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1.
Marker‐assisted genetic evaluation needs to infer genotypes at quantitative trait loci (QTL) based on the information of linked markers. As the inference usually provides the probability distribution of QTL genotypes rather than a specific genotype, marker‐assisted genetic evaluation is characterized by the mixture model because of the uncertainty of QTL genotypes. It is, therefore, necessary to develop a statistical procedure useful for mixture model analyses. In this study, a set of mixture model equations was derived based on the normal mixture model and the EM algorithm for evaluating linear models with uncertain independent variables. The derived equations can be seen as an extension of Henderson's mixed model equations to mixture models and provide a general framework to deal with the issues of uncertain incidence matrices in linear models. The mixture model equations were applied to marker‐assisted genetic evaluation with different parameterizations of QTL effects. A sire‐QTL‐effect model and a founder‐QTL‐effect model were used to illustrate the application of the mixture model equations. The potential advantages of the mixture model equations for marker‐assisted genetic evaluation were discussed. The mixed‐effect mixture model equations are flexible in modelling QTL effects and show desirable properties in estimating QTL effects, compared with Henderson's mixed model equations.  相似文献   

2.
Quantitative trait loci (QTL) analysis in designed experiments is investigated using a mixed model framework through the modification of segment mapping techniques. Allele effects are modelled in the F1 generation allowing the estimation of additive substitution effects while accounting for QTL segregation within lines and differences in mean QTL effects between lines. The resulting approach is called F1 segment mapping. Simulation is used to illustrate the method and its properties. F1 segment mapping has advantages over F2 segment mapping in the derivation of exact additive genetic covariances and in the computation time for variance component estimation.  相似文献   

3.
Reliabilities for genomic estimated breeding values (GEBV) were investigated by simulation for a typical dairy cattle breeding setting. Scenarios were simulated with different heritabilites ( h 2) and for different haplotype sizes, and seven generations with only genotypes were generated to investigate reliability of GEBV over time. A genome with 5000 single nucleotide polymorphisms (SNP) at distances of 0.1 cM and 50 quantitative trait loci (QTL) was simulated, and a Bayesian variable selection model was implemented to predict GEBV. Highest reliabilities were obtained for 10 SNP haplotypes. At optimal haplotype size, reliabilities in generation 1 without phenotypes ranged from 0.80 for h 2 = 0.02 to 0.93 for h 2 = 0.30, and in the seventh generation without phenotypes ranged from 0.69 for h 2 = 0.02 to 0.86 for h 2 = 0.30. Reliabilities of GEBV were found sufficiently high to implement dairy selection schemes without progeny testing in which case a data time-lag of two to three generations may be present. Reliabilities were also relatively high for low heritable traits, implying that genomic selection could be especially beneficial to improve the selection on, e.g. health and fertility.  相似文献   

4.
Genomic selection   总被引：2，自引：0，他引：2  
Genomic selection is a form of marker-assisted selection in which genetic markers covering the whole genome are used so that all quantitative trait loci (QTL) are in linkage disequilibrium with at least one marker. This approach has become feasible thanks to the large number of single nucleotide polymorphisms (SNP) discovered by genome sequencing and new methods to efficiently genotype large number of SNP. Simulation results and limited experimental results suggest that breeding values can be predicted with high accuracy using genetic markers alone but more validation is required especially in samples of the population different from that in which the effect of the markers was estimated. The ideal method to estimate the breeding value from genomic data is to calculate the conditional mean of the breeding value given the genotype of the animal at each QTL. This conditional mean can only be calculated by using a prior distribution of QTL effects so this should be part of the research carried out to implement genomic selection. In practice, this method of estimating breeding values is approximated by using the marker genotypes instead of the QTL genotypes but the ideal method is likely to be approached more closely as more sequence and SNP data is obtained. Implementation of genomic selection is likely to have major implications for genetic evaluation systems and for genetic improvement programmes generally and these are discussed.  相似文献   

5.
The aim of study was to investigate the effect of genotype on carcass measurements and meat quality characteristics of purebred Hair Goat, Saanen × Hair Goat (F1 and B1) kids under an intensive production system. In total, 24 kids were slaughtered at the age of approximately 133 days. Kids were fattened for 56 days immediately after weaning. Hot carcass weights were 6.78, 7.61 and 7.02 kg and dressing percentages were 49.71, 49.27 and 48.78%, respectively ( P  > 0.05). Differences between genotypes for carcass measurements and indexes were not significant. Effect of genotype on pH measurements, drip loss, water holding capacity, cooking loss and Warner Bratzler shear force values were not significant. Meat lightness values at 0 h, 1 h and 1 day after cutting were higher in crossbred kids than Hair Goat kids ( P  < 0.05). Redness value was significantly higher in meat samples of Hair goat kids at 0 h, 1 h and 1 day measurements ( P  < 0.05). Kid genotype had no significant effect on meat sensory characteristics, except tenderness. Panelists gave lower scores for meat tenderness to F1 and B1 crosses compared to purebred Hair Goat kids. In conclusion, higher meat lightness values of crossbred kids, at particularly B1 level, might have a positive effect on the consumer choices.  相似文献   

6.
The principle of interval mapping for quantitative trait loci (QTL) was originally developed for the analysis of single backcross data but it has been increasingly applied to more complicated experimental designs and data structures. It is important to study whether accounting for the heterogeneity of variance would improve the precision of QTL mapping based on data of multiple populations or families. This study compared homogeneous and heterogeneous maximum likelihood approaches for QTL mapping. The data consisted of 433 sons from six sire families with 69 microsatellite markers distributed over 12 chromosomes. The results of this study indicate that the heterogeneous approach generally produced a smaller residual variance and thus provided a better fit to the data than the homogeneous approach, meaning that the heterogeneous approach offers better precision in estimating both positions and effects of QTL. The results further showed that accounting for the heterogeneity of residual variance led to different statistical inferences from ignoring the heterogeneity of variance in QTL mapping. The heterogeneous approach is useful for QTL mapping based on the joint data of diverse reference populations or heteroscedastic data obtained from crossing animals with different genetic backgrounds.  相似文献   

7.
Quantitative trait locus mapping based on selective DNA pooling   总被引：1，自引：0，他引：1  
Concepts of a simple method to map quantitative trait loci (QTL) based on selective DNA pooling in half-sib family, backcross, and F2 designs were developed. It is shown that the position of a QTL can be estimated from differences in allele frequencies for two flanking markers between individuals with high and low phenotypes and does not depend on the phenotypic means of the selected groups. An estimate of the QTL effect was obtained by relating group differences in phenotypic means to differences in QTL frequencies, which can be estimated from the QTL position and marker allele frequencies. Simulation of a half-sib family and a F2 family of 2000 individuals showed that the method gives close to unbiased results when power is high. Biases increased when measurement errors on marker allele frequencies increased and when the effect of the QTL was small. Similarities of QTL mapping based on selective DNA pooling data and on individual genotyping data are discussed, as are opportunities to extend the selective DNA pooling method to the use of multiple markers and multiple half-sib family designs. This study shows that the use of selective DNA pooling can be extended from the detection of marker associations to the mapping of QTL. Selective DNA pooling can greatly reduce the number of genotypings required.  相似文献   

8.
The extraction of the hepatobiliary radiopharmaceutical 99mTc-mebrofenin ( Choletec ) by the liver can be used to evaluate the severity of hepatocellular disease. The hepatic parenchymal cells extract mebrofenin from the blood by the same active transport mechanism as bilirubin. The ability of the liver to extract 99mTc-membrofenin is a measure of hepatic parenchymal cell function. In this study, we induced hepatocellular disease by administration of a hepatotoxic drug and compared a direct method of determining the hepatic extraction of 99mTc-membrofenin to hepatic extraction fraction derived from deconvolutional analysis. We also compared both methods of calculating the hepatic extraction of 99mTc-membrofenin to liver histopathology. Hepatic extraction fraction derived from deconvolutional analysis correlated very well to the direct measurement technique (R=0.922, p<0.001). Both methods of determining hepatic extraction correlated well to quantitative histopathology, having the same correlation coefficient and p values. (R=-0.833, p=0.003). As the hepatic extraction 99mTc-membrofenin decreased, the severity of the histopathologic lesions of the liver increased in a linear fashion. There was a significant correlation of the hepatic excretion T1/2 to quantititative histopathology (R=0.949, p<0.001). The hepatic excretion T1/2 increased as the severity of the histopathologic lesions of the liver increased. Hepatic extraction (HEF) and excretion of 99mTc-membrofenin are good predictors of the severity of hepatocellular damage in toxic induced liver disease. This study helps validate the premise that HEF derived from deconvolutional analysis ois a good predictor of the actual first pass hepatic extraction of 99mTc-membrofenin.  相似文献   

9.
This study quantified the efficiency of quantitative traits loci (QTL)‐assisted selection in the presence of correlations (ρqr) between identified (q) and residual (r) genotypes. Two levels of heritability (h2 = 0.1 or 0.3), two levels of correlation (ρqr = ?0.3 or 0.3) and five proportions of genetic variance explained by QTL detected (= 0.1, 0.2, 0.4, 0.6 or 0.8) were combined to give 20 scenarios in all. QTL‐assisted selection placed a larger index weight on the QTL genotype than on the phenotype in 17 of 20 scenarios, yielding a greater response in the QTL genotype than in residual genotype. Although QTL‐assisted selection was superior to phenotypic selection in all 20 scenarios, QTL‐assisted selection showed a greater advantage over phenotypic selection when ρqr was positive than when ρqr was negative. Doubling the proportion of detected QTL variance to genetic variance does not result in a twofold increase in the genetic response to QTL‐assisted selection, suggesting that economic returns diminish for each additional cost of detecting extra QTL. The correlation between q and r would make the interpretation (or prediction) of QTL effects difficult and QTL‐assisted selection strategy must consider the joint effect of q and r. When q and r are not independent, a failure to account for ρqr in QTL‐assisted selection would underestimate the genetic responses when ρqr is positive, but overestimate the genetic responses when ρqr is negative. Estimation bias is more serious at high heritability than at low heritability. Accounting for ρqr would improve the efficiency of QTL‐assisted selection and the accuracy of QTL detection. The generalized procedure developed in this study allows for quantifying the efficiency of QTL‐assisted selection and assessing estimation bias for ignoring the correlation between q and r for all possible combinations of h2, ρqr, and .  相似文献   

10.
Estimation of genome-wide haplotype effects in half-sib designs   总被引：2，自引：1，他引：1  
Genome-wide estimated breeding values can be computed from the simultaneous estimates of the effects of small intervals of DNA throughout the genome on a trait or traits of interest. Small intervals or segments of DNA can be created by the use of thousands of single nucleotide polymorphisms (SNP) available in panels of 10, 25 and 50 thousand SNP. A simulation study was conducted to compare factors that could influence the accuracy of genome-wide selection. Factors studied were the heritability of the trait, dispersion of quantitative trait loci (QTL) across the genome and size of the QTL effects. A 100-cM genome was assumed with 100 equally spaced SNP markers and 10 QTL. A granddaughter design was constructed with 20 sires and 100 sons per sire. Population-wide linkage disequilibrium was assumed to be sufficient after 25 generations of random mating starting with 30 sires and 400 dams. Best linear unbiased prediction was used to simultaneously estimate the effects of 99 SNP intervals, based on determining the SNP haplotype of each son inherited from the sire. Indicator variables were used in the model to indicate haplotype transmission. A genome-wide estimated breeding value was calculated as the sum of the appropriate haplotype interval estimates for each son. Correlations between estimated and true breeding values ranged from 0.60 to 0.79. Situations with unequally sized QTL effects and randomly dispersed QTL gave higher correlations. QTL positions could be estimated to within 2 cM or less.  相似文献   

11.
This paper provides an investigation into some of the key practical issues for minimizing the cost of DNA testing. Previous studies focused on maximizing the utility of genotyping by prioritizing individuals for genotyping. For logistical reasons, individuals may have to be genotyped in groups rather than individually, and the best group to genotype is expected to differ from the same-sized group chosen when individuals are genotyped sequentially. In a calibration step, simulated populations and full knowledge of genotypes were used to discover the best group(s) to genotype. The characteristics of these groups were then targeted in an optimization step, using normally available information for group formation in targeted populations. Contrasts were made among predictive indices for: (i) individuals, with genotyping between each individual; (ii) individuals, with genotyping occurring group-at-a-time; and (iii) groups, using group variables as criteria. The results of this investigation allow the determination of the value of moving from individual to group genotyping, reveal the favourable attributes of individuals for group formation, and lead to methods to form groups for genotyping. The approach used has applications in reducing genotyping costs in both experimental and commercial populations for both quantitative trait loci (QTL) detection and monitoring.  相似文献   

12.
Metabolites of Monascus ruber in silages   总被引：2，自引：0，他引：2  
A total of 233 silages were examined and found that Monascus ruber was present in 43 samples with counts between 1 × 103 and 9 × 106 colony-forming units (CFU)/g (mean: 2 × 105 CFU/g). Monacolin KL and the hydroxy acid monacolin KA were detected by liquid chromatography-mass spectrometry in 45 and 50 of 233 samples at levels ranging from 25–15 600 and 28–65 400  μ g/kg, respectively. Citrinin was found with high-performance liquid chromatography-fluorescence detection (FLD) in 14 (6%) samples, the concentrations varied between 2.4 and 64.2  μ g/kg. The concentrations of citrinin were low and toxic effects are not anticipated. Monacolin KA and monacolin KL occur frequently and in considerable amounts in silages. These metabolites are believed to influence the metabolic activity of rumen anaerobic fungi resulting in a poorer digestion of crude fibre.  相似文献   

13.
The effectiveness of five selection methods for genetic improvement of net merit comprising trait 1 of low heritability (h2 = 0.1) and trait 2 of high heritability (h2 = 0.4) was examined: (i) two‐trait quantitative trait loci (QTL)‐assisted selection; (ii) partial QTL‐assisted selection based on trait 1; (iii) partial QTL‐assisted selection based on trait 2; (iv) QTL‐only selection; and (v) conventional selection index without QTL information. These selection methods were compared under 72 scenarios with different combinations of the relative economic weights, the genetic correlations between traits, the ratio of QTL variance to total genetic variance of the trait, and the ratio of genetic variances between traits. The results suggest that the detection of QTL for multiple‐trait QTL‐assisted selection is more important when the index traits are negatively correlated than when they are positively correlated. In contrast to literature reports that single‐trait marker‐assisted selection (MAS) is the most efficient for low heritability traits, this study found that the identified QTL of the low heritability trait contributed negligibly to total response in net merit. This is because multiple‐trait QTL‐assisted selection is designed to maximize total net merit rather than the genetic response of the individual index trait as in the case of single‐trait MAS. Therefore, it is not economical to identify the QTL of the low heritability traits for the improvement of total net merit. The efficient, cost‐effective selection strategy is to identify the QTL of the moderate or high heritability traits of the QTL‐assisted selection index to facilitate total economic returns. Detection of the QTL of the low h2 traits for the QTL‐assisted index selection is justified when the low h2 traits have high negative genetic correlation with the other index traits and/or when both economic weights and genetic variances of the low h2 traits are larger as compared to the other index traits of higher h2. This study deals with theoretical efficiency of QTL‐assisted selection, but the same principle applies to SNP‐based genomic selection when the proportion of the genetic variance ‘explained by the identified QTLs’ in this study is replaced by ‘explained by SNPs’.  相似文献   

14.
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15.
The objective of the present study was to detect quantitative trait loci for economically important traits in a family from a Bos indicus x Bos taurus sire. A Brahman x Hereford sire was used to develop a half-sib family (n = 547). The sire was mated to Bos taurus cows. Traits analyzed were birth (kg) and weaning weights (kg); hot carcass weight (kg); marbling score; longissimus area (cm2); USDA yield grade; estimated kidney, pelvic, and heart fat (%); fat thickness (cm); fat yield (%); and retail product yield (%). Meat tenderness was measured as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem. Two hundred and thirty-eight markers were genotyped in 185 offspring. One hundred and thirty markers were used to genotype the remaining 362 offspring. A total of 312 markers were used in the final analysis. Seventy-four markers were common to both groups. Significant QTL (expected number of false-positives < 0.05) were observed for birth weight and longissimus area on chromosome 5, for longissimus area on chromosome 6, for retail product yield on chromosome 9, for birth weight on chromosome 21, and for marbling score on chromosome 23. Evidence suggesting (expected number of false-positives < 1) the presence of QTL was detected for several traits. Putative QTL for birth weight were detected on chromosomes 1, 2, and 3, and for weaning weight on chromosome 29. For hot carcass weight, QTL were detected on chromosomes 10, 18, and 29. Four QTL for yield grade were identified on chromosomes 2, 11, 14, and 19. Three QTL for fat thickness were detected on chromosomes 2, 3, 7, and 14. For marbling score, QTL were identified on chromosomes 3, 10, 14, and 27. Four QTL were identified for retail product yield on chromosomes 12, 18, 19, and 29. A QTL for estimated kidney, pelvic, and heart fat was detected on chromosome 15, and a QTL for meat tenderness measured as Warner-Bratzler shear force at 3 d postmortem was identified on chromosome 20. Two QTL were detected for meat tenderness measured as Warner-Bratzler shear force at 14 d postmortem on chromosomes 20 and 29. These results present a complete scan in all available progeny in this family. Regions underlying QTL need to be assessed in other populations.  相似文献   

16.
Several reports have demonstrated that bovine chromosome 26 (BTA26) harbours significant or suggestive quantitative trait loci (QTL) for milk production and composition traits in dairy cattle. Our previous study showed that a C/T substitution in the bovine TCF7L2 gene on BTA26 was significantly linked to QTL for protein yield (PY) in a Canadian dairy cattle population. Actually, this polymorphism was one of the markers derived from a genome‐wide screening of QTL for milk PY using an amplified fragment length polymorphism technique combined with a DNA pooling strategy. In the present study, 990 Holstein bulls with complete genotype and phenotype data from 14 sire families were analysed to confirm, if the QTL effects exist in other populations. Statistical analysis revealed that this marker was significantly associated with PY, protein percentage, milk yield and fat yield (FY) (p < 0.001) in the US Holstein population. These results indicate that this QTL region has a pleiotrophic effect on different milk traits and is portable in different populations.  相似文献   

17.
In dairy cattle, many studies have reported quantitative trait loci (QTL) on the centromeric end of chromosome 14 that affect milk production traits. One of the candidate genes in this QTL region – thyroglobulin (TG) – was previously found to be significantly associated with marbling in beef cattle. Thus, based on QTL studies in dairy cattle and because of possible effects of this gene on fat metabolism, we investigated the association of TG with milk yield and composition in Holstein dairy cattle. A total of 1279 bulls from the Cooperative Dairy DNA Repository Holstein population were genotyped for a single nucleotide polymorphism in TG used previously in beef cattle studies. Analysis of 29 sire families showed no significant association between TG variants and milk production traits. Within‐sire family analysis suggests that TG is neither the responsible gene nor a genetic marker in association with milk production traits.  相似文献   

18.
为初步鉴定与紫花苜蓿(Medicago sativa)粗灰分、钾、钙、镁、磷含量调控相关的数量性状基因座(Quantitative trait loci, QTL)和分子标记,本研究用低产早熟苜蓿和高产晚熟苜蓿杂交,构建了由392个个体组成的F1群体,对这些性状进行3年表型数据测定,且基于前期已构建的高密度遗传连锁图谱开展QTL定位。结果表明：共检测到63个与粗灰分和4种矿质元素含量相关的QTL,分布于22个染色体上,单个QTL的贡献率为2.50%～29.85%;其中重复定位的QTL共8个(qCa-3C-1和qCa-3C-2,qCa-6B-1和qCa-6B-2,qCa-6D-1和qCa-6D-2,qAsh-8B-1和qAsh-8B-2),共定位的QTL有6个(qP-2C和qK-2C,qP-3A和qMg-3A,qP-6D-3和qMg-6D-2);经进一步验证,与这些QTL紧密连锁的标记可用于分子标记辅助选择育种。本研究为选育矿质营养更丰富的苜蓿新品种奠定了基础。  相似文献   

19.
This report describes the use of 99mtechnetium pertechnetate (99mTcO4−) and 131[for imaging of a metastatic thyroid carcinoma in a dog. The 131] imaging showed metastatic lesions undetected by the 99mTcO4− imaging on 2 separate occasions. The possible mechanisms for the discrepancies between 131I and 99mTcO4− imaging of thyroid carcinomas are discussed. The use of 131I for the imaging of functional thyroid carcinomas in the dog is recommended.  相似文献   

20.
A confirmatory scan for the regions of bovine chromosome 1 segregating the quantitative trait loci (QTL) influencing birthweight, weaning weight, yearling weight, and preweaning and postweaning average daily gains was performed by genotyping half‐sib progeny of four Japanese Black sires using microsatellite DNA markers. Data were analyzed by generating an F‐statistic every 1 cM on a linkage map by the regression of phenotype on the probabilities of inheriting an allele from the sire after adjusting for the fixed effects of sire, sex, parity and season of birth as well as age as a covariate. Permutation tests at chromosome‐wide significance thresholds were carried out over 10 000 iterations. A significant QTL for birthweight at 114 cM was detected in the sire 2 family. This identification of a birthweight QTL in Japanese Black cattle may be useful for the implementation of marker‐assisted selection.  相似文献   

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