Genet Sel EvolThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

This page shows you the latest items in this publication.

Pages: 1 2 3 4

163 records returned

Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL) analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE)...
Source: Genet Sel Evol - November 19, 2009 Category: Genetics & Stem Cells Authors: Raadsma HW, Thomson PC, Zenger KR, Cavanagh C, Lam MK, Jonas E, Jones M, Attard G, Palmer D, Nicholas FW Tags: Genet Sel Evol Source Type: journals

A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: For an autosomal locus, four transmission events are possible from the parents to a progeny, specified by the grand parental origin of the alleles inherited by this individual. Computing the probabilities of these transmission events is essential to perform QTL detection methods. A fast algorithm for the estimation of these probabilities conditional to parental phases is developed. It is adapted to classical QTL detection designs applied to outbred populations, in particular to designed composed of half and / or full sib families. It assumes the absence of interference. The theory is fully developed and an ex...
Source: Genet Sel Evol - November 17, 2009 Category: Genetics & Stem Cells Authors: Elsen JM, Filangi O, Gilbert H, Le Roy P, Moreno C Tags: Genet Sel Evol Source Type: journals

Assessing population genetic structure via the maximisation of genetic distance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present. PMID: 19900278 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - November 9, 2009 Category: Genetics & Stem Cells Authors: Rodriguez-Ramilo ST, Toro MA, Fernandez J Tags: Genet Sel Evol Source Type: journals

Estimated breeding values and association mapping for persistency and total milk yield using natural cubic smoothing splines.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: NCSS can be used to estimate EBV for lactation persistency and total milk yield, which in turn can be used in whole-genome association studies. PMID: 19891765 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - November 5, 2009 Category: Genetics & Stem Cells Authors: Verbyla KL, Verbyla AP Tags: Genet Sel Evol Source Type: journals

Inheritance of fertility in broiler chickens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: There are opportunities for improving fertility in broiler stocks by selection on both sexes which would have impact throughout the laying period. PMID: 19874616 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - October 29, 2009 Category: Genetics & Stem Cells Authors: Wolc A, White IM, Olori VE, Hill WG Tags: Genet Sel Evol Source Type: journals

Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: This study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate common underlying loci affecting parasite resistance traits in different sheep breeds. The identification of new QTL may suggest the existence of complex host-parasite relationships that have unique features depending on the host-parasite combination, perhaps due to the different m...
Source: Genet Sel Evol - October 28, 2009 Category: Genetics & Stem Cells Authors: Gutierrez-Gil B, Perez J, Alvarez L, Martinez-Valladares M, de la Fuente LF, Bayon Y, Meana A, San Primitivo F, Rojo-Vazquez FA, Arranz JJ Tags: Genet Sel Evol Source Type: journals

Mapping Quantitative Trait Loci (QTL) in Sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: An (Awassi x Merino) x Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation an...
Source: Genet Sel Evol - October 21, 2009 Category: Genetics & Stem Cells Authors: Raadsma HW, Jonas E, McGill D, Hobbs M, Lam MK, Thomson PC Tags: Genet Sel Evol Source Type: journals

Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Detection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs. PMID: 19807906 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - October 5, 2009 Category: Genetics & Stem Cells Authors: Nagamine Y, Pong-Wong R, Visscher PM, Haley CS Tags: Genet Sel Evol Source Type: journals

Linear models for joint association and linkage QTL mapping.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward. PMID: 19788745 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - September 28, 2009 Category: Genetics & Stem Cells Authors: Legarra A, Fernando RL Tags: Genet Sel Evol Source Type: journals

Fuzzy classification of phantom parent groups in an animal model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Fuzzy-classification provides the potential to describe the genetic level of unknown parents in a more parsimonious and structured manner, and thereby increases the precision of predicted breeding values. PMID: 19785735 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - September 27, 2009 Category: Genetics & Stem Cells Authors: Fikse F Tags: Genet Sel Evol Source Type: journals

Genetic variation in the pleiotropic association between physical activity and body weight in mice.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: It was concluded that individuals with specific combinations of genotypes at the relQTLs and epiQTLs may account for some of the variation typically seen in plots of the association of physical activity with body weight. PMID: 19775457 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - September 22, 2009 Category: Genetics & Stem Cells Authors: Leamy LJ, Pomp D, Lightfoot JT Tags: Genet Sel Evol Source Type: journals

GSE is now an open access journal published by BioMed Central.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19674488 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - August 15, 2009 Category: Genetics & Stem Cells Authors: Hayes H, Baret P, Boichard D Tags: Genet Sel Evol Source Type: journals

Haplotype inference in crossbred populations without pedigree information.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating. PMID: 19671130 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - August 10, 2009 Category: Genetics & Stem Cells Authors: Coster A, Heuven HC, Fernando RL, Dekkers JC Tags: Genet Sel Evol Source Type: journals

History and structure of the closed pedigreed population of Icelandic Sheepdogs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: Although the base population consisted of 36 Icelandic Sheepdog founders, the current diversity is equivalent to that of only 2.2 equally contributing founders with no loss of founder alleles in descendants. The maximum attainable diversity is 4.7, unlikely achievable in a non-supervised breeding population like the Icelandic Sheepdog. Cluster analysis of kinship coefficients can provide a supporting tool to assess the distribution of available genetic diversity for captive population management. PMID: 19660133 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - August 5, 2009 Category: Genetics & Stem Cells Authors: Oliehoek PA, Bijma P, van der Meijden A Tags: Genet Sel Evol Source Type: journals

Introgression of a major QTL from an inferior into a superior population using genomic selection.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Substantial differences between introgression programs using classical and genomic selection were observed, and the former was generally inferior with respect to both genetic gain and the ability to preserve the target QTL. Combining genomic selection with gene-assisted selection for the target QTL acted as an extra precaution against loss of the target QTL and gave additional genetic gain for disease resistance. However, the effect on total merit index was limited. PMID: 19635140 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - July 26, 2009 Category: Genetics & Stem Cells Authors: Odegard J, Sonesson AK, Yazdi MH, Meuwissen TM Tags: Genet Sel Evol Source Type: journals

Testing strategies for genomic selection in aquaculture breeding programs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Various strategies were evaluated to reduce the amount of sib-testing and genotyping, but all resulted in loss of selection accuracy and thus of genetic gain. Rates of inbreeding were reduced by 81% in genomic selection schemes compared to traditional selection schemes for the parameters of the basic scheme, due to within-family selection. PMID: 19566932 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - June 29, 2009 Category: Genetics & Stem Cells Authors: Sonesson AK, Meuwissen TH Tags: Genet Sel Evol Source Type: journals

Association of selected SNP with carcass and taste panel assessed meat quality traits in a commercial population of Aberdeen Angus-sired beef cattle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: The results of this study confirm some previously documented associations. Furthermore, novel associations have been identified which, following validation in other populations, could be incorporated into breeding programmes to improve meat quality. PMID: 19555501 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - June 24, 2009 Category: Genetics & Stem Cells Authors: Gill JL, Bishop SC, McCorquodale C, Williams JL, Wiener P Tags: Genet Sel Evol Source Type: journals

Accuracy of breeding values of 'unrelated' individuals predicted by dense SNP genotyping.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: For livestock populations, 1NeL requires about ~30,000 training records, but this may be reduced if training and evaluation animals are related. A prediction equation is presented, that predicts accuracy when training and evaluation individuals are related. For humans, 1NeL requires ~350,000 individuals, which means that human disease risk prediction is possible only for diseases that are determined by a limited number of genes. Otherwise, genotyping and phenotypic recording need to become very common in the future. PMID: 19519896 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - June 10, 2009 Category: Genetics & Stem Cells Authors: Meuwissen TH Tags: Genet Sel Evol Source Type: journals

Estimation in a multiplicative mixed model involving a genetic relationship matrix.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the extension to the standard formulation necessary for estimation with a factor analytic structure across multiple environments. PMID: 19356255 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - April 9, 2009 Category: Genetics & Stem Cells Authors: Kelly AM, Cullis BR, Gilmour AR, Eccleston JA, Thompson R Tags: Genet Sel Evol Source Type: journals

Eleven generations of selection for the duration of fertility in the intergeneric crossbreeding of ducks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: A 12-generation selection experiment involving a selected line (S) and a control line (C) has been conducted since 1992 with the aim of increasing the number of fertile eggs laid by the Brown Tsaiya duck after a single artificial insemination (AI) with pooled Muscovy semen. On average, 28.9% of the females and 17.05% of the males were selected. The selection responses and the predicted responses showed similar trends. The average predicted genetic responses per generation in genetic standard deviation units were 0.40 for the number of fertile eggs, 0.45 for the maximum duration of fertility, and 0.32 for the ...
Source: Genet Sel Evol - March 31, 2009 Category: Genetics & Stem Cells Authors: Cheng YS, Rouvier R, Liu HL, Huang SC, Huang YC, Liao CW, Tai JJ, Tai C, Poivey JP Tags: Genet Sel Evol Source Type: journals

Reducing the bias of estimates of genotype by environment interactions in random regression sire models.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: The combination of a sire model and a random regression term describing genotype by environment interactions may lead to biased estimates of genetic variance components due to heterogeneous residual variance. In order to test different models, data simulated with genotype by environment interactions and dairy cattle data, assumed to contain such interactions, were analyzed. Two animal models were compared to four sire models. Models differed in their ability to handle heterogeneous variance from different sources. Including an individual effect with a (co)variance matrix restricted to three times the sire (co...
Source: Genet Sel Evol - March 19, 2009 Category: Genetics & Stem Cells Authors: Lillehammer M, Odegard J, Meuwissen TH Tags: Genet Sel Evol Source Type: journals

Correction: Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: After the recent publication of our article (Leroy, Genetics Selection Evolution 2009 41:5), we found several errors in the published Table Three, concerning the computation of contribution to within-breed diversity (CW). We apologize to the readers for these errors, which are corrected in the present erratum. PMID: 19298654 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - March 19, 2009 Category: Genetics & Stem Cells Authors: Leroy G, Callede L, Verrier E, Meriaux JC, Ricard A, Danchin-Burge C, Rognon X Tags: Genet Sel Evol Source Type: journals

Reducing dimensionality for prediction of genome-wide breeding values.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Partial least square regression (PLSR) and principal component regression (PCR) are methods designed for situations where the number of predictors is larger than the number of records. The aim was to compare the accuracy of genome-wide breeding values (EBV) produced using PLSR and PCR with a Bayesian method, 'BayesB'. Marker densities of 1, 2, 4 and 8 Ne markers/Morgan were evaluated when the effective population size (Ne) was 100. The correlation between true breeding value and estimated breeding value increased with density from 0.611 to 0.681 and 0.604 to 0.658 using PLSR and PCR respectively, with an over...
Source: Genet Sel Evol - March 18, 2009 Category: Genetics & Stem Cells Authors: Solberg TR, Sonesson AK, Woolliams JA, Meuwissen TH Tags: Genet Sel Evol Source Type: journals

Duck (Anas platyrhynchos) linkage mapping by AFLP fingerprinting.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Amplified fragment length polymorphism (AFLP) with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos) genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands) were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymo...
Source: Genet Sel Evol - March 17, 2009 Category: Genetics & Stem Cells Authors: Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang HL, Huang MC Tags: Genet Sel Evol Source Type: journals

Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: A QTL analysis of pig chromosome X (SSCX) was carried out using an approach that accurately takes into account the specific features of sex chromosomes i.e. their heterogeneity, the presence of a pseudoautosomal region and the dosage compensation phenomenon. A three-generation full-sib population of 386 animals was created by crossing Pietrain sires with a crossbred dam line. Phenotypic data on 72 traits were recorded for at least 292 and up to 315 F2 animals including chemical body composition measured on live animals at five target weights ranging from 30 to 140 kg, daily gain and feed intake measured throu...
Source: Genet Sel Evol - March 11, 2009 Category: Genetics & Stem Cells Authors: Duthie CA, Simm G, Perez-Enciso M, Doeschl-Wilson A, Kalm E, Knap PW, Roehe R Tags: Genet Sel Evol Source Type: journals

Precision of genetic parameters and breeding values estimated in marker assisted BLUP genetic evaluation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: In practical implementations of marker-assisted selection economic and logistic restrictions frequently lead to incomplete genotypic data for the animals of interest. This may result in bias and larger standard errors of the estimated parameters and, as a consequence, reduce the benefits of applying marker-assisted selection. Our study examines the impact of the following factors: phenotypic information, depth of pedigree, and missing genotypes in the application of marker-assisted selection. Stochastic simulations were conducted to generate a typical dairy cattle population. Genetic parameters and breeding v...
Source: Genet Sel Evol - March 4, 2009 Category: Genetics & Stem Cells Authors: Neuner S, Edel C, Emmerling R, Thaller G, Gotz KU Tags: Genet Sel Evol Source Type: journals

Inclusion of genetically identical animals to a numerator relationship matrix and modification of its inverse.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: In the field of animal breeding, estimation of genetic parameters and prediction of breeding values are routinely conducted by analyzing quantitative traits. Using an animal model and including the direct inverse of a numerator relationship matrix (NRM) into a mixed model has made these analyses possible. However, a method including a genetically identical animal (GIA) in NRM if genetic relationships between pairs of GIAs are not perfect, is still lacking. Here, we describe a method to incorporate GIAs into NRM using a K matrix in which diagonal elements are set to 1.0, off-diagonal elements between pairs of ...
Source: Genet Sel Evol - March 3, 2009 Category: Genetics & Stem Cells Authors: Oikawa T, Yasuda K Tags: Genet Sel Evol Source Type: journals

Factor-analytic models for genotype x environment type problems and structured covariance matrices.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: Factor analytic models provide a natural framework for modelling genotype x environment interaction type problems. Mixed model analyses fitting such models are likely to see increasing use due to the parsimonious description of covariance structures available, the scope for direct interpretation of factors as well as computational advantages. PMID: 19284520 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 30, 2009 Category: Genetics & Stem Cells Authors: Meyer K Tags: Genet Sel Evol Source Type: journals

Large-scale association study for structural soundness and leg locomotion traits in the pig.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses. PMID: 19284518 [PubMed - as supplied by publisher] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 21, 2009 Category: Genetics & Stem Cells Authors: Fan B, Onteru SK, Mote BE, Serenius T, Stalder KJ, Rothschild MF Tags: Genet Sel Evol Source Type: journals

Detecting selection-induced departures from Hardy-Weinberg proportions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Viability selection influences the genotypic contexts of alleles and leads to quantifiable departures from Hardy-Weinberg proportions. One measure of these departures is Wright's inbreeding coefficient (F), where observed heterozygosity is compared with expected heterozygosity. Here, I extend population genetics theory to describe post-selection genotype frequencies in terms of post-selection allele frequencies and fitness dominance. The resulting equations correspond to non-equilibrium populations, allowing the following questions to be addressed: When selection is present, how large a sample size is needed ...
Source: Genet Sel Evol - January 21, 2009 Category: Genetics & Stem Cells Authors: Lachance J Tags: Genet Sel Evol Source Type: journals

Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Quantitative trait loci (QTL) affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A) for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA), several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham) and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. T...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Heuven HC, van Wijk RH, Dibbits B, van Kampen TA, Knol EF, Bovenhuis H Tags: Genet Sel Evol Source Type: journals

Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and con...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Calus MP, Meuwissen TH, Windig JJ, Knol EF, Schrooten C, Vereijken ALj, Veerkamp RF Tags: Genet Sel Evol Source Type: journals

Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects. PMID: 19284678 [PubMed - in process] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Rowe SJ, Pong-Wong R, Haley CS, Knott SA, De Koning DJ Tags: Genet Sel Evol Source Type: journals

A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Genomic selection uses genome-wide dense SNP marker genotyping for the prediction of genetic values, and consists of two steps: (1) estimation of SNP effects, and (2) prediction of genetic value based on SNP genotypes and estimates of their effects. For the former step, BayesB type of estimators have been proposed, which assume a priori that many markers have no effects, and some have an effect coming from a gamma or exponential distribution, i.e. a fat-tailed distribution. Whilst such estimators have been developed using Monte Carlo Markov chain (MCMC), here we derive a much faster non-MCMC based estimator b...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Meuwissen TH, Solberg TR, Shepherd R, Woolliams JA Tags: Genet Sel Evol Source Type: journals

Changes in muscle cell cation regulation and meat quality traits are associated with genetic selection for high body weight and meat yield in broiler chickens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Between-breed genetic variation for muscle and meat quality traits was determined at eight weeks of age in 34 lines of purebred commercial broiler and layer lines and traditional breeds (categories) of chickens. Between-breed genetic variation for plasma ion concentrations and element concentration in muscle dry matter and ash were determined. Plasma from broilers had higher concentrations of Na+, K+, Mg++, total and free Ca++ and lower free:total Ca++ than plasma from layer and traditional lines. Muscle from broilers contained more Na and higher concentrations of K, Mg and Ca per mg of ash but not of dry mat...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Sandercock DA, Barker ZE, Mitchell MA, Hocking PM Tags: Genet Sel Evol Source Type: journals

GSE is now an open access journal published by BioMed Central.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19284684 [PubMed - in process] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Hayes H, Baret P, Boichard D Tags: Genet Sel Evol Source Type: journals

Ovine progressive pneumonia provirus levels are unaffected by the prion 171R allele in an Idaho sheep flock.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides further support to the adoption of PRNP 171R selection as a scrapie control measure. PMID: 19284685 [PubMed - in process] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Harrington RD, Herrmann-Hoesing LM, White SN, O'Rourke KI, Knowles DP Tags: Genet Sel Evol Source Type: journals

Effects of pedigree errors on the efficiency of conservation decisions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Conservation schemes often aim at increasing genetic diversity by minimizing kinship, and the best method to achieve this goal, when pedigree data is available, is to apply optimal contributions. Optimal contributions calculate contributions per animal so that the weighted average mean kinship among candidate parents is minimized. This approach assumes that pedigree data is correct and complete. However, in practice, pedigrees often contain errors: parents are recorded incorrectly or even missing. We used simulations to investigate the effect of these two types of errors on minimizing kinship. Our findings sh...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Oliehoek PA, Bijma P Tags: Genet Sel Evol Source Type: journals

Purging of inbreeding depression within the Irish Holstein-Friesian population.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this study was to investigate whether inbreeding depression in milk production or fertility performance has been partially purged due to selection within the Irish Holstein-Friesian population. Classical, ancestral (i.e., the inbreeding of an individual's ancestors according to two different formulae) and new inbreeding coefficients (i.e., part of the classical inbreeding coefficient that is not accounted for by ancestral inbreeding) were computed for all animals. The effect of each coefficient on 305-day milk, fat and protein yield as well as calving interval, age at first calving and survival to second l...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Mc Parland S, Kearney F, Berry DP Tags: Genet Sel Evol Source Type: journals

Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we concl...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X Tags: Genet Sel Evol Source Type: journals

A mating method accounting for inbreeding and multi-trait selection in dairy cattle populations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
: Selection in dairy cattle populations usually takes into account both the breed profiles for many traits and their overall estimated breeding values (EBV). This can result in effective contributions of breeding animals departing substantially from contributions optimised for saving future genetic variability. In this work, we propose a mating method that considers not only inbreeding but also the detailed EBV of progeny or the EBV of sires in reference to acceptance thresholds. Penalties were defined for inbreeding and for inadequate EBV profiles. Relative reductions of penalties yielded by any mating design were exp...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Colleau JJ, Tual K, de Preaumont H, Regaldo D Tags: Genet Sel Evol Source Type: journals

Genetic architecture of trout from Albania as revealed by mtDNA control region variation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this ...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Snoj A, Marić S, Berrebi P, Crivelli AJ, Shumka S, Susnik S Tags: Genet Sel Evol Source Type: journals

Genome-assisted prediction of a quantitative trait measured in parents and progeny: application to food conversion rate in chickens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Accuracy of prediction of yet-to-be observed phenotypes for food conversion rate (FCR) in broilers was studied in a genome-assisted selection context. Data consisted of FCR measured on the progeny of 394 sires with SNP information. A Bayesian regression model (Bayes A) and a semi-parametric approach (Reproducing kernel Hilbert Spaces regression, RKHS) using all available SNPs (p = 3481) were compared with a standard linear model in which future performance was predicted using pedigree indexes in the absence of genomic data. The RKHS regression was also tested on several sets of pre-selected SNPs (p = 400) usi...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: González-Recio O, Gianola D, Rosa GJ, Weigel KA, Kranis A Tags: Genet Sel Evol Source Type: journals

A genetic epidemiological model to describe resistance to an endemic bacterial disease in livestock: application to footrot in sheep.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Selection for resistance to an infectious disease not only improves resistance of animals, but also has the potential to reduce the pathogen challenge to contemporaries, especially when the population under selection is the main reservoir of pathogens. A model was developed to describe the epidemiological cycle that animals in affected populations typically go through; viz. susceptible, latently infected, diseased and infectious, recovered and reverting back to susceptible through loss of immunity, and the rates at which animals move from one state to the next, along with effects on the pathogen population. T...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Nieuwhof GJ, Conington J, Bishop SC Tags: Genet Sel Evol Source Type: journals

Genomic breeding value estimation using nonparametric additive regression models.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: Genomic selection refers to the use of genomewide dense markers for breeding value estimation and subsequently for selection. The main challenge of genomic breeding value estimation is the estimation of many effects from a limited number of observations. Bayesian methods have been proposed to successfully cope with these challenges. As an alternative class of models, non- and semiparametric models were recently introduced. The present study investigated the ability of nonparametric additive regression models to predict genomic breeding values. The genotypes were modelled for each marker or pair of flanking ma...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Bennewitz J, Solberg T, Meuwissen T Tags: Genet Sel Evol Source Type: journals

Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this study was to compare the convergence rate of different formulations of the prediction error variance calculated using Monte Carlo sampling. Four of these formulations were published, four were corresponding alternative versions, and two were derived as part of this study. The different formulations had different convergence rates and these were shown to depend on the number of samples and on the level of prediction error variance. Four formulations were competitive and these made use of information on either the variance of the estimated breeding value and on the variance of the true breeding value mi...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Hickey JM, Veerkamp RF, Calus MP, Mulder HA, Thompson R Tags: Genet Sel Evol Source Type: journals

Model for fitting longitudinal traits subject to threshold response applied to genetic evaluation for heat tolerance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: A semi-parametric non-linear longitudinal hierarchical model is presented. The model assumes that individual variation exists both in the degree of the linear change of performance (slope) beyond a particular threshold of the independent variable scale and in the magnitude of the threshold itself; these individual variations are attributed to genetic and environmental components. During implementation via a Bayesian MCMC approach, threshold levels were sampled using a Metropolis step because their fully conditional posterior distributions do not have a closed form. The model was tested by simulation following...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Sánchez JP, Rekaya R, Misztal I Tags: Genet Sel Evol Source Type: journals

Genomic selection of purebreds for crossbred performance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: In conclusion, GS can be conducted in crossbred population and models that fit breed-specific effects of SNP alleles may not be necessary, especially with high marker density. This opens great opportunities for genetic improvement of purebreds for performance of their crossbred descendents in the field, without the need to track pedigrees through the system. PMID: 19284703 [PubMed - in process] (Source: Genet Sel Evol)
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Ibánez-Escriche N, Fernando RL, Toosi A, Dekkers JC Tags: Genet Sel Evol Source Type: journals

Casein haplotypes and their association with milk production traits in Norwegian Red cattle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: A high resolution SNP map was constructed for the bovine casein region to identify haplotype structures and study associations with milk traits in Norwegian Red cattle. Our analyses suggest separation of the casein cluster into two haplotype blocks, one consisting of the CSN1S1, CSN2 and CSN1S2 genes and another one consisting of the CSN3 gene. Highly significant associations with both protein and milk yield were found for both single SNPs and haplotypes within the CSN1S1-CSN2-CSN1S2 haplotype block. In contrast, no significant association was found for single SNPs or haplotypes within the CSN3 block. Our res...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Nilsen H, Olsen HG, Hayes B, Sehested E, Svendsen M, Nome T, Meuwissen T, Lien S Tags: Genet Sel Evol Source Type: journals

Comparison of classification methods for detecting associations between SNPs and chick mortality.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective was to select a subset of whole genome SNPs associated with chick mortality. This was done by categorizing mortality rates and using a filter-wrapper feature selection procedure in each of the classification methods evaluated. Different numbers of categories (2, 3, 4, 5 and 10) and three classification algorithms (naïve Bayes classifiers, Bayesian networks and neural networks) were compared, using early and late chick mortality rates in low and high hygiene environments. Evaluation of SNPs selected by each classification method was done by predicted residual sum of squares and a significance test-related...
Source: Genet Sel Evol - January 1, 2009 Category: Genetics & Stem Cells Authors: Long N, Gianola D, Rosa GJ, Weigel KA, Avendaño S Tags: Genet Sel Evol Source Type: journals