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Breeding Values (breeding + value)
Selected AbstractsEstimation of Breeding Values Using Selected Pedigree RecordsBIOMETRICS, Issue 2 2005Richard Morton Summary Fish bred in tanks or ponds cannot be easily tagged individually. The parentage of any individual may be determined by DNA fingerprinting, but is sufficiently expensive that large numbers cannot be so fingerprinted. The measurement of the objective trait can be made on a much larger sample relatively cheaply. This article deals with experimental designs for selecting individuals to be fingerprinted and for the estimation of the individual and family breeding values. The general setup provides estimates for both genetic effects regarded as fixed or random and for fixed effects due to known regressors. The family effects can be well estimated when even very small numbers are fingerprinted, provided that they are the individuals with the most extreme phenotypes. [source] Including an additional systematic environmental effect within a generation in an evaluation model improves accuracy of prediction of breeding values in a closed herd of pigsANIMAL SCIENCE JOURNAL, Issue 2 2004Masahiro SATOH ABSTRACT The present study evaluated the advantage of mixed-model techniques over a selection index under different magnitudes of an additional systematic environmental effect (ASEE) in terms of accuracy of prediction and expected genetic gain. The data attempted to simulate a closed herd in a pig breeding program. The base population (G0) consisted of 10 males and 50 females. Six generations (G0 to G5) were selected by using a selection index of three traits without overlapping. Additional systematic environmental constants with four levels in a generation were assigned from a uniform distribution at different ranges. Breeding values of animals in the last generation (G5) were estimated on the basis of an index of individual phenotype (SI-U), SI-U adjusted for ASEE using a least-squares mean (SI-A), best linear unbiased prediction using an animal model excluding ASEE (AM-E), and an animal model including ASEE (AM-I). Accuracy of prediction and expected genetic gain were larger by the animal model than by the selection index, even if heritability of the traits selected was high and ASEE was set to zero. When ASEE was zero, the accuracy of prediction and expected genetic gain given by SI-U and AM-I were similar to those given by SI-A and AM-E, respectively. However, the differences in accuracy and expected gain between SI-U and AI-A and between AM-I and AM-E increased as the range of ASEE increased. It was concluded that selection based on an animal model was more effective than index selection, even if the herd environment was uniform and traits with high heritability were selected, and that it should be always included in an evaluation model, however slight any systematic environmental effect may be in a closed herd. [source] IS INBREEDING DEPRESSION LOWER IN MALADAPTED POPULATIONS?EVOLUTION, Issue 7 2009A QUANTITATIVE GENETICS MODEL Despite abundant empirical evidence that inbreeding depression varies with both the environment and the genotypic context, theoretical predictions about such effects are still rare. Using a quantitative genetics model, we predict amounts of inbreeding depression for fitness emerging from Gaussian stabilizing selection on some phenotypic trait, on which, for simplicity, genetic effects are strictly additive. Given the strength of stabilizing selection, inbreeding depression then varies simply with the genetic variance for the trait under selection and the distance between the mean breeding value and the optimal phenotype. This allows us to relate the expected inbreeding depression to the degree of maladaptation of the population to its environment. We confront analytical predictions with simulations, in well-adapted populations at equilibrium, as well as in maladapted populations undergoing either a transient environmental shift, or gene swamping in heterogeneous habitats. We predict minimal inbreeding depression in situations of extreme maladaptation. Our model provides a new basis for interpreting experiments that measure inbreeding depression for the same set of genotypes in different environments, by demonstrating that the history of adaptation, in addition to environmental harshness per se, may account for differences in inbreeding depression. [source] CLIMATIC AND TEMPORAL EFFECTS ON THE EXPRESSION OF SECONDARY SEXUAL CHARACTERS: GENETIC AND ENVIRONMENTAL COMPONENTSEVOLUTION, Issue 3 2004Dany Garant Abstract Despite great interest in sexual selection, relatively little is known in detail about the genetic and environmental determinants of secondary sexual characters in natural populations. Such information is important for determining the way in which populations may respond to sexual selection. We report analyses of genetic and large-scale environmental components of phenotypic variation of two secondary sexual plumage characters (forehead and wing patch size) in the collared flycatcher Ficedula albicollis over a 22-year period. We found significant heritability for both characters but little genetic covariance between the two. We found a positive association between forehead patch size and a large-scale climatic index, the North Atlantic Oscillation (NAO) index, but not for wing patch. This pattern was observed in both cross-sectional and longitudinal data suggesting that the population response to NAO index can be explained as the result of phenotypic plasticity. Heritability of forehead patch size for old males, calculated under favorable conditions (NAO index median), was greater than that under unfavorable conditions (NAO index < median). These changes occurred because there were opposing changes in additive genetic variance (VA) and residual variance (VR) under favorable and unfavorable conditions, with VA increasing and VR decreasing in good environments. However, no such effect was detected for young birds, or for wing patch size in either age class. In addition to these environmental effects on both phenotypic and genetic variances, we found evidence for a significant decrease of forehead patch size over time in older birds. This change appears to be caused by a change in the sign of viability selection on forehead patch size, which is associated with a decline in the breeding value of multiple breeders. Our data thus reveal complex patterns of environmental influence on the expression of secondary sexual characters, which may have important implications for understanding selection and evolution of these characters. [source] Optimized management of genetic variability in selected pig populationsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2008J.J. Colleau Summary Controlling the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed to breeding animals, given the current situation with regard to genetic diversity, and further, through optimal design of matings. The potential of such an approach for pig breeding was tested by retrospective optimization on the French Landrace population in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall estimated breeding value (EBV) should be the same as the observed one, for not decreasing short-term genetic gain. Optimizing breeding allocations to boars would have led one to decrease coancestry and inbreeding coefficients by approximately 20%. This decrease would have even increased to approximately 30%, would have replacements and disposals been optimized after accounting for genetic variability, keeping the same constraint of genetic level identical to the observed one. These results showed the potential value, in the future, of completing each periodical calculation of EBVs by optimizations considering genetic variability and of releasing corresponding information to breeders, in order to enhance maintenance of genetic variability. [source] Strategy for applying genome-wide selection in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2006L.R. Schaeffer Summary Animals can be genotyped for thousands of single nucleotide polymorphisms (SNPs) at one time, where the SNPs are located at roughly 1-cM intervals throughout the genome. For each contiguous pair of SNPs there are four possible haplotypes that could be inherited from the sire. The effects of each interval on a trait can be estimated for all intervals simultaneously in a model where interval effects are random factors. Given the estimated effects of each haplotype for every interval in the genome, and given an animal's genotype, a ,genomic' estimated breeding value is obtained by summing the estimated effects for that genotype. The accuracy of that estimator of breeding values is around 80%. Because the genomic estimated breeding values can be calculated at birth, and because it has a high accuracy, a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian-like dairy cattle situation. Costs of proving bulls were reduced by 92% and genetic change was increased by a factor of 2. Genome-wide selection may become a popular tool for genetic improvement in livestock. [source] Genetic evaluation of dairy cattle using a simple heritable genetic groundJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 11 2010Josef Pribyl Abstract The evaluation of an animal is based on production records, adjusted for environmental effects, which gives a reliable estimation of its breeding value. Highly reliable daughter yield deviations are used as inputs for genetic marker evaluation. Genetic variability is explained by particular loci and background polygenes, both of which are described by the genomic breeding value selection index. Automated genotyping enables the determination of many single-nucleotide polymorphisms (SNPs) and can increase the reliability of evaluation of young animals (from 0.30 if only the pedigree value is used to 0.60 when the genomic breeding value is applied). However, the introduction of SNPs requires a mixed model with a large number of regressors, in turn requiring new algorithms for the best linear unbiased prediction and BayesB. Here, we discuss a method that uses a genomic relationship matrix to estimate the genomic breeding value of animals directly, without regressors. A one-step procedure evaluates both genotyped and ungenotyped animals at the same time, and produces one common ranking of all animals in a whole population. An augmented pedigree,genomic relationship matrix and the removal of prerequisites produce more accurate evaluations of all connected animals. Copyright © 2010 Society of Chemical Industry [source] Genetic mapping of quantitative trait loci for milk production in sheepANIMAL GENETICS, Issue 5 2010R. G. Mateescu Summary A backcross pedigree using dairy East Friesian rams and non-dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test-day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here. [source] Association of single nucleotide polymorphisms in the endothelial differentiation sphingolipid G-protein-coupled receptor 1 gene with marbling in Japanese Black beef cattleANIMAL GENETICS, Issue 2 2009T. Yamada Summary Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. The endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene, involved in blood vessel formation, has been previously shown to be expressed at different levels in musculus longissimus muscle between low-marbled and high-marbled steer groups. It is located within the genomic region of a quantitative trait locus for marbling, and thus was considered as a positionally functional candidate for the gene responsible for marbling. In this study, two single nucleotide polymorphisms (SNPs) in the 5, untranslated region (UTR) and the 3, UTR of EDG1, referred to as c. - 312A>G and c.*446G>A, respectively, were detected between the two steer groups. The two SNPs were associated with the predicted breeding value for beef marbling standard number by analyses using a population of Japanese Black beef cattle. The effect of genotypes at each of the SNPs on the predicted breeding value for subcutaneous fat thickness was not statistically significant (P > 0.05). Reporter gene assays revealed no significant differences in gene expression between alleles at each of the SNPs. These findings suggest that EDG1 SNPs, although they may not be regarded as a causal mutation, may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. [source] An insertion/deletion variant of a thymine base in exon 2 of the porcine beta 3-adrenergic receptor gene associated with loin eye muscle areaANIMAL SCIENCE JOURNAL, Issue 6 2009Kensuke HIROSE ABSTRACT An insertion/deletion variant of a thymine base (T5 and T6) in exon 2 of porcine beta 3-adrenergic receptor (ADRB3) gene has been described. In the current study, we made an association study between the ADRB3 polymorphisms and production traits in 735 Duroc pigs. The allele frequencies for the T5 and T6 alleles in our study population were 0.433 and 0.567, respectively. Any associations between ADRB3 genotype and average daily weight gain during test period, or backfat thickness and intramuscular fat content were not detected in either sex. However the size of the loin eye muscle area (EMA) was significantly associated with ADRB3 genotypes in gilts. T6-homozygous gilts had a higher mean of EMA (40.6 ± 0.6 cm2) than T5-homozygous (38.1 ± 0.4 cm2, P = 0.002) and heterozygous (38.8 ± 0.3 cm2, P = 0.034) gilts. This association was not detected in males. In addition, a multiple traits animal model best linear unbiased predictor (BLUP) analysis revealed that the T6-homozygous genotype had positive effects on breeding value of EMA. Accordingly, we suggest that ADRB3 polymorphism has the potential to be an important genetic marker for prediction of EMA in Duroc pigs. [source] Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattleANIMAL SCIENCE JOURNAL, Issue 6 2009Takahisa YAMADA ABSTRACT Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2-11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. [source] Novel SNP in 5, flanking region of EDG1 associated with marbling in Japanese Black beef cattleANIMAL SCIENCE JOURNAL, Issue 4 2009Takahisa YAMADA ABSTRACT Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A>G in the 5, untranslated region (UTR) and c.*446G>A in the 3, UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G>A and g.1471620G>T, in the 5, flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G>A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G>T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G>T SNP might have an impact on EDG1 expression and also marbling. [source] Effect of mate selection on fuzzy selective mating criteria in closed dairy multiple ovulation and embryo transfer nucleus programsANIMAL SCIENCE JOURNAL, Issue 3 2002Atsushi NAKAMURA ABSTRACT In order to control rates of response and inbreeding, mate selection using fuzzy selective mating criteria (FMC) was investigated in adult multiple ovulation and embryo transfer nucleus schemes for dairy cattle. Stochastic simulation was used to model the closed nucleus scheme. This mate selection was examined in four alternative mating and male selection schemes: (i) a hierarchical scheme; (ii) a hierarchical sibship scheme (two males per sibship); (iii) a factorial scheme (two sires per dam); and (iv) a factorial sibship scheme (two males per sibship and two sires per dam). Genetic response and inbreeding rate tended to be reduced by increasing the trade-off parameter of FMC between the expected breeding value and inbreeding of progeny. Inbreeding rates in all schemes were reduced by reducing the variance of family size through selection and the average coancestry of mating pairs through mate allocation. [source] Cybrids and tetrad sterility for developing true potato seed hybridsANNALS OF APPLIED BIOLOGY, Issue 2 2003ALI M GOLMIRZAIE Summary Potato cybrids result from the fusion between cytoplasm and nuclear gene donors. Such genetic materials are an alternative means to broaden the breeding pool by non-sexual gene transfer. Tetrad pollen sterility provides also another source of male sterility with some potential for true potato seed breeding. The objective of this research was to investigate cybrid-derived offspring for both agronomic and reproductive characteristics in two contrasting Peruvian locations, and to examine new exotic germplasm for tetrad sterility, with the aim of broadening the breeding pool available at the Centro Internacional de la Papa (CIP). The cybrids were derived from fusions between Y-245.7, a clone with tetrad sterility, and Atzimba. These cybrids were crossed with selected male parents from the CIP breeding population, and their hybrid offspring were tested in La Molina (coastal desert) and Huancayo (cool highlands). In addition, other clones with tetrad sterility were also crossed with selected testers to determine their breeding value. There were significant differences for tuber yield, style length, and berry number among the hybrid offspring, and the genotype by environment interaction was significant for tuber yield and berry number. The top 25% highest yielding cybrid-derived offspring across both locations showed the same tuber yield although they were significantly different for some of the reproductive characteristics. With the exception of one cybrid, the others did not exhibit segregation for tetrad sterility in their hybrid offspring, which were male fertile. However, the offspring derived from crosses between other sources of tetrad sterility and the same testers all showed tetrad sterility, and some of them had outstanding tuber yield at La Molina. The lack of segregation for tetrad sterility in these new crosses suggests that the non-cybrid, male sterile, female parents are triplex or quadriplex for the Tr nuclear locus, which interacts with a sensitive cytoplasm (e.g. Trs from S. verrucosum or S. stoloniferum) to produce tetrad sterility in potato. [source] How is female mate choice affected by male competition?BIOLOGICAL REVIEWS, Issue 4 2005Bob B. M. Wong ABSTRACT The plethora of studies devoted to the topics of male competition and female mate choice belie the fact that their interaction remains poorly understood. Indeed, on the question of whether competition should help or hinder the choice process, opinions scattered throughout the sexual selection literature seem unnecessarily polarised. We argue, in the light of recent theoretical and empirical advances, that the effect of competition on mate choice depends on whether it results in the choosy sex attaining high breeding value for total fitness, considering both direct and indirect fitness benefits. Specifically, trade-offs may occur between different fitness benefits if some are correlated with male competitive ability whilst others are not. Moreover, the costs and benefits of mating with competitive males may vary in time and/or space. These considerations highlight the importance of injecting a life-history perspective into sexual selection studies. Within this context, we turn to the sexual selection literature to try to offer insights into the circumstances when competition might be expected to have positive or negative implications for pre-copulatory female choice. In this regard, we elaborate on three stages where competition might impact upon the choice process: (i) during mate detection, (ii) mate evaluation, and (iii) in dictating actual mating outcomes. We conclude by offering researchers several potentially rewarding avenues for future research. [source] The importance of haplotype length and heritability using genomic selection in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2009T.M. Villumsen Summary Reliabilities for genomic estimated breeding values (GEBV) were investigated by simulation for a typical dairy cattle breeding setting. Scenarios were simulated with different heritabilites (h2) 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 h2 = 0.02 to 0.93 for h2 = 0.30, and in the seventh generation without phenotypes ranged from 0.69 for h2 = 0.02 to 0.86 for h2 = 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. [source] Comparison of models for genetic evaluation of survival traits in dairy cattle: a simulation studyJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2008J. Jamrozik Summary Three models for the analysis of functional survival data in dairy cattle were compared using stochastic simulation. The simulated phenotype for survival was defined as a month after the first calving (from 1 to 100) in which a cow was involuntarily removed from the herd. Parameters for simulation were based on survival data of the Canadian Jersey population. Three different levels of heritability of survival (0.100, 0.050 and 0.025) and two levels of numbers of females per generation (2000 or 4000) were considered in the simulation. Twenty generations of random mating and selection (on a second trait, uncorrelated with survival) with 20 replicates were simulated for each scenario. Sires were evaluated for survival of their daughters by three models: proportional hazard (PH), linear multiple-trait (MT), and random regression (RR) animal models. Different models gave different ranking of sires with respect to survival of their daughters. Correlations between true and estimated breeding values for survival to five different points in a cow's lifetime after the first calving (120 and 240 days in milk after first, second, third and fourth calving) favoured the PH model, followed by the RR model evaluations. Rankings of models were independent of the heritability level, female population size and sire progeny group size (20 or 100). The RR model, however, showed a slight superiority over MT and PH models in predicting the proportion of sire's daughters that survived to the five different end-points after the first calving. [source] Multivariate analyses of carcass traits for Angus cattle fitting reduced rank and factor analytic modelsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2007K. Meyer Summary Multivariate analyses of carcass traits for Angus cattle, consisting of six traits recorded on the carcass and eight auxiliary traits measured by ultrasound scanning of live animals, are reported. Analyses were carried out by restricted maximum likelihood, fitting a number of reduced rank and factor analytic models for the genetic covariance matrix. Estimates of eigenvalues and eigenvectors for different orders of fit are contrasted and implications for the estimates of genetic variances and correlations are examined. Results indicate that at most eight principal components (PCs) are required to model the genetic covariance structure among the 14 traits. Selection index calculations suggest that the first seven of these PCs are sufficient to obtain estimates of breeding values for the carcass traits without loss in the expected accuracy of evaluation. This implied that the number of effects fitted in genetic evaluation for carcass traits can be halved by estimating breeding values for the leading PCs directly. [source] Application of robust procedures for estimation of breeding values in multiple-trait random regression test-day modelJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2007J. Jamrozik Summary Robust procedures for estimation of breeding values were applied to multiple-trait random regression test-day (TD) model to reduce the influence of outliers on inferences. Robust estimation methods consisted of correcting selected observations (defined as outliers) in the process of solving mixed-model equations in such a way that ,new' observations gave residuals (actual observation minus predicted) within k residual standard deviations for a given day in milk in 305-day lactation. Data were 980 503 TD records on 63 346 Canadian Jersey cows. Milk, fat, protein and somatic cell score in the first three lactations were analysed jointly in the model that included fixed herd-TD effect and regressions within region,age,season of calving, and regressions with random coefficients for animal genetic and permanent environmental effects. All regressions were orthogonal polynomials of order 4. Robust procedures for k = 1.5, 2.0, 2.5, 2.75 and 3.0 were contrasted with the regular best linear unbiased prediction (BLUP) method in terms of numbers and distributions of outliers, and estimated breeding values (EBV) of animals. Distributions of outliers were similar across traits and lactations. Early days in milk (from 5 to 15) were associated with larger frequency of outliers compared with the remaining part of lactation. Several, computationally simple, robust methods (for k > 2.0) reduced the influence of outlier observations in the model and improved the overall model performance. Differences in rankings of animals from robust evaluations were small compared with the regular BLUP method. No clear associations between changes in EBV (rankings) of top animals from different methods and the occurrence of outliers were detected. [source] Strategy for applying genome-wide selection in dairy cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2006L.R. Schaeffer Summary Animals can be genotyped for thousands of single nucleotide polymorphisms (SNPs) at one time, where the SNPs are located at roughly 1-cM intervals throughout the genome. For each contiguous pair of SNPs there are four possible haplotypes that could be inherited from the sire. The effects of each interval on a trait can be estimated for all intervals simultaneously in a model where interval effects are random factors. Given the estimated effects of each haplotype for every interval in the genome, and given an animal's genotype, a ,genomic' estimated breeding value is obtained by summing the estimated effects for that genotype. The accuracy of that estimator of breeding values is around 80%. Because the genomic estimated breeding values can be calculated at birth, and because it has a high accuracy, a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian-like dairy cattle situation. Costs of proving bulls were reduced by 92% and genetic change was increased by a factor of 2. Genome-wide selection may become a popular tool for genetic improvement in livestock. [source] Association of a melanocortin 4 receptor (MC4R) polymorphism with performance traits in Lithuanian White pigsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2006R. Jokubka Summary The melanocortin 4 receptor is expressed in virtually all brain regions of mammals and plays an important role in energy homeostasis. Polymorphisms in this gene may thus be related to growth and obesity. In pigs, a non-synonymous polymorphic site was described (Asp298Asn) and demonstrated to affect cAMP production and to alter adenylyl cyclase signalling. Association studies revealed significant linkage of this mutation with production trait in pigs. In this study, 207 Lithuanian White pigs were genotyped at the MC4R locus and analysed on relationships between genotype and breeding values for several performance traits. The observed allele and genotype frequencies did not deviate significantly from Hardy,Weinberg equilibrium (wildtype allele 0.59; mutant allele 0.41) and are comparable with those described in other Large White populations. The mutant Asn298 allele of the MC4R gene was significantly associated with increased test daily gain, higher lean meat percentage and lower backfat thickness. There was a trend towards an improved feed conversion ratio (p = 0.065) in animals with the mutant allele whereas no significant effect was found on lifetime daily gain. These results indicate that the MC4R polymorphism should be integrated in selection programmes in the Lithuanian White to improve carcass composition. [source] Prediction of accuracy of estimated Mendelian sampling termsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2005S. Avendaño Summary This study describes a general framework for predicting the accuracy of Mendelian sampling terms when truncation selection is applied on best linear unbiased prediction (BLUP) estimated breeding values. A selection index approach is followed. The pseudo-BLUP index is extended to include terms related to the Mendelian sampling term. Predicted accuracies are compared with those obtained through stochastic computer simulation. Good predictions for the accuracy of the Mendelian sampling term were obtained both at selection time and at convergence of long-term contributions of selected candidates for a range of heritabilities and population structures. The prediction approach developed provides a key tool for obtaining predictions of genetic response from quadratic optimization that maximizes the rate of genetic progress while restricting the rate of inbreeding. [source] Simple preconditioners for the conjugate gradient method: experience with test day modelsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2002I. STRANDÉN Preconditioned conjugate gradient method can be used to solve large mixed model equations quickly. Convergence of the method depends on the quality of the preconditioner. Here, the effect of simple preconditioners on the number of iterations until convergence was studied by solving breeding values for several test day models. The test day records were from a field data set, and several simulated data sets with low and high correlations among regression coefficients. The preconditioner matrices had diagonal or block diagonal parts. Transformation of the mixed model equations by diagonalization of the genetic covariance matrix was studied as well. Preconditioner having the whole block of the fixed effects was found to be advantageous. A block diagonal preconditioner for the animal effects reduced the number of iterations the higher the correlations among animal effects, but increased memory usage of the preconditioner. Diagonalization of the animal genetic covariance matrix often reduced the number of iterations considerably without increased memory usage. Einfache Preconditioners für die `Conjugate Gradient Method': Erfahrungen mit Testtagsmodellen Die `Preconditioned Conjugate Gradient Methode' kann benutzt werden um große `Mixed Model' Gleichungssysteme schnell zu lösen. In diesem Beitrag wurde der Einfluss von einfachen Preconditioners auf die Anzahl an Iterationen bis zur Konvergenz bei der Schätzung von Zuchtwerten bei verschiedenen Testtagsmodellen untersucht. Die Testtagsdaten stammen aus einem Felddatensatz und mehreren simulierten Datensätzen mit unterschiedlichen Korrelationen zwischen den Regressionskoeffizienten. Die Preconditioner Matrix bestand aus Diagonalen oder Blockdiagonalen Teilen. Eine Transformation der Mixed Modell Gleichungen durch Diagonalisierung der genetischen Kovarianzmatrix wurde ebenfalls untersucht. Preconditioners mit dem Block der fixen Effekte zeigten sich immer überlegen. Ein Blockdiagonaler Preconditioner für den Tiereffekt reduzierte die Anzahl an Iterationen mit höher werden Korrelationen zwischen den Tiereffekten, aber erhöhte den Speicherbedarf. Eine Diagonalisierung der genetischen Kovarianzmatrix reduzierte sehr oft die Anzahl an Iterationen erheblich ohne den Speicherbedarf zu erhöhen. [source] Comparison of estimated breeding values, daughter yield deviations and de-regressed proofs within a whole genome scan for QTLJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2001H. Thomsen An important issue in quantitative trait loci (QTL) detection is the use of phenotypic measurement as a dependent variable. Daughter yield deviations (DYDs) as the unit of choice are not available for all traits of interest. The use of de-regressed proofs (DRPFs) of estimated breeding values (EBVs) is an alternative to using daughter yield deviations. The objective of this study was to examine possible differences between DYDs and DRPFs within the use of QTL detection. The pedigree used was part of the granddaughter design of the German QTL effort. Consisting marker maps for livestock species were derived from all available data of 16 German Holstein paternal half-sib families with a total of 872 sires. The number of progeny ranged from 19 to 127. A whole genome scan was performed using weighted and unweighted multimarker regression with DYDs, DRPFs and EBVs as dependent variables for the traits milk, fat and protein yields. Results were compared with respect to the number of QTL detected. A similar number of QTL was detected with DRPFs and DYDs. Also, when dependent variables were weighted according to the variance of the trait, a higher number of QTL was detected at the desired level of significance as compared to using unweighted variables. Vergleich von Zuchtwerten, Daughter Yield Deviation und deregressierten Zuchtwerten bei der Genomanalyse zum Nachweis für QTL Ein bedeutender Einflussfaktor in der QTL-Analyse (QTL: Genorte für quantitativemarkmale) ist die Wahl der abhängigen Leistungsvariablen. Da Daughter Yield Deviations (DYDs) aber nicht für jedes Leistungsmerkmal zur Verfügung stehen, sollte untersucht werden, ob die De-regression von Zuchtwerten als alternative Variable in der QTL Analyse verwendet werden kann. Für die Untersuchung wurde ein Teil des Tiermaterials verwendet, das im Rahmen des Genomanalyseprojektes der Arbeitsgemeinschaft Deutscher Rinderzüchter untersucht wurde. Es standen 872 Bullen aus 16 väterlichen Halbgeschwisterfamilien der Rasse Deutsche Holsteins zur Verfügung. Die Zahl der Nachkommen pro Familie variierte von 19 bis 127. Unter Verwendung eines gewichteten als auch ungewichteten Multi-Marker Regressionsansatzes wurde ein Genomscan für die Leistungsmerkmale Milch-kg, Fett-kg und Eiweiss-kg durchgeführt, wobei als abhängige Variablen Zuchtwerte (EBV), Daughter Yield Deviations (DYD) und de-regressierte Zuchtwerte (DRPF) verwendet wurden. Die De-regression wurde auf der Basis der effektiven Töchterzahl, der Heritabilität des Merkmals und der additiv genetischen Verwandtschaftsmatrix durchgeführt. Alle Ergebnisse wurden in Hinblick auf die Anzahl der entdeckten QTL verglichen. Es zeigten sich dabei keine wesentlichen Unterschiede bei der Verwendung von DYDs und DRPFs. Die Rate der QTL Entdeckungen war bei beiden verwendeten Zuchtwerten annähernd gleich. Über den Vergleich unterschiedlicher Leistungsvariablen hinaus wurden die Ergebnisse der ungewichteten und gewichteten Analyse einander gegenübergestellt. Es konnte gezeigt werden, dass bei einer Gewichtung des Merkmals die Rate der QTL-Entdeckungen bei einem bestimmten Signifikanzniveau deutlich höher ist. [source] Reducing the effect of parent averages from animal solutions in mixed model equationsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2000L. Wu Summary Selection of animals based on their BLUP evaluations from an animal model results in animals that are closely related which leads to increased rates of inbreeding. The tendency for higher inbreeding rates is greater at low heritability values. Several attempts have been made to reduce the impact of parent average breeding values from animals evaluations in order to reduce inbreeding while not sacrificing genetic response. A method that modifies the rules for forming the inverse of the additive genetic relationship matrix for use in best linear unbiased estimation of breeding values via an animal model was developed. This method and several others were compared analytically and empirically, from the perspective of partitioning the animal solutions into contributions from the data, from progeny, and from the parent average. The ratio of genetic progress to average level of inbreeding showed that the modified relationship matrix method was superior to the other methods. Similar results could be obtained by using artificially high heritability in a usual BLUP analysis. Zusammenfassung Die Selektion von Tieren aufgrund ihrer geschätzten BLUP-Zuchtwerte unter einem Tiermodell ergibt verwandte Tiere, was zu gesteigerten Inzuchtraten führt. Einige Versuche wurden unternommen, um die Wirkung des elterlichen Zuchtwertduchschnitts auf die geschätzten Tierzuchtwerte zu reduzieren, um einerseits die Inzucht einzugrenzen, aber andererseits den Zuchtfortschritt nicht zu beeinträchtigen. Es wurde eine Methode entwickelt, welche die Regeln zur Aufstellung der additiven genetischen Verwandtschaftsmatrix im Tiermodell für die BLUP-Zuchtwertschätzung modifiziert. Diese und einige andere Methoden wurden empirisch und analytisch verglichen. Das geschah aus der Sicht, die Lösungen für die Tiereffekte in Bezug auf den Beitrag der Eltern, der Eigenleistung und der Nachkommen aufzuteilen. Das Verhältnis des Zuchtfortschritts zum mittleren Inzuchtniveau zeigte, dass die modifizierte Verwandtschaftsmatrix als Methode allen anderen überlegen war. Ähnliche Ergebnisse konnten erreicht werden, wenn in einer gewöhnlichen BLUP-Analyse der Heritabilitätsparameter künstlich hochgesetzt wird. [source] Implications of the difference between true and predicted breeding values for the study of natural selection and micro-evolutionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2006E. POSTMA Abstract The ability to predict individual breeding values in natural populations with known pedigrees has provided a powerful tool to separate phenotypic values into their genetic and environmental components in a nonexperimental setting. This has allowed sophisticated analyses of selection, as well as powerful tests of evolutionary change and differentiation. To date, there has, however, been no evaluation of the reliability or potential limitations of the approach. In this article, I address these gaps. In particular, I emphasize the differences between true and predicted breeding values (PBVs), which as yet have largely been ignored. These differences do, however, have important implications for the interpretation of, firstly, the relationship between PBVs and fitness, and secondly, patterns in PBVs over time. I subsequently present guidelines I believe to be essential in the formulation of the questions addressed in studies using PBVs, and I discuss possibilities for future research. [source] Sources of Phenotypic and Genetic Variation for Seawater Growth in Five North American Atlantic Salmon, Salmo salar, StocksJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 3 2010William R. Wolters In 2003, pedigreed families were obtained from two St. John's River sources, Penobscot River, Gaspè, and landlocked salmon stocks. Eyed eggs were disinfected upon arrival, and incubated in separate hatching jars. Fry were transferred prior to first feeding into individual 0.1-m3 tanks receiving 8 L/min of oxygen-saturated freshwater from a recirculating biological filtration system. At approximately 30 d after the initiation of feeding, fish densities were equalized to 250 fish/tank, fed 5% of the tank's total biomass in 3,4 daily feedings. When the fish were approximately 40 g, approximately 30 fish from each family were pit tagged and stocked communally into three replicated 10-m3 smolt tanks. Approximately 1 mo prior to stocking into sea cages for performance evaluations, evaluations of serum chloride levels and gill Na+, K+ -ATPase activity were measured on subsamples from all stocks in freshwater and following seawater challenge. Smolts were stocked into sea cages in June 2005, harvested in February 2007, and evaluated for carcass weight, sex, and stage of sexual maturity. Data were analyzed by the mixed model ANOVA to determine the random effects of sire and dam (sire), and the fixed effects of sex, salmon stock, ploidy level, and replicate smolt tank on carcass weight with smolt weight as a covariate. Sire and dam variance components were significantly different from zero, and the fixed effects of salmon stock, sex × stock interaction, and smolt weight at stocking were significant (P < 0.05). There were no significant differences among sexes, replicate smolt tank, or ploidy level for carcass weight. Overall, St. John's River fish had the fastest growth with a carcass weight >4.1 kg compared with the slowest growth in landlocked fish at 1.7 kg. Grilsing was also highest in St. John's River fish (ca. 4,6%) and lowest in Penobscot River fish (0%). The sire heritability for carcass weight calculated from the sire variance component using the mixed model ANOVA or MTDFREML was 0.26 ± 0.14. Data were used to calculate breeding values on captive sibling adult brood fish, and a line selected for carcass weight was spawned in the fall of 2007, and eggs from these fish were released to industry. [source] INHBA -Associated Markers as Candidates for Stallion FertilityREPRODUCTION IN DOMESTIC ANIMALS, Issue 2 2010K Giesecke Contents The inhibin beta A (INHBA) gene was chosen as candidate for stallion fertility and analysed for intragenic markers to find associations with pregnancy rate per oestrus. Intragenic single nucleotide polymorphisms (SNPs) were developed in order to perform an association and haplotype analysis using the least square means (LSM) of the pregnancy rate per oestrus for stallions as well as breeding values (BVs) for the embryonic and paternal component of the pregnancy rate per oestrus. The polymorphisms were genotyped in 161 Hanoverian warmblood stallions. Insemination records from approximately 20 000 Hanoverian warmblood mares were used to calculate LSM for stallions and to predict the paternal and embryonic component of BVs for the pregnancy rate per oestrus. We demonstrated significant associations of single markers and haplotypes with the LSM and the embryonic and paternal component of BVs for the pregnancy rate per oestrus. This is the first report on INHBA as an associated candidate gene with the LSM of stallions and the paternal and embryonic component of BVs for the pregnancy rate per oestrus. [source] Assignment of the locus for arachnomelia syndrome to bovine chromosome 23 in Simmental cattleANIMAL GENETICS, Issue 6 2009J. Buitkamp Summary Arachnomelia syndrome is a lethal inherited malformation mainly of the limbs, vertebral column and skull in cattle, which poses a severe impairment to farmers and breeders. Recently, a number of cases of arachnomelia syndrome have occurred in the Simmental breed and some sires with excellent breeding values had been shown to be carriers of the disease. We herein report the genetic mapping of the mutation underlying arachnomelia in cattle. The disease was mapped using a two-stage genome scan. A first round autosomal genome-wide screening using a limited number of cases identified three chromosomal regions with lod-scores > 1. The position of the arachnomelia syndrome locus was identified to be on BTA 23 by genotyping an additional, independent set of animals with markers that provided positive lod-scores in the course of the initial genome-wide screen. Using a denser set of regional microsatellites, the locus could be mapped to a region about 9 cM in length. The most significant linkage signal with arachnomelia syndrome was obtained with marker NRKM-17 (lod-score > 20) using a recessive model. Interestingly, different genes seem to be responsible for the disease in Brown Swiss and Simmental breeds, as arachnomelia syndrome was mapped to a different location in Brown Swiss. The results provide sufficient information for the development of a genetic test system and also allow the identification of positional candidate genes. [source] Evaluation of SPATA1 -associated markers for stallion fertilityANIMAL GENETICS, Issue 4 2009K. Giesecke Summary Stallion fertility is an economically important trait because the use of artificial insemination is increasing in the horse industry and superior sires are used more intensely. Molecular genetic markers may be useful as early indicators for a stallion's fertility and genetic improvement programmes. The testis-specific SPATA1 protein is involved in shaping the sperm head during spermatogenesis. Thus, the spermatogenesis associated 1 (SPATA1) gene was chosen as candidate for stallion fertility, and we analysed intragenic single nucleotide polymorphisms (SNPs) as genetic markers for the least square means (LSM) of the pregnancy rate per oestrus of stallions and breeding values (BV) for the paternal and embryonic component of the pregnancy rate per oestrus. We sequenced the cDNA of SPATA1 to verify the annotated mRNA sequence. One SPATA1 -associated intronic SNP (BIEC2-968854) showed a significant association with the embryonic component of BVs of stallions for the pregnancy rate per oestrus. The embryonic component of BVs was positively associated with homozygous C/C stallions. Both the additive and dominance effects were significant with values of ,5.8% (P = 0.01) and ,6.4% (P = 0.02) for the embryonic component of BVs. For the same SNP, a suggestive association was found for the LSM of the pregnancy rate per oestrus of stallions. Heterozygous stallions had higher pregnancy rates per oestrus than homozygous stallions. The dominance effect was 4.1% with a nominal P -value of 0.02. The SNP BIEC2-968854 can change an SP1 binding site and thus we assume that gene regulation may be influenced through this intronic mutation. This is the first report on SPATA1 being associated with the pregnancy rate per oestrus for stallions. [source] | |||||||||||||||||||