data. In this article we present a new statistical framework for mapping epistasis in inbred line crosses. It is based on reducing the high dimensionality of the problem in two ways. First, epistatic QTL are mapped in a one-dimensional genome scan for high interactions between QTL and the genetic background. Second, the dimension of the search is bounded by penalized likelihood methods. We use simulated backcross data to illustrate the new approach.

Chromosome Mapping↗
PubMed2003

Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.).

Low-temperature germination is one of the major determinants for stable stand establishment in the direct seeding method in temperate regions, and at high altitudes of tropical regions. Quantitative trait loci (QTLs) controlling low-temperature germinability in rice were identified using 122 backcross inbred lines (BILs) derived from a cross between temperate japonica varieties, Italica Livorno and Hayamasari. The germination rate at 15 degrees C was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15 degrees C for 7 days of Italica Livorno and Hayamasari was 98.7 and 26.8%, respectively, and that of BILs ranged from 0 to 83.3%. Using restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers, we constructed a linkage map which corresponded to about 90% of the rice genome. Three putative QTLs associated with low-temperature germination were detected. The most effective QTL, qLTG-3-1 on chromosome 3, accounted for 35.0% of the total phenotypic variation for low-temperature germinability. Two additional QTLs, qLTG-3-2 on chromosome 3 and qLTG-4 on chromosome 4, were detected and accounted for 17.4 and 5.5% of the total phenotypic variation, respectively. The Italica Livorno alleles in all detected QTLs increased the low-temperature germination rate.

Base Sequence↗
PubMed1998

Mapping of quantitative trait loci on porcine chromosome 4.

A F2 population derived from a cross between European Large White and Chinese Meishan pigs was established in order to study the genetic basis of breed differences for growth and fat traits. Chromosome 4 was chosen for initial study as previous work had revealed quantitative trait loci (QTLs) on this chromosome affected growth and fat traits in a Wild Boar x Large White cross. Individuals in the F2 population were typed for nine markers spanning a region of approximately 124 CM. We found evidence for QTLs affecting growth between weaning and the end of test (additive effect: 43.4 g/day) and fat depth measured in the mid-back position (additive effect: 1.82 mm). There was no evidence of interactions between the QTLs and sex, grandparents or F1 sires, suggesting that the detected QTLs were fixed for alternative alleles in the Meishan and Large White breeds. Comparison of locations suggests that these QTLs could be the same as those found in the Wild Boar x Large White cross.

Animals↗
PubMed2006

High-resolution mapping of quantitative trait loci affecting increased life span in Drosophila melanogaster.

Limited life span and senescence are near-universal characteristics of eukaryotic organisms, controlled by many interacting quantitative trait loci (QTL) with individually small effects, whose expression is sensitive to the environment. Analyses of mutations in model organisms have shown that genes affecting stress resistance and metabolism affect life span across diverse taxa. However, there is considerable segregating variation for life span in nature, and relatively little is known about the genetic basis of this variation. Replicated lines of Drosophila that have evolved increased longevity as a correlated response to selection for postponed senescence are valuable resources for identifying QTL affecting naturally occurring variation in life span. Here, we used deficiency complementation mapping to identify at least 11 QTL on chromosome 3 that affect variation in life span between five old (O) lines selected for postponed senescence and their five base (B) population control lines. Most QTL were sex specific, and all but one affected multiple O lines. The latter observation is consistent with alleles at intermediate frequency in the base population contributing to the response to selection for postponed senescence. The QTL were mapped with high resolution and contained from 12 to 170 positional candidate genes.

Animals↗
PubMed2002

Genetic linkage mapping of quantitative trait loci for behavioral and neuroendocrine stress response traits in pigs.

A QTL analysis of behavioral and neuroendocrine responses to a "novel environment" stress was conducted in a three-generation experimental cross between Meishan and Large White pig breeds. A total of 186 F2 males and 182 F2 females were studied for their behavioral and neuroendocrine reactivity to a novel environment test at 6 wk of age. Locomotion, vocalization, and defecation rate, as well as exploration time, were measured for 10 min. Blood samples were taken immediately before and after the test to measure plasma levels of ACTH, cortisol, and glucose. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using two interval mapping methods: a line-cross regression method, where founder lines were assumed to be fixed for different QTL alleles, and a half-/full-sib maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Both methods revealed a highly significant gene effect for poststress cortisol level (P < 0.001) and a significant effect for basal cortisol level (P < 0.05) at the end of the q arm of chromosome 7, explaining, respectively, 20% and 7% of the phenotypic variance. Meishan alleles are associated with higher cortisol levels and are partially dominant (for poststress levels) over Large White alleles. Other significant gene effects on biological measures were detected on chromosomes 1 and 17 (ACTH response to stress), 3, 5, and 8 (glucose levels). The SSC 17 QTL explains 12% of the phenotypic variance of poststress ACTH levels, with a suggestive evidence of imprinting effects. Meishan alleles are associated with lower poststress ACTH levels. Gene effects of low amplitude only were found for behavioral reactivity traits. Considering the effects of stress neuroendocrine systems on energy fluxes and protein deposition, and the importance of stress reactivity for meat quality and animal welfare, these results open new perspectives for pig selection.

Adrenocorticotropic Hormone↗
PubMed2005

Mapping of quantitative trait loci affecting organ weights and blood variables in a broiler layer cross.

1. A genome scan was performed to locate genomic regions associated with traits that are known to vary in birds (most commonly broilers) suffering from heart, lung or muscular dysfunction and for weight of the dressed carcass and some internal organs. 2. The F2 population studied was derived from a cross between a broiler and a layer line and consisted of over 460 birds that were genotyped for 101 markers. 3. There was strong support for segregation of quantitative trait loci (QTL) for carcass and organ weights and blood variables. We identified 11 genome-wide significant QTL (most of them for dressed carcass weight) and several genome-wide suggestive QTL. 4. The results point to some genome regions that may be associated with health-related traits and merit further study, with the final aim of identifying linked genetic markers that could be used in commercial breeding programmes to decrease the incidence of muscular and metabolic disorders in broiler populations.

Animals↗
PubMed1999

Mapping of quantitative trait loci for seminal vesicle mass and litter size to rat chromosome 8.

The spontaneously hypertensive rat (SHR) and the Brown Norway (BN) rat differ significantly in litter size (7.6 versus 4.5 pups). In the HXB and BXH sets of recombinant inbred (RI) strains derived from SHR and BN rats, heritability of litter size and of selected male reproductive parameters such as sperm production, sperm count, sperm morphology and motility, and the mass of the testis, epididymides, and seminal vesicles were estimated and a search was undertaken for quantitative trait loci (QTL) associated with these phenotypes. The mass of seminal vesicles was significantly associated with a QTL near the D8Cebr204S21 marker on chromosome 8 (LOD score = 4.1, P = 0.00001); this QTL was responsible for 46% of the genetic variability of the trait. The same gene marker on chromosome 8 also showed a suggestive association with the litter size. Litter size was significantly correlated with the mass of seminal vesicles (r = 0.58, P = 0.003). These findings indicate that the variability in litter size among RI strains may be due in part to differences in the mass of seminal vesicles and it is possible that both mass of seminal vesicles and litter size are determined by a pleiotropic effect of the same QTL on rat chromosome 8.

Animals↗
PubMed2001

Further characterization and high-resolution mapping of quantitative trait loci for ethanol-induced locomotor activity.

Differential sensitivity to the stimulant effects of ethanol on locomotor activity is determined in part by genetic differences. Among inbred strains of mice, moderate doses of ethanol (1-2 g/kg) stimulate locomotor activity in some strains, e.g., the DBA/2J (D2), but only mildly affect activity in other strains, e.g., C57BL/6J (B6) (Crabbe et al., 1982, 1983; Crabbe, 1986; Dudek and Phillips, 1990; Dudek et al., 1991; Dudek and Tritto, 1994). Quantitative trait loci (QTL) for the acute ethanol (1.5 g/kg) locomotor response has been identified in the BXD recombinant inbred (RI) series (N = 25 strains), a C57BL/6J x DBA/2J (B6D2) F2 intercross (N = 1800), and heterogeneous stock (HS) mice (N = 550). QTLs detected (p < .01) in the RI series were found on chromosomes 1, 2, and 6 and these QTLs were expressed in a time-dependent fashion. The QTLs on chromosomes 1 and 2 were confirmed in the F2 intercross at p < 10(-7) or better. HS mice from G32 to G35 were used to fine-map the chromosome 2 QTL. Compared to the consensus map, the genetic map in the HS animals was expanded 10- to 15-fold. Over the region flanked by D2Mit94 to D2Mit304, three separate QTLs were detected in the HS animals. The data obtained confirm the usefulness of HS mice for the fine-mapping of QTLs to a resolution of 2 cM or less.

Animals↗
PubMed2001

Bayesian mapping of quantitative trait loci under complicated mating designs.

Quantitative trait loci (QTL) are easily studied in a biallelic system. Such a system requires the cross of two inbred lines presumably fixed for alternative alleles of the QTL. However, development of inbred lines can be time consuming and cost ineffective for species with long generation intervals and severe inbreeding depression. In addition, restriction of the investigation to a biallelic system can sometimes be misleading because many potentially important allelic interactions do not have a chance to express and thus fail to be detected. A complicated mating design involving multiple alleles mimics the actual breeding system. However, it is difficult to develop the statistical model and algorithm using the classical maximum-likelihood method. In this study, we investigate the application of a Bayesian method implemented via the Markov chain Monte Carlo (MCMC) algorithm to QTL mapping under arbitrarily complicated mating designs. We develop the method under a mixed-model framework where the genetic values of founder alleles are treated as random and the nongenetic effects are treated as fixed. With the MCMC algorithm, we first draw the gene flows from the founders to the descendants for each QTL and then draw samples of the genetic parameters. Finally, we are able to simultaneously infer the posterior distribution of the number, the additive and dominance variances, and the chromosomal locations of all identified QTL.

Analysis of Variance↗
PubMed2004

Mapping major quantitative trait loci for postnatal growth in an intersubspecific backcross between C57BL/6J and Philippine wild mice by using principal component analysis.

A number of quantitative trait loci (QTLs) for postnatal growth have previously been reported in mice. As effects of the QTLs are usually small and similar to one another in magnitude, it is generally difficult to know which loci are major contributors to postnatal growth. We applied principal component analysis to a genome-wide search for QTLs affecting postnatal growth in body weight weekly recorded from 3 to 10 weeks of age in an intersubspecific backcross population of C57BL/6J inbred mice (Mus musculus domesticus) and wild mice (M. m. castaneus) captured in the Philippines, in order to discover new QTLs from a gene pool of the wild mice and uncover major loci underlying variation in postnatal growth. Principal component analysis classified phenotypic variation in body weights at different ages into two independent principal components: the first principal component (PC1) extracted information on the entire growth process and the second principal component (PC2) contrasted middle (3-6 weeks of age) with late (6-10 weeks) growth phases. Simple interval mapping and composite interval mapping revealed 10 significant QTLs with main effects on PC1 or PC2 on eight chromosomes. Of these, the six main-effect QTLs interacted epistatically with one another or three new additional QTLs on different chromosomal regions without main effects. Several of the identified QTLs with main effects and/or epistatic interaction effects appeared to be sex specific. These results suggest that the identified 13 QTLs, most of which affected the entire growth process, are very important contributors to complex genetic networks of postnatal growth.

Animals↗
PubMed2005

Mapping of quantitative trait loci associated with chilling tolerance in maize (Zea mays L.) seedlings grown under field conditions.

The effect of low growth temperature on morpho-physiological traits of maize was investigated by the means of a QTL analysis in a segregating F(2:3) population grown under field conditions in Switzerland. Chlorophyll fluorescence parameters, leaf greenness, leaf area, shoot dry weight, and shoot nitrogen content were investigated at the seedling stage for two years. Maize was sown on two dates in each year; thus, plants sown early were exposed to low temperature, whereas those sown later developed under more favourable conditions. The main QTLs involved in the functioning of the photosynthetic apparatus at low temperature were stable across the cold environments and were also identified under controlled conditions with suboptimal temperature in a previous study. Based on the QTL analysis, relationships between chlorophyll fluorescence parameters and leaf greenness were moderate. This indicates that the extent and functioning of the photosynthetic machinery may be under different genetic control. The functioning of the photosynthetic apparatus in plants developed at low temperature in the field did not noticeably affect biomass accumulation; since there were no co-locations between QTLs for leaf area and shoot dry weight, biomass accumulation did not seem to be carbon-limited at the seedling stage under cool conditions in the field.

Acclimatization↗
PubMed2006

Genetic mapping of seed shape in three populations of recombinant inbred lines of soybean (Glycine max L. Merr.).

Round soybean seeds are sought-after for food-type soybean. Also the genetic control of seed geometry is of scientific interest. The objectives of this study were to estimate heritability and map quantitative trait loci (QTLs) responsible for seed shape traits. Three densely mapped recombinant inbred populations each with 192 segregants were used, Minsoy x Archer, Minsoy x Noir1, and Noir1 x Archer. A two rep two location experiment was conducted in Los Andes, Chile, and East Lansing, MI, USA. Seed height (SH), width (SW), length (SL), and seed volume (SV) as width x height x length were measured to determine seed shape. Heritability was estimated by variance component analysis. A total of 19 significant QTLs (LOD >or= 3.7) in ten linkage groups (LG) were detected for all the traits. Only one QTL was stable across populations and environments and six were stable in at least two populations in both environments. The amount of phenotypic variation explained by a single QTL varied from 7.5% for SH, to 18.5% for SW and at least 30% of the genetic variation for the traits is controlled by four QTL or less. All traits were highly correlated with each other in all populations with values ranging from 0.5 to 0.9, except for SL and SW that were not significantly correlated or had a low correlation in all populations. Narrow sense heritabilities for all traits ranged from 0.42 to 0.88. We note that LG u9, u11, and u14 are hot points of the genome for QTLs for various traits. The number and genomic distribution of the QTLs confirms the complex genetic control of seed shape. Transgressive segregation was observed for all traits suggesting that careful selection of parents with similar phenotypes but different genotypes using molecular markers can result in desirable transgressive segregants.

Chromosome Mapping↗
PubMed2006

Fine mapping of quantitative trait nucleotides underlying thrombin-activatable fibrinolysis inhibitor antigen levels by a transethnic study.

Recent studies revisiting the association between plasma thrombin-activatable fibrinolysis inhibitor (TAFI) Ag levels and polymorphisms of the CPB2 gene (coding for TAFI) suggested that TAFI Ag levels were influenced by 2 major quantitative trait nucleotides (QTNs) in European whites. However, the strong linkage disequilibrium (LD) between CPB2 polymorphisms in European whites did not allow one to distinguish which polymorphisms could be the putative QTNs. To get a better insight into the identification of QTNs, a transethnic haplotype analysis contrasting 2 populations of African and European subjects was performed using 13 CPB2 polymorphisms. Results of the haplotype analyses suggested that 3 QTNs had independent effects and explained about 15% of the TAFI variability, consistently in the 2 populations. The lower LD observed in the African population enabled us to identify the 1583T>A SNP located in 3'UTR as one of these QTNs, whereas the -2599C>G and -2345--2344insG SNPs located in the 5' region might be the 2 other QTNs. A phylogenetic study suggested that these 3 polymorphisms occurred before the period of migration "out of Africa." Although this transethnic comparison contributed to better map the putative CPB2 QTNs, further studies are required to clarify the role of the promoter region.

3' Untranslated Regions↗
PubMed2002

Score test for mapping quantitative-trait loci with sibships of arbitrary size when the dominance effect is not negligible.

In the linakge analysis of quantitative traits, an additive model that assumes no dominance effect is often adopted. Intuitively, when the no-dominance-effect assumption does not hold, such a practice does not make efficient use of the data, and its power to detect linkage can be improved. Here we introduce a score statistic for detecting quantitative trait loci when the dominance effect is not neglible or the dominance effect is a concern. This statistic is derived from a normal likelihood function for sibships of arbitrary size. In the derivation, the inherent genetic constraints on model parameters are fully taken into consideration. This score statistic is asymptotically equivalent to the corresponding likelihood ratio statistic, but it is much easier to compute. The asymptotic distribution of this statistic is derived, which is a mixture of chi(0) (2), chi(1) (2), and chi(2) (2). Weights for distribution components are functions of the informativeness of the marker data. The type I error rate and the power of the proposed statistic in finite sample are evaluated via simulations.

Chromosome Mapping↗
PubMed2002

Provisional mapping of quantitative trait loci modulating the acoustic startle response and prepulse inhibition of acoustic startle.

Prepulse inhibition (PPI) of the acoustic startle response (ASR) is a form of sensorimotor gating, defined as an inhibition of the startle response when a low intensity stimulus, the prepulse, precedes the startling stimulus. Deficits in PPI have been reported in schizophrenia and other psychiatric/neurological disorders, and correlate with symptom severity in schizophrenia, suggesting that deficient PPI per se or abnormalities in neural circuits regulating PPI may cause some symptoms of schizophrenia. If so, then genes conferring reduced PPI may contribute toward genetic vulnerability to schizophrenia. Studies with selectively bred rodent strains indicate that PPI is under genetic control; however, the identity of the relevant genes is unknown. The current study used recombinant congenic mouse strains derived from C57BL/6J and A/J parents to assess genetic variability in PPI and in ASR and to identify provisional quantitative trait loci (QTLs) modulating these phenotypes. Significant between-strain differences in ASR and in PPI at each of several prepulse intensities (75, 80, 85, 90, 95 dB) were found. Correlations between PPI at the various prepulse intensities were highly significant, suggesting appreciable overlap in genetic regulation of PPI across prepulse intensities. Five QTLs (chromosomes 3, 5, 7, 16) associated with PPI across all prepulse intensities, but not with ASR, were identified. Two additional QTLs (chromosomes 2, 11) associated with both PPI and ASR were found. Fifteen QTLs were associated with ASR alone. Data on genotypes of informative congenic strains were used to support probable involvement of loci modulating PPI and to narrow the probable chromosomal location of QTLs. If confirmed, these QTLs may suggest candidate genes directing novel mechanisms for regulation of PPI

Acoustic Stimulation↗
PubMed1995

Mapping of quantitative trait loci for blood pressure and cardiac mass in the rat by genome scanning of recombinant inbred strains.

In the HXB and BXH recombinant inbred strains derived from the spontaneously hypertensive rat and the normotensive Brown Norway rat, we determined the strain distribution patterns of 500 genetic markers to scan the rodent genome for quantitative trait loci regulating cardiac mass and blood pressure. The markers spanned approximately 1,139 cM of the genome and were tested for correlations with left ventricular mass adjusted for body weight, and with systolic, diastolic, and mean arterial pressures. The marker for the dopamine 1A receptor (Drd1a) on chromosome 17 showed the strongest correlation with left ventricular heart weight (P = .00038, r = -0.59) and the relationship to heart weight was independent of blood pressure. The markers showing the strongest correlations with systolic, diastolic, and mean arterial pressure were D19Mit7 on chromosome 19 (P = .0012, r = .55), D2N35 on chromosome 2 (P = .0008, r = .56), and Il6 on chromosome 4 (P = .0018, r = .53), respectively. These studies demonstrate that the HXB and BXH strains can be effectively used for genome scanning studies of complex traits and have revealed several chromosome regions that may be involved in the genetic control of blood pressure and cardiac mass in the rat.

Animals↗