MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Genet Sel Evol' source. Thu, 11 Mar 2010 17:23:38 +0100 http://www.medworm.com/index.php?rid=3327761&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20193071%26dopt%3DAbstract CONCLUSIONS: International genomic evaluations can be computed either by modifying MACE to account for residual correlations across countries or by multi-trait evaluation of combined genotype files. The gains in reliability justify the increased computation but require more cooperation than in previous breeding programs. PMID: 20193071 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3327761 Mon, 01 Mar 2010 00:00:00 +0100 3327761 http://www.medworm.com/index.php?rid=3315225&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20184760%26dopt%3DAbstract CONCLUSIONS: The degree of connectedness in a bovine population bred by natural service mating, such as Bruna del Pirineus beef cattle, measured as the CD of comparisons among herds, is high. It is possible to define a pool of animals for which estimated breeding values can be compared after an across-herds genetic evaluation, especially for highly heritable traits. PMID: 20184760 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3315225 Thu, 25 Feb 2010 00:00:00 +0100 3315225 http://www.medworm.com/index.php?rid=3299827&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20170500%26dopt%3DAbstract CONCLUSIONS: GEBV accuracy of current selection candidates varies due to different genetic relationships relative to the training data. Accuracy of future candidates can be lower than reported in previous studies because information from close relatives will not be available when selection on GEBVs is applied. A Bayesian model averaging approach exploits LD information considerably better than G-BLUP and thus is the most promising method. Cross-validations should account for family structure in the data to allow for long-lasting genomic based breeding plans in animal and plant breeding. PMID: 20170500 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3299827 Fri, 19 Feb 2010 00:00:00 +0100 3299827 http://www.medworm.com/index.php?rid=3236454&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20113462%26dopt%3DAbstract CONCLUSIONS: Both mutations reduced fatness and increased muscle mass, although the effect of the frameshift mutation (c.960delG) was more important as compared to the 3'-UTR mutation (c.2360G>A). Lambs homozygous for the c.960delG mutation grew more slowly than those with other MSTN genotypes, but had the least fat and the largest muscle mass. Only c.960delG showed dominance effects. PMID: 20113462 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3236454 Fri, 29 Jan 2010 00:00:00 +0100 3236454 http://www.medworm.com/index.php?rid=3223755&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20109204%26dopt%3DAbstract CONCLUSIONS: The underlying model was validated. A correct drawing of liabilities for the Gibbs sampler was provided. For a structured competition, the mixture model with a group effect assigned to horses gave the best results. PMID: 20109204 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3223755 Thu, 28 Jan 2010 00:00:00 +0100 3223755 http://www.medworm.com/index.php?rid=3223756&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20105297%26dopt%3DAbstract CONCLUSIONS: The extension of the method to non-genotyped animals presented in this paper makes it possible to integrate all the genomic, pedigree and phenotype information into a one-step procedure for genomic prediction. Such a one-step procedure results in more accurate estimated breeding values and has the potential to become the standard tool for genomic prediction of breeding values in future practical evaluations in pig and cattle breeding. PMID: 20105297 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3223756 Wed, 27 Jan 2010 00:00:00 +0100 3223756 http://www.medworm.com/index.php?rid=3209431&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20100345%26dopt%3DAbstract CONCLUSIONS: The applications examined in this study suggest the plausibility of a nonlinear recursive effect from GL onto CD and SB. Also, the fact that the most restrictive model RMM3, which assumes that the only cause of correlation is phenotypic recursion, performs as well as the others indicates that the phenotypic recursion may be an important cause of the observed patterns of genetic and environmental correlations. PMID: 20100345 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3209431 Mon, 25 Jan 2010 00:00:00 +0100 3209431 http://www.medworm.com/index.php?rid=3136971&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20043827%26dopt%3DAbstract CONCLUSIONS: Phenotypic information on some individuals and deregressed data on others can be combined in genomic analyses using appropriate weighting. PMID: 20043827 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3136971 Thu, 31 Dec 2009 00:00:00 +0100 3136971 http://www.medworm.com/index.php?rid=3136970&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20043835%26dopt%3DAbstract CONCLUSIONS: The four methods which use information from all SNP namely RR-BLUP, Bayes-R, PLSR and SVR generate similar accuracies of MBV prediction for genomic selection, and their use in the selection of immediate future generations in dairy cattle will be comparable. The use of FR-LS in genomic selection is not recommended. PMID: 20043835 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3136970 Thu, 31 Dec 2009 00:00:00 +0100 3136970 http://www.medworm.com/index.php?rid=3134237&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20042096%26dopt%3DAbstract In this study, we estimated the heritabilities of a wide range of immune traits, as potential biomarkers, and measured their relationship with performance within both specific pathogen-free (SPF) and non-SPF environments. Immune traits were measured in 674 SPF pigs and 606 non-SPF pigs, which were subsets of the populations for which we had performance measurements (average daily gain), viz. 1549 SPF pigs and 1093 non-SPF pigs. Immune traits measured included total and differential white blood cell counts, peripheral blood mononuclear leucocyte (PBML) subsets (CD4+ cells, total CD8alpha+ cells, classical CD8alphabeta+ cells, CD11R1+ cells (CD8alpha+ and CD8alpha-), B cells, monocytes and CD16+ cells) and acute phase proteins (alpha-1 acid glycoprotein (AGP), haptoglobin, C-reactive protein... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3134237 Wed, 30 Dec 2009 00:00:00 +0100 3134237 http://www.medworm.com/index.php?rid=3134238&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040081%26dopt%3DAbstract CONCLUSIONS: Including a polygenic effect had no impact on the selection accuracy, but showed reduced bias, which is especially important when estimates of genome-wide markers are used to estimate breeding values over more than one generation. PMID: 20040081 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3134238 Tue, 29 Dec 2009 00:00:00 +0100 3134238 http://www.medworm.com/index.php?rid=3060461&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19958551%26dopt%3DAbstract Authors: Totir LR, Fernando RL, Abraham J ABSTRACT: BACKGROUND: Marginal posterior genotype probabilities need to be computed for genetic analyses such as genetic counseling in humans and selective breeding in animal and plant species. METHODS: In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing int... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3060461 Thu, 03 Dec 2009 00:00:00 +0100 3060461 http://www.medworm.com/index.php?rid=3030881&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19930712%26dopt%3DAbstract CONCLUSIONS: Predicting genomic breeding values using a genomic relationship matrix is an attractive approach to implement genomic selection as expected accuracies of GEBV can be readily derived. However in multi-breed populations, Bayesian approaches give higher accuracies for some traits. Finally, multi-breed reference populations will be a valuable resource to fine map QTL. PMID: 19930712 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3030881 Tue, 24 Nov 2009 00:00:00 +0100 3030881 http://www.medworm.com/index.php?rid=3008683&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19389264%26dopt%3DAbstract Authors: Raadsma HW, Thomson PC, Zenger KR, Cavanagh C, Lam MK, Jonas E, Jones M, Attard G, Palmer D, Nicholas FW 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) and is freely available on request. The new analysis pa... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3008683 Thu, 19 Nov 2009 21:44:03 +0100 3008683 http://www.medworm.com/index.php?rid=3008682&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19919698%26dopt%3DAbstract Authors: Elsen JM, Filangi O, Gilbert H, Le Roy P, Moreno C 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 example given. PMID: 19919698 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3008682 Tue, 17 Nov 2009 00:00:00 +0100 3008682 http://www.medworm.com/index.php?rid=2982167&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19900278%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2982167 Mon, 09 Nov 2009 00:00:00 +0100 2982167 http://www.medworm.com/index.php?rid=2972105&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19891765%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2972105 Thu, 05 Nov 2009 00:00:00 +0100 2972105 http://www.medworm.com/index.php?rid=2951321&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19874616%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2951321 Thu, 29 Oct 2009 00:00:00 +0100 2951321 http://www.medworm.com/index.php?rid=2940478&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19863786%26dopt%3DAbstract 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 mechanisms underlying resistance in adult sheep (hypersensitivity reactions) and lambs (immunity). The most significant QTL identified on chromosome 6 for LFEC1 may be the... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2940478 Wed, 28 Oct 2009 00:00:00 +0100 2940478 http://www.medworm.com/index.php?rid=2923791&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19849860%26dopt%3DAbstract Authors: Raadsma HW, Jonas E, McGill D, Hobbs M, Lam MK, Thomson PC 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 and regression analysis. A total of 15 significant (P < 0.01) and additional 25 suggestive (P < 0.... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2923791 Wed, 21 Oct 2009 23:00:00 +0100 2923791 http://www.medworm.com/index.php?rid=2876919&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19807906%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2876919 Mon, 05 Oct 2009 23:00:00 +0100 2876919 http://www.medworm.com/index.php?rid=2852974&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19788745%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2852974 Mon, 28 Sep 2009 23:00:00 +0100 2852974 http://www.medworm.com/index.php?rid=2846678&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19785735%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2846678 Sun, 27 Sep 2009 23:00:00 +0100 2846678 http://www.medworm.com/index.php?rid=2834729&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19775457%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2834729 Tue, 22 Sep 2009 23:00:00 +0100 2834729 http://www.medworm.com/index.php?rid=2702759&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19674488%26dopt%3DAbstract Authors: Hayes H, Baret P, Boichard D PMID: 19674488 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2702759 Sat, 15 Aug 2009 21:32:04 +0100 2702759 http://www.medworm.com/index.php?rid=2696357&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19671130%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2696357 Mon, 10 Aug 2009 23:00:00 +0100 2696357 http://www.medworm.com/index.php?rid=2684318&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19660133%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2684318 Wed, 05 Aug 2009 23:00:00 +0100 2684318 http://www.medworm.com/index.php?rid=2650373&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19635140%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2650373 Sun, 26 Jul 2009 23:00:00 +0100 2650373 http://www.medworm.com/index.php?rid=2562248&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19566932%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2562248 Mon, 29 Jun 2009 23:00:00 +0100 2562248 http://www.medworm.com/index.php?rid=2543623&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19555501%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2543623 Wed, 24 Jun 2009 23:00:00 +0100 2543623 http://www.medworm.com/index.php?rid=2543625&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19519896%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2543625 Wed, 10 Jun 2009 23:00:00 +0100 2543625 http://www.medworm.com/index.php?rid=2321519&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356255%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2321519 Thu, 09 Apr 2009 04:00:00 +0100 2321519 http://www.medworm.com/index.php?rid=2321520&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19335901%26dopt%3DAbstract Authors: Cheng YS, Rouvier R, Liu HL, Huang SC, Huang YC, Liao CW, Tai JJ, Tai C, Poivey JP 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 number of hatched mule ducklings' traits. The fertility rates for days 2-8 aft... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2321520 Tue, 31 Mar 2009 04:00:00 +0100 2321520 http://www.medworm.com/index.php?rid=2281770&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19296859%26dopt%3DAbstract Authors: Lillehammer M, Odegard J, Meuwissen TH 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)variance matrix permitted the modeling of the additive genetic variance not covered by the sire effect. This made the abi... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2281770 Thu, 19 Mar 2009 04:00:00 +0100 2281770 http://www.medworm.com/index.php?rid=2281769&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19298654%26dopt%3DAbstract Authors: Leroy G, Callede L, Verrier E, Meriaux JC, Ricard A, Danchin-Burge C, Rognon X 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2281769 Thu, 19 Mar 2009 04:00:00 +0100 2281769 http://www.medworm.com/index.php?rid=2281771&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19296851%26dopt%3DAbstract Authors: Solberg TR, Sonesson AK, Woolliams JA, Meuwissen TH 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 overall advantage to PLSR of 0.016 (s.e = 0.008). Both methods gave a lower accuracy compared to the 'BayesB', fo... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2281771 Wed, 18 Mar 2009 04:00:00 +0100 2281771 http://www.medworm.com/index.php?rid=2281772&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19291328%26dopt%3DAbstract Authors: Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang HL, Huang MC 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 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage gr... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2281772 Tue, 17 Mar 2009 04:00:00 +0100 2281772 http://www.medworm.com/index.php?rid=2272456&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284590%26dopt%3DAbstract Authors: Duthie CA, Simm G, Perez-Enciso M, Doeschl-Wilson A, Kalm E, Knap PW, Roehe R 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 throughout growth, and carcass characteristics obtained at slaughter weight (140 kg). Se... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272456 Wed, 11 Mar 2009 04:00:00 +0100 2272456 http://www.medworm.com/index.php?rid=2272458&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284530%26dopt%3DAbstract Authors: Neuner S, Edel C, Emmerling R, Thaller G, Gotz KU 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 values were estimated using a two-step approach. First, pre-corrected phenotypes (daughter yield deviations (DYD... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272458 Wed, 04 Mar 2009 05:00:00 +0100 2272458 http://www.medworm.com/index.php?rid=2272460&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284529%26dopt%3DAbstract Authors: Oikawa T, Yasuda K 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 GIAs to (1-x) and the other elements to 0, where x is a constant close to 0.0. The inverse of the K matrix is then calculated directly by a si... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272460 Tue, 03 Mar 2009 05:00:00 +0100 2272460 http://www.medworm.com/index.php?rid=2272463&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284520%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272463 Fri, 30 Jan 2009 05:00:00 +0100 2272463 http://www.medworm.com/index.php?rid=2272469&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284518%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272469 Wed, 21 Jan 2009 05:00:00 +0100 2272469 http://www.medworm.com/index.php?rid=2272466&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284519%26dopt%3DAbstract Authors: Lachance J 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 to detect significant departures from Hardy-Weinberg? How do selection-induced departures from Hardy-Weinberg vary with allele frequencies and levels ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272466 Wed, 21 Jan 2009 05:00:00 +0100 2272466 http://www.medworm.com/index.php?rid=2272454&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284675%26dopt%3DAbstract Authors: Heuven HC, van Wijk RH, Dibbits B, van Kampen TA, Knol EF, Bovenhuis H 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. These results agreed well with previous QTL-studies involving SSC2. Since our study is carr... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272454 Thu, 01 Jan 2009 05:00:00 +0100 2272454 http://www.medworm.com/index.php?rid=2272452&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284677%26dopt%3DAbstract Authors: Calus MP, Meuwissen TH, Windig JJ, Knol EF, Schrooten C, Vereijken ALj, Veerkamp RF 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 contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272452 Thu, 01 Jan 2009 05:00:00 +0100 2272452 http://www.medworm.com/index.php?rid=2272450&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284678%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272450 Thu, 01 Jan 2009 05:00:00 +0100 2272450 http://www.medworm.com/index.php?rid=2272448&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284681%26dopt%3DAbstract Authors: Meuwissen TH, Solberg TR, Shepherd R, Woolliams JA 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 by analytically performing the required integrations. The accuracy of the genome-wide breeding value estimates ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272448 Thu, 01 Jan 2009 05:00:00 +0100 2272448 http://www.medworm.com/index.php?rid=2272446&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284683%26dopt%3DAbstract Authors: Sandercock DA, Barker ZE, Mitchell MA, Hocking PM 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 matter compared with layer and traditional lines. In comparison with layer and traditional lines, broiler genotype... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272446 Thu, 01 Jan 2009 05:00:00 +0100 2272446 http://www.medworm.com/index.php?rid=2272444&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284684%26dopt%3DAbstract Authors: Hayes H, Baret P, Boichard D PMID: 19284684 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272444 Thu, 01 Jan 2009 05:00:00 +0100 2272444 http://www.medworm.com/index.php?rid=2272442&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284685%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272442 Thu, 01 Jan 2009 05:00:00 +0100 2272442 http://www.medworm.com/index.php?rid=2272440&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284686%26dopt%3DAbstract Authors: Oliehoek PA, Bijma P 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 show that a low percentage of wrong parent information reduces the effect of optimal contributions. When the percentage of wrong parent inform... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272440 Thu, 01 Jan 2009 05:00:00 +0100 2272440 http://www.medworm.com/index.php?rid=2272438&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284688%26dopt%3DAbstract 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 lactation was investigated. Ancestral inbreeding accounting for all common ancestors in the pedigree had a positive effect on 305-day milk and protein yield, increasing yi... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272438 Thu, 01 Jan 2009 05:00:00 +0100 2272438 http://www.medworm.com/index.php?rid=2272436&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284689%26dopt%3DAbstract Authors: Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X 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 conclude that particular efforts should be made to conserve five local breeds... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272436 Thu, 01 Jan 2009 05:00:00 +0100 2272436 http://www.medworm.com/index.php?rid=2272433&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284690%26dopt%3DAbstract Authors: Colleau JJ, Tual K, de Preaumont H, Regaldo D : 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 expressed on a scale ranging from 0 to 1. A value of 0 represented the average performance of random matings and a val... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272433 Thu, 01 Jan 2009 05:00:00 +0100 2272433 http://www.medworm.com/index.php?rid=2272430&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284692%26dopt%3DAbstract Authors: Snoj A, Marić S, Berrebi P, Crivelli AJ, Shumka S, Susnik S 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 study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean - ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272430 Thu, 01 Jan 2009 05:00:00 +0100 2272430 http://www.medworm.com/index.php?rid=2272427&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284693%26dopt%3DAbstract Authors: González-Recio O, Gianola D, Rosa GJ, Weigel KA, Kranis A 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) using alternative measures of the information gain provided by the SNPs. All analyses were performed ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272427 Thu, 01 Jan 2009 05:00:00 +0100 2272427 http://www.medworm.com/index.php?rid=2272424&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284695%26dopt%3DAbstract Authors: Nieuwhof GJ, Conington J, Bishop SC 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. The equilibrium prevalence was estimated as a function of these rates. The likely response to selection for increased resistan... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272424 Thu, 01 Jan 2009 05:00:00 +0100 2272424 http://www.medworm.com/index.php?rid=2272422&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284696%26dopt%3DAbstract Authors: Bennewitz J, Solberg T, Meuwissen T 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 markers (i.e. the predictors) separately. The nonparametric functions for the predictors were estimated simultaneously using ad... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272422 Thu, 01 Jan 2009 05:00:00 +0100 2272422 http://www.medworm.com/index.php?rid=2272420&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284698%26dopt%3DAbstract 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 minus the estimated breeding value or on the covariance between the true and estimated breeding values. PMID: 19284698 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272420 Thu, 01 Jan 2009 05:00:00 +0100 2272420 http://www.medworm.com/index.php?rid=2272416&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284701%26dopt%3DAbstract Authors: Sánchez JP, Rekaya R, Misztal I 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 designs similar to previous studies on genetics of heat stress. Posterior means of parameters of interest, under all simula... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272416 Thu, 01 Jan 2009 05:00:00 +0100 2272416 http://www.medworm.com/index.php?rid=2272413&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284703%26dopt%3DAbstract 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) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272413 Thu, 01 Jan 2009 05:00:00 +0100 2272413 http://www.medworm.com/index.php?rid=2272410&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284706%26dopt%3DAbstract Authors: Nilsen H, Olsen HG, Hayes B, Sehested E, Svendsen M, Nome T, Meuwissen T, Lien S 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 results point towards CSN2 and CSN1S2 as the most likely loci harbouring the underl... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272410 Thu, 01 Jan 2009 05:00:00 +0100 2272410 http://www.medworm.com/index.php?rid=2272406&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284707%26dopt%3DAbstract 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 metric. A naïve Bayes classifier, coupled with discretization into two or three categories generated the SNP subset with greatest predictive ability. Further, an al... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272406 Thu, 01 Jan 2009 05:00:00 +0100 2272406 http://www.medworm.com/index.php?rid=2272403&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19284708%26dopt%3DAbstract This study compares laying performances between two environments of dwarf laying hen lines segregating for the naked neck mutation (NA locus), a selected dwarf line of brown-egg layers and its control line. Layers with one of the three genotypes at the NA locus were produced from 11 sires from the control line and 12 sires from the selected line. Two hatches produced 216 adult hens in Taiwan and 297 hens in France. Genetic parameters for laying traits were estimated in each environment and the ranking of sire breeding values was compared between environments. Laying performance was lower, and mortality was higher in Taiwan than in France. The line by environment interaction was highly significant for body weight at 16 weeks, clutch length and egg number, with or without Box-Cox transformat... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=2272403 Thu, 01 Jan 2009 05:00:00 +0100 2272403 http://www.medworm.com/index.php?rid=1944614&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990353%26dopt%3DAbstract Authors: Martinez V Complex traits may show some degree of dominance at the gene level that may influence the statistical power of simple models, i.e. assuming only additive effects to detect quantitative trait loci (QTL) using the variance component method. Little has been published on this topic even in species where relatively large family sizes can be obtained, such as poultry, pigs, and aquacultural species. This is important, when the idea is to select regions likely to be harbouring dominant QTL or in marker assisted selection. In this work, we investigated the empirical power and accuracy to both detect and localise dominant QTL with or without incorporating dominance effects explicitly in the model of analysis. For this purpose, populations with variable family sizes and const... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944614 Sat, 01 Nov 2008 04:00:00 +0100 1944614 http://www.medworm.com/index.php?rid=1944613&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990354%26dopt%3DAbstract Authors: Grima L, Quillet E, Boujard T, Robert-Granié C, Chatain B, Mambrini M Little is known about the genetic basis of residual feed intake (RFI) variation in fish, since this trait is highly sensitive to environmental influences, and feed intake of individuals is difficult to measure accurately. The purpose of this work was (i) to assess the genetic variability of RFI estimated by an X-ray technique and (ii) to develop predictive criteria for RFI. Two predictive criteria were tested: loss of body weight during feed deprivation and compensatory growth during re-feeding. Ten heterozygous rainbow trout clones were used. Individual intake and body weight were measured three times at threeweek intervals. Then, individual body weight was recorded after two cycles of a three-week fee... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944613 Sat, 01 Nov 2008 04:00:00 +0100 1944613 http://www.medworm.com/index.php?rid=1944612&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990355%26dopt%3DAbstract Authors: Ren ZQ, Wang Y, Xu YJ, Wang LJ, Lei MG, Zuo B, Li FE, Xu DQ, Zheng R, Deng CY, Jiang SW, Xiong YZ ATP-citrate lyase (ACL), one of the lipogenic enzymes, catalyses the formation of acetyl-coenzyme A (CoA) involved in the synthesis of fatty acid and cholesterol. In pig, very little is known about the ACL gene. In this work, the mRNA differential display technique was used to analyse the differences in gene expression between Meishan and Large White pigs and the F1 hybrids of both direct and reciprocal crosses. Our results show that among the differentially expressed genes ACL is up-regulated in the backfat of the F1 hybrids. After cloning and analysing the fulllength cDNA and the 870 bp 50-flanking sequence of the porcine ACL gene, a C/T mutation at position -97 bp upstream of t... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944612 Sat, 01 Nov 2008 04:00:00 +0100 1944612 http://www.medworm.com/index.php?rid=1944611&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990356%26dopt%3DAbstract Authors: Loywyck V, Bed'hom B, Pinard-van der Laan MH, Pitel F, Verrier E, Bijma P We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed F(st) values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944611 Sat, 01 Nov 2008 04:00:00 +0100 1944611 http://www.medworm.com/index.php?rid=1944610&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990357%26dopt%3DAbstract Authors: Palhiere I, Brochard M, Moazami-Goudarzi K, Laloeë D, Amigues Y, Bed'hom B, Neuts E, Leymarie C, Pantano T, Cribiu EP, Bibé B, Verrier E Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3-4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers). The expected loss of genetic ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944610 Sat, 01 Nov 2008 04:00:00 +0100 1944610 http://www.medworm.com/index.php?rid=1944609&cid=s_33034_50_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18990358%26dopt%3DAbstract Authors: Sun W, Chen H, Lei C, Lei X, Zhang Y Genetic variability and genetic relationships were investigated among eight Chinese cattle breeds using 12 microsatellite markers. Three hundred and fifty-two alleles were detected and the average number of alleles per locus ranged from 8.33+/-1.67 in the Jiaxian breed to 21.33+/-5.60 in the Qinchuan breed with a mean value of 13.91. The total number of alleles per microsatellite ranged from 21 (INRA005, HEL1) to 40 (HEL13), with a mean of 29.33 per locus. The fixation indices at the 12 loci in the eight breeds were very low with a mean of 0.006. A principal components analysis and the construction of a neighborjoining tree showed that these eight Chinese cattle breeds cluster into three groups i.e. the Yanbian andChineseHolstein, theNanyan... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1944609 Sat, 01 Nov 2008 04:00:00 +0100 1944609 http://www.medworm.com/index.php?rid=1703916&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694545%26dopt%3DAbstract Authors: Ndumu DB, Baumung R, Hanotte O, Wurzinger M, Okeyo MA, Jianlin H, Kibogo H, Sölkner J The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall FST index ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703916 Thu, 14 Aug 2008 10:31:23 +0100 1703916 http://www.medworm.com/index.php?rid=1703915&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694546%26dopt%3DAbstract Authors: Detilleux JC A mixed hidden Markov model (HMM) was developed for predicting breeding values of a biomarker (here, somatic cell score) and the individual probabilities of health and disease (here, mastitis) based upon the measurements of the biomarker. At a first level, the unobserved disease process (Markov model) was introduced and at a second level, the measurement process was modeled, making the link between the unobserved disease states and the observed biomarker values. This hierarchical formulation allows joint estimation of the parameters of both processes. The flexibility of this approach is illustrated on the simulated data. Firstly, lactation curves for the biomarker were generated based upon published parameters (mean, variance, and probabilities of infection) for c... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703915 Thu, 14 Aug 2008 10:31:18 +0100 1703915 http://www.medworm.com/index.php?rid=1703914&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694547%26dopt%3DAbstract Authors: Carolino N, Gama LT Records from up to 19 054 registered cows and 10 297 calves in 155 herds of the Alentejana cattle breed were used to study the effects of individual (F(i)) and maternal (F(m)) inbreeding on reproductive, growth and carcass traits, as well as assessing the importance of non-linear associations between inbreeding and performance, and evaluating the differences among sire-families in the effect of F(i) and F(m) on calf weight at 7 months of age (W7M). Overall, regression coefficients of performance traits on inbreeding were small, indicating a minor but still detrimental effect of both F(i) and F(m) on most traits. The traits with the highest percentage impact of F(i) were total number of calvings through life and calf weight at 3 months of age (W3M), followed... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703914 Thu, 14 Aug 2008 10:31:13 +0100 1703914 http://www.medworm.com/index.php?rid=1703913&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694548%26dopt%3DAbstract This study confirmed the QTL for age at puberty previously identified on SSC1, 7 and 8, and reports for the first time a QTL for age at puberty in gilts on SSC17. Interestingly, the Chinese Erhualian alleles were not systematically favourable for younger age at puberty. PMID: 18694548 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703913 Thu, 14 Aug 2008 10:31:06 +0100 1703913 http://www.medworm.com/index.php?rid=1703912&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694549%26dopt%3DAbstract Authors: Ibarra AM, Famula R Shrimp is one of few marine species cultured worldwide for which several selective breeding programs are being conducted. One environmental factor that can affect the response to selection in breeding programs is the density at which the shrimp are cultured (low-medium-high). Phenotypic plasticity in the growth response to different densities might be accompanied by a significant genotype by environment interaction, evidenced by a change in heritabilities between environments and by a genetic correlation less than one for a unique trait between environments. Our goal was to understand whether different growth densities affect estimates of those genetic parameters for adult body weight (BW) in the Pacific white shrimp (Penaeus vannamei). BW heritabilities we... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703912 Thu, 14 Aug 2008 10:31:02 +0100 1703912 http://www.medworm.com/index.php?rid=1703911&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694550%26dopt%3DAbstract Authors: White S, Herrmann-Hoesing L, O'rourke K, Waldron D, Rowe J, Alverson J Scrapie eradication efforts cost 18 million dollars annually in the United States and rely heavily upon PRNP genotyping of sheep. Genetic resistance might reduce goat scrapie and limit the risk of goats serving as a scrapie reservoir, so PRNP coding sequences were examined from 446 goats of 10 breeds, 8 of which had not been previously examined at PRNP. The 10 observed alleles were all related to one of two central haplotypes by a single amino acid substitution. At least five of these alleles (M142, R143, S146, H154, and K222) have been associated with increased incubation time or decreased odds of scrapie. To the best of our knowledge, neither S146 nor K222 has been found in any goats with scrapie, though ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703911 Thu, 14 Aug 2008 10:30:58 +0100 1703911 http://www.medworm.com/index.php?rid=1703910&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18694551%26dopt%3DAbstract In this study, a full-length cDNA of the porcine ENO3 gene encoding a 434 amino acid protein was isolated. It contains 12 exons over approximately 5.4 kb. Differential splicing in the 50-untranslated sequence generates two forms of mRNA that differ from each other in the presence or absence of a 142-nucleotide fragment. Expression analysis showed that transcript 1 of ENO3 is highly expressed in liver and lung, while transcript 2 is highly expressed in skeletal muscle and heart. We provide the first evidence that in skeletal muscle expression of ENO3 is different between Yorkshire and Meishan pig breeds. Furthermore, real-time polymerase chain reaction revealed that, in Yorkshire pigs, skeletal muscle expression of transcript 1 is identical at postnatal day-1 and at other stages while that ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1703910 Thu, 14 Aug 2008 10:30:53 +0100 1703910 http://www.medworm.com/index.php?rid=1529836&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558070%26dopt%3DAbstract Authors: Wu XL, Heringstad B, Gianola D A Gaussian-threshold model is described under the general framework of structural equation models for inferring simultaneous and recursive relationships between binary and Gaussian characters, and estimating genetic parameters. Relationships between clinical mastitis (CM) and test-day milk yield (MY) in first-lactation Norwegian Red cows were examined using a recursive Gaussian-threshold model. For comparison, the data were also analyzed using a standard Gaussian-threshold, a multivariate linear model, and a recursive multivariate linear model. The first 180 days of lactation were arbitrarily divided into three periods of equal length, in order to investigate how these relationships evolve in the course of lactation. The recursive model showed ne... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529836 Thu, 19 Jun 2008 21:14:04 +0100 1529836 http://www.medworm.com/index.php?rid=1529835&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558071%26dopt%3DAbstract We present here a simple approach to obtain reliable estimates of the effective population size in real world populations via the computation of the increase in inbreeding for each individual (delta F(i)) in a given population. The values of delta F(i) are computed as t-root of 1 - (1 - F(i)) where F(i) is the inbreeding coefficient and t is the equivalent complete generations for each individual. The values of delta F computed for a pre-defined reference subset can be averaged and used to estimate effective size. A standard error of this estimate of N(e) can be further computed from the standard deviation of the individual increase in inbreeding. The methodology is demonstrated by applying it to several simulated examples and to a real pedigree in which other methodologies fail when consi... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529835 Thu, 19 Jun 2008 21:13:59 +0100 1529835 http://www.medworm.com/index.php?rid=1529834&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558072%26dopt%3DAbstract Authors: Naya H, Urioste JI, Chang YM, Rodrigues-Motta M, Kremer R, Gianola D Dark spots in the fleece area are often associated with dark fibres in wool, which limits its competitiveness with other textile fibres. Field data from a sheep experiment in Uruguay revealed an excess number of zeros for dark spots. We compared the performance of four Poisson and zero-inflated Poisson (ZIP) models under four simulation scenarios. All models performed reasonably well under the same scenario for which the data were simulated. The deviance information criterion favoured a Poisson model with residual, while the ZIP model with a residual gave estimates closer to their true values under all simulation scenarios. Both Poisson and ZIP models with an error term at the regression level performed bette... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529834 Thu, 19 Jun 2008 21:13:46 +0100 1529834 http://www.medworm.com/index.php?rid=1529833&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558073%26dopt%3DAbstract Authors: Casellas J, Ibáñez-Escriche N, García-Cortés LA, Varona L The implementation of Student t mixed models in animal breeding has been suggested as a useful statistical tool to effectively mute the impact of preferential treatment or other sources of outliers in field data. Nevertheless, these additional sources of variation are undeclared and we do not know whether a Student t mixed model is required or if a standard, and less parameterized, Gaussian mixed model would be sufficient to serve the intended purpose. Within this context, our aim was to develop the Bayes factor between two nested models that only differed in a bounded variable in order to easily compare a Student t and a Gaussian mixed model. It is important to highlight that the Student t density c... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529833 Thu, 19 Jun 2008 21:13:40 +0100 1529833 http://www.medworm.com/index.php?rid=1529832&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558074%26dopt%3DAbstract Authors: Colleau JJ, Avon L The development of inbreeding in rotation breeding schemes, sequentially using artificial insemination (AI) sires over generations, was investigated for a full AI scheme. Asymptotic prediction formulae of inbreeding coefficients were established when the first rotation list of AI sires (possibly related) was in use. Simulated annealing provided the optimal rotation order of sires within this list, when the sires were related. These methods were also used for subsequent rotation lists, needed by the exhaustion of semen stores for the first bulls. Simulation was carried out starting with groups of independent sires, with different sizes. To generate a yearly inbreeding rate substantially lower than 0.05% (considered to be within reach by conventional conservat... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529832 Thu, 19 Jun 2008 21:13:25 +0100 1529832 http://www.medworm.com/index.php?rid=1529831&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558075%26dopt%3DAbstract Authors: Gizaw S, Komen H, Windig JJ, Hanotte O, van Arendonk JA Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers) and current merits (economic, ecological and cultural merits). Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merit... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529831 Thu, 19 Jun 2008 21:13:20 +0100 1529831 http://www.medworm.com/index.php?rid=1529830&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18558076%26dopt%3DAbstract Authors: Shang X, Cheng H, Zhou R S100 proteins are calcium-binding proteins, which exist only in vertebrates and which constitute a large protein family. The origin and evolution of the S100 family in vertebrate lineages remain a challenge. Here, we examined the synteny conservation of mammalian S100A genes by analysing the sequence of available vertebrate S100 genes in databases. Five S100A gene members, unknown previously, were identified by chromosome mapping analysis. Mammalian S100A genes are duplicated and clustered on a single chromosome while two S100A gene clusters are found on separate chromosomes in teleost fish, suggesting that S100A genes existed in fish before the fish-specific genome duplication took place. During speciation, tandem gene duplication events within the cl... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1529830 Thu, 19 Jun 2008 21:12:43 +0100 1529830 http://www.medworm.com/index.php?rid=1365880&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400148%26dopt%3DAbstract Authors: Doeschl-Wilson AB, Vagenas D, Kyriazakis I, Bishop SC The wide range of genetic parameter estimates for production traits and nematode resistance in sheep obtained from field studies gives rise to much speculation. Using a mathematical model describing host - parasite interactions in a genetically heterogeneous lamb population, we investigated the consequence of: (i) genetic relationships between underlying growth and immunological traits on estimated genetic parameters for performance and nematode resistance, and (ii) alterations in resource allocation on these parameter estimates. Altering genetic correlations between underlying growth and immunological traits had large impacts on estimated genetic parameters for production and resistance traits. Extreme parameter values obs... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365880 Fri, 11 Apr 2008 19:14:42 +0100 1365880 http://www.medworm.com/index.php?rid=1365879&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400149%26dopt%3DAbstract We present an approach using a mixed linear model nested in an empirical Bayesian approach, which simultaneously takes into account additive, dominance and epistatic effects due to multiple QTL. The covariance structure used in the mixed linear model is based on combined linkage disequilibrium and linkage information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously map interacting QTL into a small region using the proposed approach. The estimated variance components are accurate and less biased with the proposed approach compared with traditional models. PMID: 18400149 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365879 Fri, 11 Apr 2008 19:14:39 +0100 1365879 http://www.medworm.com/index.php?rid=1365878&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400150%26dopt%3DAbstract Authors: Ibáñez-Escriche N, Moreno A, Nieto B, Piqueras P, Salgado C, Gutiérrez JP Data from an experimental mice population selected from 18 generations to increase weight gain were used to estimate the genetic parameters associated with environmental variability. The analysis involved three traits: weight at 21 days, weight at 42 days and weight gain between 21 and 42 days. A dataset of 5273 records for males was studied. Data were analysed using Bayesian procedures by comparing the Deviance Information Criterion (DIC) value of two different models: one assuming homogeneous environmental variances and another assuming them as heterogeneous. The model assuming heterogeneity was better in all cases and also showed higher additive genetic variances and lower common enviro... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365878 Fri, 11 Apr 2008 19:14:37 +0100 1365878 http://www.medworm.com/index.php?rid=1365877&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400151%26dopt%3DAbstract Authors: Tarres J, Liu Z, Ducrocq V, Reinhardt F, Reents R Since many countries use multiple lactation random regression test day models in national evaluations for milk production traits, a random regression multiple across-country evaluation (MACE) model permitting a variable number of correlated traits per country should be used in international dairy evaluations. In order to reduce the number of within country traits for international comparison, three different MACE models were implemented based on German daughter yield deviation data and compared to the random regression MACE. The multiple lactation MACE model analysed daughter yield deviations on a lactation basis reducing the rank from nine random regression coefficients to three lactations. The lactation breeding values were v... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365877 Fri, 11 Apr 2008 19:14:34 +0100 1365877 http://www.medworm.com/index.php?rid=1365876&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400152%26dopt%3DAbstract Authors: Pritchard T, Cahalan C, Ap Dewi I Cytoplasmic effects were investigated using a dataset comprising three breeding groups of Welsh Mountain sheep. The influences of cytoplasmic effects were investigated by comparing animal models with and without a random term representing cytoplasmic effects. The models were applied to the eight-week weight, scan weight (mean 152 days) and ultrasonically scanned muscle and fat depth. The animal model included the random effects of animals and the maternal additive genetic, maternal permanent environmental and maternal common environmental effects. In total there were 24 569, 10 509, 8389, 8369 records for the eight-week weight, scan weight, muscle depth and fat depth respectively. Four subsets were further analysed containing maternal lines wi... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365876 Fri, 11 Apr 2008 19:14:31 +0100 1365876 http://www.medworm.com/index.php?rid=1365875&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18400153%26dopt%3DAbstract Authors: Cinkulov M, Tapio M, Ozerov M, Kiselyova T, Marzanov N, Pihler I, Olsaker I, Vegara M, Kantanen J Two Tsigai sheep populations exist in Serbia: the Old type, called Cokan, and the New type. It is assumed that the New type results from upgrading Tsigai sheep with exotic genetic material. We investigated genetic diversity and differentiation of these types by analysing 23 autosomal microsatellites. Tests for Hardy-Weinberg proportions, linkage equilibrium between genotypes across loci and the calculation of inbreeding coefficients were performed and the deficiency in the number of alleles within the Tsigai types was examined using a Wilcoxon sign-rank test. The New type displayed a higher level of genetic variability than the Cokan in terms of allele numbers, but the New Tsigai ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1365875 Fri, 11 Apr 2008 19:14:28 +0100 1365875 http://www.medworm.com/index.php?rid=1260785&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298932%26dopt%3DAbstract Authors: Fouilloux MN, Clément V, Laloë D A procedure to measure connectedness among groups in large-sized genetic evaluations is presented. It consists of two steps: (a) computing coefficients of determination (CD) of comparisons among groups of animals; and (b) building sets of connected groups. The CD of comparisons were estimated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample. A clustering method that may handle a large number of comparisons and build compact clusters of connected groups was developed. An aggregation criterion (Caco) that reflects the level of connectedness of each herd was computed. This procedure was validated using a small beef data set. It was applied to the French genet... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260785 Wed, 27 Feb 2008 20:17:07 +0100 1260785 http://www.medworm.com/index.php?rid=1260784&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298933%26dopt%3DAbstract Authors: Waagepetersen R, Ibánez-Escriche N, Sorensen D In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications in quantitative genetics is to obtain efficient updates of the high-dimensional vectors of genetic random effects and the associated covariance parameters. We discuss various strategies to approach this problem including reparameterization, Langevin-Hastings updates, and updates based on normal approximations. The methods are compared in applications to Bayesian inference for three data sets using a model with genetically structured... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260784 Wed, 27 Feb 2008 20:17:05 +0100 1260784 http://www.medworm.com/index.php?rid=1260783&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298934%26dopt%3DAbstract Authors: Lund MS, Sorensen P, Madsen P, Jaffrézic F A longitudinal approach is proposed to map QTL affecting function-valued traits and to estimate their effect over time. The method is based on fitting mixed random regression models. The QTL allelic effects are modelled with random coefficient parametric curves and using a gametic relationship matrix. A simulation study was conducted in order to assess the ability of the approach to fit different patterns of QTL over time. It was found that this longitudinal approach was able to adequately fit the simulated variance functions and considerably improved the power of detection of time-varying QTL effects compared to the traditional univariate model. This was confirmed by an analysis of protein yield data in dairy cattle, where the m... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260783 Wed, 27 Feb 2008 20:17:02 +0100 1260783 http://www.medworm.com/index.php?rid=1260782&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298935%26dopt%3DAbstract Authors: Schulman NF, Sahana G, Lund MS, Viitala SM, Vilkki JH A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. S... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260782 Wed, 27 Feb 2008 20:17:00 +0100 1260782 http://www.medworm.com/index.php?rid=1260781&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298936%26dopt%3DAbstract Authors: Tao X, Jihong Y, Li G, Bin F, Yi Z, Xiaodong C, Peichao Z, Yang Z The PAT proteins, named after the three PLIN/ADRP/TIP47 (PAT) proteins, PLIN for perilipin, ADRP for adipose differentiation-related protein and TIP47 for tail-interacting protein of 47 kDa, now officially named M6PRBP1 for mannose-6-phosphate receptor binding protein 1, is a set of intracellular lipid droplet binding proteins. They are localized in the outer membrane monolayer enveloping lipid droplets and are involved in the metabolism of intracellular lipid. This work describes the cloning and sequencing of porcine PLIN and M6PRBP1 cDNAs, the chromosome mapping of these two genes, as well as the expression pattern of porcine PAT genes. Sequence analysis shows that the porcine PLIN cDNA contains an open readin... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260781 Wed, 27 Feb 2008 20:16:57 +0100 1260781 http://www.medworm.com/index.php?rid=1260780&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18298937%26dopt%3DAbstract Authors: Wu J, Zhou D, Deng C, Xiong Y, Lei M, Li F, Jiang S, Zuo B, Zheng R Carbonic anhydrase III (CA3) is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibres. In order to further understand the functions of the porcine CA3 protein in muscle, the temporal and spatial distributions of its gene product were analysed and the association between the presence of specific polymorphisms and carcass traits in the pig was also examined. Real-time PCR revealed that the CA3 mRNA expression showed no differences with age in skeletal muscles from Yorkshire pigs at postnatal day-1, month-2, and month-4. We provide the first evidence that CA3 is differentially expressed in the skeletal muscle of Yorkshire and Meishan pig breeds. In addition, the whole pig genomic D... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1260780 Wed, 27 Feb 2008 20:16:53 +0100 1260780 http://www.medworm.com/index.php?rid=1113008&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096112%26dopt%3DAbstract Authors: Meyer K Parameter expanded and standard expectation maximisation algorithms are described for reduced rank estimation of covariance matrices by restricted maximum likelihood, fitting the leading principal components only. Convergence behaviour of these algorithms is examined for several examples and contrasted to that of the average information algorithm, and implications for practical analyses are discussed. It is shown that expectation maximisation type algorithms are readily adapted to reduced rank estimation and converge reliably. However, as is well known for the full rank case, the convergence is linear and thus slow. Hence, these algorithms are most useful in combination with the quadratically convergent average information algorithm, in particular in the initial stages... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113008 Sun, 23 Dec 2007 00:53:45 +0100 1113008 http://www.medworm.com/index.php?rid=1113007&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096113%26dopt%3DAbstract Authors: Gao G, Hoeschele I Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of th... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113007 Sun, 23 Dec 2007 00:53:43 +0100 1113007 http://www.medworm.com/index.php?rid=1113006&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096114%26dopt%3DAbstract The objective was to investigate the effects of genetic parameters, breeding goal, number of progeny per sire and breeding scheme on selection responses in mean and variance when applying index selection. Genetic parameters were obtained from the literature. Economic values for the mean and variance were derived for some standard non-linear profit equations, e.g. for traits with an intermediate optimum. The economic value of variance was in most situations negative, indicating that selection for reduced variance increases profit. Predicted responses in residual variance after one generation of selection were large, in some cases when the number of progeny per sire was at least 50, by more than 10% of the current residual variance. Progeny testing schemes were more efficient than sib-testin... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113006 Sun, 23 Dec 2007 00:53:40 +0100 1113006 http://www.medworm.com/index.php?rid=1113005&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096115%26dopt%3DAbstract Authors: Tribout T, Iannuccelli N, Druet T, Gilbert H, Riquet J, Gueblez R, Mercat MJ, Bidanel JP, Milan D, Le Roy P A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat t... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113005 Sun, 23 Dec 2007 00:53:37 +0100 1113005 http://www.medworm.com/index.php?rid=1113004&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096116%26dopt%3DAbstract In this study we introduce a method that accounts for false positive and false negative results in attempting to estimate the true proportion of quantitative trait loci that affect two different traits. This method was applied to data from a genome scan that was used to detect QTL for three independent milk production traits, Australian Selection Index (ASI), protein percentage (P%) and fat percentage corrected for protein percentage (F% - P%). These four different scenarios are attributed to four biological pathways: QTL that (1) increase or decrease total mammary gland production (affecting ASI only); (2) increase or decrease lactose synthesis resulting in the volume of milk being changed but without a change in protein or fat yield (affecting P% only); (3) increase or decrease protein s... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113004 Sun, 23 Dec 2007 00:53:35 +0100 1113004 http://www.medworm.com/index.php?rid=1113003&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096117%26dopt%3DAbstract Authors: Guillaume F, Fritz S, Boichard D, Druet T The efficiency of the French marker-assisted selection (MAS) was estimated by a simulation study. The data files of two different time periods were used: April 2004 and 2006. The simulation method used the structure of the existing French MAS: same pedigree, same marker genotypes and same animals with records.The program simulated breeding values and new records based on this existing structure and knowledge on the QTL used in MAS (variance and frequency). Reliabilities of genetic values of young animals (less than one year old) obtained with and without marker information were compared to assess the efficiency of MAS for evaluation of milk, fat and protein yields and fat and protein contents. Mean gains of reliability ranged from 0.01... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113003 Sun, 23 Dec 2007 00:53:33 +0100 1113003 http://www.medworm.com/index.php?rid=1113002&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096118%26dopt%3DAbstract Authors: Megens HJ, Crooijmans RP, San Cristobal M, Hui X, Li N, Groenen MA Microsatellite diversity in European and Chinese pigs was assessed using a pooled sampling method on 52 European and 46 Chinese pig populations. A Neighbor Joining analysis on genetic distances revealed that European breeds were grouped together and showed little evidence for geographic structure, although a southern European and English group could tentatively be assigned. Populations from international breeds formed breed specific clusters. The Chinese breeds formed a second major group, with the Sino-European synthetic Tia Meslan in-between the two large clusters. Within Chinese breeds, in contrast to the European pigs, a large degree of geographic structure was noted, in line with previous classification sc... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113002 Sun, 23 Dec 2007 00:53:30 +0100 1113002 http://www.medworm.com/index.php?rid=1113001&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18096119%26dopt%3DAbstract Authors: Robic A, Larzul C, Bonneau M High levels of androstenone and skatole in fat tissues are considered the primary causes of boar taint, an unpleasant odour and flavour of the meat from non-castrated male pigs. The aim of this article is to review our current knowledge of the biology and genetic control of the accumulation of androstenone and skatole in fat tissue. Two QTL mapping studies have shown the complexity of the genetic control of these traits. During the last ten years, several authors have taken a more physiological approach to investigate the involvement of genes controlling the metabolism of androstenone and skatole. Although some authors have claimed the identification of candidate genes, it is more appropriate to talk about target genes. This suggests that genes aff... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1113001 Sun, 23 Dec 2007 00:53:28 +0100 1113001 http://www.medworm.com/index.php?rid=1078355&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053572%26dopt%3DAbstract Authors: de Koning DJ, Jaffrézic F, Lund MS, Watson M, Channing C, Hulsegge I, Pool MH, Buitenhuis B, Hedegaard J, Hornshøj H, Jiang L, Sørensen P, Marot G, Delmas C, Lê Cao KA, San Cristobal M, Baron MD, Malinverni R, Stella A, Brunner RM, Seyfert HM, Jensen K, Mouzaki D, Waddington D, Jiménez-Marín A, Pérez-Alegre M, Pérez-Reinado E, Closset R, Detilleux JC, Dovc P, Lavric M, Nie H, Janss L Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078355 Thu, 01 Nov 2007 04:00:00 +0100 1078355 http://www.medworm.com/index.php?rid=1078354&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053573%26dopt%3DAbstract Authors: Jaffrézic F, de Koning DJ, Boettcher PJ, Bonnet A, Buitenhuis B, Closset R, Déjean S, Delmas C, Detilleux JC, Dovc P, Duval M, Foulley JL, Hedegaard J, Hornshøj H, Hulsegge I, Janss L, Jensen K, Jiang L, Lavric M, Lê Cao KA, Lund MS, Malinverni R, Marot G, Nie H, Petzl W, Pool MH, Robert-Granié C, San Cristobal M, van Schothorst EM, Schuberth HJ, Sørensen P, Stella A, Tosser-Klopp G, Waddington D, Watson M, Yang W, Zerbe H, Seyfert HM A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078354 Thu, 01 Nov 2007 04:00:00 +0100 1078354 http://www.medworm.com/index.php?rid=1078353&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053574%26dopt%3DAbstract Authors: Sørensen P, Bonnet A, Buitenhuis B, Closset R, Déjean S, Delmas C, Duval M, Glass L, Hedegaard J, Hornshøj H, Hulsegge I, Jaffrézic F, Jensen K, Jiang L, de Koning DJ, Lê Cao KA, Nie H, Petzl W, Pool MH, Robert-Granié C, San Cristobal M, Lund MS, van Schothorst EM, Schuberth HJ, Seyfert HM, Tosser-Klopp G, Waddington D, Watson M, Yang W, Zerbe H The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expres... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078353 Thu, 01 Nov 2007 04:00:00 +0100 1078353 http://www.medworm.com/index.php?rid=1078352&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053575%26dopt%3DAbstract Authors: Watson M, Pérez-Alegre M, Baron MD, Delmas C, Dovc P, Duval M, Foulley JL, Garrido-Pavón JJ, Hulsegge I, Jaffrézic F, Jiménez-Marín A, Lavric M, Lê Cao KA, Marot G, Mouzaki D, Pool MH, Robert-Granié C, San Cristobal M, Tosser-Klopp G, Waddington D, de Koning DJ Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. Wi... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078352 Thu, 01 Nov 2007 04:00:00 +0100 1078352 http://www.medworm.com/index.php?rid=1078351&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053576%26dopt%3DAbstract In this study, two interval mapping methods for analysis of selective DNA pooling data were developed and evaluated. One was based on least squares regression (LS-pool) and the other on approximate maximum likelihood (ML-pool). Both methods simultaneously utilize information from multiple markers and multiple families and can be applied to different family structures (half-sib, F2 cross and backcross). The results from these two interval mapping methods were compared with results from single marker analysis by simulation. The results indicate that both LS-pool and ML-pool provided greater power to detect the QTL than single marker analysis. They also provide separate estimates of QTL location and effect. With large family sizes, both LS-pool and ML-pool provided similar power and estimates... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078351 Thu, 01 Nov 2007 04:00:00 +0100 1078351 http://www.medworm.com/index.php?rid=1078350&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18053577%26dopt%3DAbstract Authors: Man WY, Lewis RM, Boulton K, Villanueva B Selection programmes based on prion protein (PrP) genotypes are being implemented for increasing resistance to scrapie. Commercial meat sheep populations participating in sire-referencing schemes were simulated to investigate the effect of selection on PrP genotypes on ARR and VRQ allele frequencies, inbreeding and genetic gain in a performance trait under selection. PrP selection strategies modelled included selection against the VRQ allele and in favour of the ARR allele. Assuming realistic initial PrP frequencies, selection against the VRQ allele had a minimal impact on performance and inbreeding. However, when selection was also in favour of the ARR allele and the frequency of this allele was relatively low, there was a loss of up ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=1078350 Thu, 01 Nov 2007 04:00:00 +0100 1078350 http://www.medworm.com/index.php?rid=910337&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897592%26dopt%3DAbstract We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (co)variance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model. PMID: 17897592 [PubMed - in proces... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910337 Sat, 01 Sep 2007 04:00:00 +0100 910337 http://www.medworm.com/index.php?rid=910336&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897593%26dopt%3DAbstract This study investigated a marker-assisted introgression programme in Australian Merino sheep. The goal was to introgress an allele with a large negative effect on fibre diameter into a Merino flock possessing medium average fibre diameter. The influence of two factors was explored: the strategy used to select animals from the purebred and backcross line for backcrossing purposes and the use of selection on background markers to accelerate the return to the purebred line's genome. The results were compared to introgression based on EBVs only. Introgression using EBVs only produced almost the same response in the dollar index as marker-based introgression methods. However, this study did not account for some of the costs associated with implementing the programmes, including the costs of phe... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910336 Sat, 01 Sep 2007 04:00:00 +0100 910336 http://www.medworm.com/index.php?rid=910335&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897594%26dopt%3DAbstract Authors: N'dri AL, Sellier N, Tixier-Boichard M, Beaumont C, Mignon-Grasteau S Since feed conversion ratio (FCR) is higher in slow-growing "Label Rouge" chickens than in broiler chickens, it is important to work on its improvement in this breed. However, this involves rearing animals in cages (C), an environment very different from that used for selection (in floor pens, S) and production (outdoor, E). The aim of this study was to evaluate the importance of genotype by environment (G x E) interactions between S, C, and E environments, to find the best way to select for FCR, using 2002 related animals. Growth curve parameters were estimated and body composition measured. Individual feed conversion ratios (FCR) were recorded between 8 and 10 weeks in C. The presence of G x E interactions... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910335 Sat, 01 Sep 2007 04:00:00 +0100 910335 http://www.medworm.com/index.php?rid=910334&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897595%26dopt%3DAbstract Authors: Kause A, Ritola O, Paananen T Genetic analysis of disorder incidence in farmed animals is challenged by two factors. Disorders in different cohorts and environments could be caused by different factors, leading to changes in heritability and to less than unity genetic correlations across cohorts. Moreover, due to computational limitations, liability scale heritabilities at very low incidence may differ from those estimated at higher incidence. We tested whether these two dilemmas occur in skeletal deformations of farmed salmonids using multigeneration data from the Finnish rainbow trout breeding programme and previous salmonid studies. The results showed that heritability was close to zero in cohorts in which management practices maintained incidence at a low level. When there... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910334 Sat, 01 Sep 2007 04:00:00 +0100 910334 http://www.medworm.com/index.php?rid=910333&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897596%26dopt%3DAbstract In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality". PMID: 17897596 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910333 Sat, 01 Sep 2007 04:00:00 +0100 910333 http://www.medworm.com/index.php?rid=910332&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897597%26dopt%3DAbstract Authors: Rao Y, Shen X, Xia M, Luo C, Nie Q, Zhang D, Zhang X An F2 chicken population was established from a crossbreeding between a Xinghua line and a White Recessive Rock line. A total of 502 F2 chickens in 17 full-sib families from six hatches was obtained, and phenotypic data of 488 individuals were available for analysis. A total of 46 SNP on GGA1 was initially selected based on the average physical distance using the dbSNP database of NCBI. After the polymorphism levels in all F0 individuals (26 individuals) and part of the F1 individuals (22 individuals) were verified, 30 informative SNP were potentially available to genotype all F2 individuals. The linkage map was constructed using Cri-Map. Interval mapping QTL analyses were carried out. QTL for body weight (BW) of 35 d and 42... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910332 Sat, 01 Sep 2007 04:00:00 +0100 910332 http://www.medworm.com/index.php?rid=910331&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897598%26dopt%3DAbstract Authors: Ducos A, Berland HM, Bonnet N, Calgaro A, Billoux S, Mary N, Garnier-Bonnet A, Darré R, Pinton A The chromosomal control of pig populations has been widely developed in France over the last ten years. By December 31st, 2006, 13 765 individuals had been karyotyped in our laboratory, 62% of these since 2002. Ninety percent were young purebred boars controlled before service in artificial insemination centres, and 3% were hypoprolific boars. So far, 102 constitutional structural chromosomal rearrangements (67 since 2002) have been described. Fifty-six were reciprocal translocations and 8 peri- or paracentric inversions. For the first time since the beginning of the programme and after more than 11 000 pigs had been karyotyped, one Robertsonian translocation was identified in... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910331 Sat, 01 Sep 2007 04:00:00 +0100 910331 http://www.medworm.com/index.php?rid=910330&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897599%26dopt%3DAbstract In this study, the polymorphism-based approach was used to detect the imprinting status of NNAT and DIRAS3 genes in five heterozygous pigs (based on SNP) of Large White and Meishan F(1) hybrids. The results show that both genes were paternally expressed in all the tested tissues (heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, fat, uterus, ovary and pituitary). In addition, the NNAT gene had two transcripts in all tested tissues, which is consistent with its counterpart in man and cattle. PMID: 17897599 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910330 Sat, 01 Sep 2007 04:00:00 +0100 910330 http://www.medworm.com/index.php?rid=910329&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17897600%26dopt%3DAbstract Authors: Głazewska I, Wysocka A, Gralak B, Sell J Polish Arabian horses are one of the oldest and the most important Arab populations in the world. The Polish Arabian Stud Book and the Genealogical Charts by Skorkowski are the main sources of information on the ancestors of Polish Arabs. Both publications were viewed as credible sources of information until the 1990s when the data regarding one of the dam lines was questioned. The aim of the current study was to check the accuracy of the pedigree data of Polish dam lines using mtDNA analysis. The analyses of a 458 bp mtDNA D-loop fragment from representatives of 15 Polish Arabian dam lines revealed 14 distinct haplotypes. The results were inconsistent with pedigree data in the case of two lines. A detailed analysis of the histori... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=910329 Sat, 01 Sep 2007 04:00:00 +0100 910329 http://www.medworm.com/index.php?rid=719168&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612477%26dopt%3DAbstract In this study, estimation of genetic parameters for breeding value estimation using models corresponding to the ones used for prediction of breeding values increased the accuracy on the breeding values and thereby the genetic progress. PMID: 17612477 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719168 Sun, 01 Jul 2007 04:00:00 +0100 719168 http://www.medworm.com/index.php?rid=719167&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612478%26dopt%3DAbstract Authors: Haile-Mariam M, Bowman PJ, Goddard ME A method that predicts the genetic composition and inbreeding (F) of the future dairy cow population using information on the current cow population, semen use and progeny test bulls is described. This is combined with information on genetic merit of bulls to compare bull selection methods that minimise F and maximise breeding value for profit (called APR in Australia). The genetic composition of the future cow population of Australian Holstein-Friesian (HF) and Jersey up to 6 years into the future was predicted. F in Australian HF and Jersey breeds is likely to increase by about 0.002 and 0.003 per year between 2002 and 2008, respectively. A comparison of bull selection methods showed that a method that selects the best bull from all avai... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719167 Sun, 01 Jul 2007 04:00:00 +0100 719167 http://www.medworm.com/index.php?rid=719166&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612479%26dopt%3DAbstract Authors: González-Recio O, Alenda R Bivariate analyses of functional longevity in dairy cattle measured as survival to next lactation (SURV) with milk yield and fertility traits were carried out. A sequential threshold-linear censored model was implemented for the analyses of SURV. Records on 96 642 lactations from 41 170 cows were used to estimate genetic parameters, using animal models, for longevity, 305 d-standardized milk production (MY305), days open (DO) and number of inseminations to conception (INS) in the Spanish Holstein population; 31% and 30% of lactations were censored for DO and INS, respectively. Heritability estimates for SURV and MY305 were 0.11 and 0.27 respectively; while heritability estimates for fertility traits were lower (0.07 for DO and 0.03 for INS). Antagon... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719166 Sun, 01 Jul 2007 04:00:00 +0100 719166 http://www.medworm.com/index.php?rid=719165&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612480%26dopt%3DAbstract Authors: David I, Druart X, Lagriffoul G, Manfredi E, Robert-Granié C, Bodin L Data from 51 107 and 11 839 ejaculates collected on rams of the "Lacaune" and "Manech tête rousse" breeds, respectively, were analysed to determine environmental and genetic factors affecting semen production traits (ejaculate volume, semen concentration, number of spermatozoa and motility) in young ([Formula: see text][Formula: see text] 1 year) and adult ([Formula: see text][Formula: see text] 2 years) rams. Fixed effects and variance components were estimated using multiple trait animal models within each breed. For all traits, the main environmental effects identified were year, season, number of ejaculations, daily variation, interval from previous to current collection and age. Heritability estimates... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719165 Sun, 01 Jul 2007 04:00:00 +0100 719165 http://www.medworm.com/index.php?rid=719164&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612481%26dopt%3DAbstract In this study, the potential association of PrP genotypes with health and productive traits was investigated. Data were recorded on animals of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. The population consisted of 30 rams and 852 ewes, which produced 1310 lambs. The animals were categorized into three PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR allele. Two analyses differing in the approach considered were carried out. Firstly, the potential association of the PrP genotype with disease (Salmonella resistance) and production (wool and carcass) traits was studied. The data used included 1042, 1043 and 1013 genotyped animals for the Salmonella resistance, wool and carcass traits, respectively. The different traits were ana... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719164 Sun, 01 Jul 2007 04:00:00 +0100 719164 http://www.medworm.com/index.php?rid=719163&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612482%26dopt%3DAbstract Authors: Quinton CD, Kause A, Koskela J, Ritola O The aquaculture industry is increasingly replacing fishmeal in feeds for carnivorous fish with soybean meal (SBM). This diet change presents a potential for genotype-environment (G x E) interactions. We tested whether current salmonid breeding programmes that evaluate and select within fishmeal diets also improve growth and efficiency on potential future SBM diets. A total of 1680 European whitefish from 70 families were reared with either fishmeal- or SBM-based diets in a split-family design. Individual daily gain (DG), daily feed intake (DFI) and feed efficiency (FE) were recorded. Traits displayed only weak G x E interactions as variances and heritabilities did not differ substantially between the diets, and cross-diet genetic correl... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719163 Sun, 01 Jul 2007 04:00:00 +0100 719163 http://www.medworm.com/index.php?rid=719162&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612483%26dopt%3DAbstract Authors: Veit-Kensch CE, Medugorac I, Jedrzejewski W, Bunevich AN, Foerster M Methods based on genetic distance matrices usually lose information during the process of tree-building by converting a multi-dimensional matrix into a phylogenetic tree. We applied a heuristic method of two-dimensional presentation to achieve a better resolution of the relationship between breeds and individuals investigated. Four hundred and nine individuals from nine German dog breed populations and one free-living wolf population were analysed with a marker set of 23 microsatellites. The result of the two-dimensional presentation was partly comparable with and complemented a model-based analysis that uses genotype patterns. The assignment test and the neighbour-joining tree based on allele sharing estimat... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719162 Sun, 01 Jul 2007 04:00:00 +0100 719162 http://www.medworm.com/index.php?rid=719161&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612484%26dopt%3DAbstract Authors: Gandini G, Pizzi F, Stella A, Boettcher PJ The aim of this work was to compare costs, in the horse, cattle, sheep, swine, and rabbit species, for the creation of gene banks for reconstruction of an extinct breed, using different strategies: embryos-only, embryos in combination with semen, and semen-only. Three cost measures were used: time required for population reconstruction, cost for creation of the gene bank, number of years-keeping-female to reach reconstruction. Semen costs were estimated across four scenarios: the presence or absence of a commercial market for semen, purchase of semen donors, and semen extracted from the epididymus. The number of cells were doubled to take into account the creation of two storage sites. The strategy embryos-only required the shortest t... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=719161 Sun, 01 Jul 2007 04:00:00 +0100 719161 http://www.medworm.com/index.php?rid=549007&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433239%26dopt%3DAbstract This study compares alternative strategies to connect small units and assesses the ability of different connectedness statistics to quantify potential bias in BV prediction. Connections established using common sires across units were most effective in reducing bias. The coefficient of determination of the mean difference in predicted BV was a perfect indicator of potential bias remaining when comparing individuals in separate units. However, this measure is difficult to calculate; correlated measures such as prediction errors of differences in unit means and correlations among prediction errors are suggested as practical alternatives. PMID: 17433239 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549007 Tue, 17 Apr 2007 18:50:12 +0100 549007 http://www.medworm.com/index.php?rid=549006&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433240%26dopt%3DAbstract Authors: Chang YM, Gianola D, Heringstad B, Klemetsdal G A Bayesian procedure for analyzing longitudinal binary responses using a periodic cosine function was developed. It was assumed that, after adjustment for "seasonal" effects, the oscillation of the underlying latent variables for longitudinal binary responses was a stationary series. Based on this assumption, a single dimension sinusoidal analysis of longitudinal binary responses using the Gibbs sampling and Metropolis algorithms was implemented in a study of clinical mastitis records of Norwegian Red cows taken over five lactations. PMID: 17433240 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549006 Tue, 17 Apr 2007 18:50:12 +0100 549006 http://www.medworm.com/index.php?rid=549005&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433241%26dopt%3DAbstract This study represents the first attempt at an empirical evaluation of the DNA pooling methodology by comparing it to individual genotyping and interval mapping to detect QTL in a dairy half-sib design. The findings indicated that the use of peak heights from the pool electropherograms without correction for stutter (shadow) product and preferential amplification performed as well as corrected estimates of frequencies. However, errors were found to decrease the power of the experiment at every stage of the pooling and analysis. The main sources of errors include technical errors from DNA quantification, pool construction, inconsistent differential amplification, and from the prevalence of sire alleles in the dams. Additionally, interval mapping using individual genotyping gains information ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549005 Tue, 17 Apr 2007 18:50:12 +0100 549005 http://www.medworm.com/index.php?rid=549004&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433242%26dopt%3DAbstract Authors: Uleberg E, Meuwissen TH Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large (>90 cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL m... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549004 Tue, 17 Apr 2007 18:50:12 +0100 549004 http://www.medworm.com/index.php?rid=549003&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433243%26dopt%3DAbstract Authors: Sonesson AK A within-family marker-assisted selection scheme was designed for typical aquaculture breeding schemes, where most traits are recorded on sibs of the candidates. Here, sibs of candidates were tested for the trait and genotyped to establish genetic marker effects on the trait. BLUP breeding values were calculated, including information of the markers (MAS) or not (NONMAS). These breeding values were identical for all family members in the NONMAS schemes, but differed between family members in the MAS schemes, making within-family selection possible. MAS had up to twice the total genetic gain of the corresponding NONMAS scheme. MAS was somewhat less effective when heritability increased from 0.06 to 0.12 or when the frequency of the positive allele was <0.5. The r... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549003 Tue, 17 Apr 2007 18:50:12 +0100 549003 http://www.medworm.com/index.php?rid=549002&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433244%26dopt%3DAbstract Authors: David L, Rosenberg NA, Lavi U, Feldman MW, Hillel J Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, suppor... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549002 Tue, 17 Apr 2007 18:50:12 +0100 549002 http://www.medworm.com/index.php?rid=549000&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17433245%26dopt%3DAbstract In this report, we describe a simple, PCR-based typing method to distinguish rabbit CSN3 alleles. We analyse both ancient wild rabbit populations from the Iberian Peninsula and France, and the more recently derived English wild rabbits and domestic stocks. A new allele (C) showing another major indel (250 bp) in intron 1 was found, but exclusively detected in Iberian wild rabbits. In addition, our survey revealed the occurrence of new haplotypes in wild populations, suggesting that intragenic recombination is important in creating genetic diversity at this locus. This easy and low cost single-step PCR-based method results in an improvement over previous described techniques, can be easily set up in a routine molecular laboratory and would probably be a valuable tool in the management of ra... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=549000 Tue, 17 Apr 2007 18:50:12 +0100 549000 http://www.medworm.com/index.php?rid=433570&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306196%26dopt%3DAbstract Authors: Lillehammer M, Odegård J, Meuwissen TH Two random regression models, where the effect of a putative QTL was regressed on an environmental gradient, are described. The first model estimates the correlation between intercept and slope of the random regression, while the other model restricts this correlation to 1 or -1, which is expected under a bi-allelic QTL model. The random regression models were compared to a model assuming no gene by environment interactions. The comparison was done with regards to the models ability to detect QTL, to position them accurately and to detect possible QTL by environment interactions. A simulation study based on a granddaughter design was conducted, and QTL were assumed, either by assigning an effect independent of the environment or as a lin... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433570 Sat, 24 Feb 2007 08:35:02 +0100 433570 http://www.medworm.com/index.php?rid=433569&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306197%26dopt%3DAbstract Authors: Stock KF, Distl O, Hoeschele I Simulated data were used to investigate the influence of the choice of priors on estimation of genetic parameters in multivariate threshold models using Gibbs sampling. We simulated additive values, residuals and fixed effects for one continuous trait and liabilities of four binary traits, and QTL effects for one of the liabilities. Within each of four replicates six different datasets were generated which resembled different practical scenarios in horses with respect to number and distribution of animals with trait records and availability of QTL information. (Co)Variance components were estimated using a Bayesian threshold animal model via Gibbs sampling. The Gibbs sampler was implemented with both a flat and a proper prior for the genetic cova... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433569 Sat, 24 Feb 2007 08:35:02 +0100 433569 http://www.medworm.com/index.php?rid=433568&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306198%26dopt%3DAbstract Authors: Gilbert H, Le Roy P A new multiple trait strategy based on discriminant analysis was studied for efficient detection of linked QTL in outbred sib families, in comparison with a multivariate likelihood technique. The discriminant analysis technique describes the segregation of a linear combination of the traits in a univariate likelihood. This combination is calculated for each pair of positions depending on the inheritance of the pairs of QTL haplotypes in the progeny. The gains in power and accuracy for position estimations of multiple trait methods in grid searches were evaluated in reference to single trait detections of linked QTL. The methods were applied to simulated designs with two correlated traits submitted to various effects from the linked QTL. Multiple trait strat... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433568 Sat, 24 Feb 2007 08:35:02 +0100 433568 http://www.medworm.com/index.php?rid=433567&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306199%26dopt%3DAbstract Authors: Flury C, Weigend S, Ding X, Täubert H, Simianer H To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three sub-populations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated wit... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433567 Sat, 24 Feb 2007 08:35:02 +0100 433567 http://www.medworm.com/index.php?rid=433566&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306200%26dopt%3DAbstract Authors: Palucci V, Schaeffer LR, Miglior F, Osborne V The effects of additive, dominance, additive by dominance, additive by additive and dominance by dominance genetic effects on age at first service, non-return rates and interval from calving to first service were estimated. Practical considerations of computing additive and dominance relationships using the genomic relationship matrix are discussed. The final strategy utilized several groups of 1000 animals (heifers or cows) in which all animals had a non-zero dominance relationship with at least one other animal in the group. Direct inversion of relationship matrices was possible within the 1000 animal subsets. Estimates of variances were obtained using Bayesian methodology via Gibbs sampling. Estimated non-additive genetic varian... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433566 Sat, 24 Feb 2007 08:35:02 +0100 433566 http://www.medworm.com/index.php?rid=433565&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306201%26dopt%3DAbstract The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2) and to analyze the effects of these variants and the well known intronic ESR1 PvuII polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP) in the ESR1 cDNA: c.669T > C (exon 3), c.1227C > T (exon 5), c.1452C > T (exon 7), c.1665T > C and c.1755A > G (exon 8). One pair of these SNP (c.1665T > C and c.1755A > G) co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the PvuII polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433565 Sat, 24 Feb 2007 08:35:02 +0100 433565 http://www.medworm.com/index.php?rid=433564&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17306202%26dopt%3DAbstract Authors: Theilgaard P, Sánchez JP, Pascual JJ, Berg P, Friggens NC, Baselga M The aim of the present study was to investigate differences in reproductive and body traits during successive parities between two genetic lines. The LP line was constituted by means of selection of animals having an extremely high number of parities (at least 25) and an average reproductive performance compared to the V line selected for litter size at weaning during 31 generations. The two lines were found to have an equal reproductive performance in the first three parities, but the LP line had higher reproductive performance from the fourth parturition onwards. The low reproductive performance after the third parity in the V line was suggested to be caused by constrained environmental conditions in the t... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=433564 Sat, 24 Feb 2007 08:35:02 +0100 433564 http://www.medworm.com/index.php?rid=352319&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212945%26dopt%3DAbstract In conclusion SDP is a reliable and flexible method for solving contribution problems. PMID: 17212945 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352319 Sat, 13 Jan 2007 05:33:02 +0100 352319 http://www.medworm.com/index.php?rid=352318&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212946%26dopt%3DAbstract Authors: Abraham KJ, Totir LR, Fernando RL Markov chain Monte Carlo (MCMC) methods have been widely used to overcome computational problems in linkage and segregation analyses. Many variants of this approach exist and are practiced; among the most popular is the Gibbs sampler. The Gibbs sampler is simple to implement but has (in its simplest form) mixing and reducibility problems; furthermore in order to initiate a Gibbs sampling chain we need a starting genotypic or allelic configuration which is consistent with the marker data in the pedigree and which has suitable weight in the joint distribution. We outline a procedure for finding such a configuration in pedigrees which have too many loci to allow for exact peeling. We also explain how this technique could be used to implement a bl... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352318 Sat, 13 Jan 2007 05:33:02 +0100 352318 http://www.medworm.com/index.php?rid=352317&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212947%26dopt%3DAbstract Authors: Casellas J, Piedrafita J, Varona L The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging c... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352317 Sat, 13 Jan 2007 05:33:02 +0100 352317 http://www.medworm.com/index.php?rid=352316&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212948%26dopt%3DAbstract The objective of this study was to build a character process model taking into account serial correlations for the analysis of repeated measurements of semen volume in AI rams. For each ram, measurements were repeated within and across years. Therefore, we considered a model including three environmental effects: the long-term environmental effect, which is a random year(*)subject effect, the short-term environmental effect, which is a random within year subject(*)collection effect, and the classical measurement error. We used a four-step approach to build the model. The first step explored graphically the serial correlations. The second step compared four models with different correlation structures for the short-term environmental effect. We selected fixed effects in the third step. In t... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352316 Sat, 13 Jan 2007 05:33:02 +0100 352316 http://www.medworm.com/index.php?rid=352315&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212949%26dopt%3DAbstract Authors: Ye X, Brown SR, Nones K, Coutinho LL, Dekkers JC, Lamont SJ Myostatin is a negative regulator of skeletal muscle growth. We evaluated effects of myostatin polymorphisms in three elite commercial broiler chicken lines on mortality, growth, feed conversion efficiency, ultrasound breast depth, breast percentage, eviscerated carcass weight, leg defects, blood oxygen level, and hen antibody titer to infectious bursal disease virus vaccine. Progeny mean data adjusted for fixed and mate effects and DNA from 100 sires per line were used. Single nucleotide polymorphisms (SNPs) of the myostatin gene segregating in these lines were identified by designing specific primers, amplifying individual DNA in each line by polymerase chain reaction, cloning, sequencing and aligning the correspond... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352315 Sat, 13 Jan 2007 05:33:02 +0100 352315 http://www.medworm.com/index.php?rid=352314&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212950%26dopt%3DAbstract Authors: Pedrosa S, Arranz JJ, Brito N, Molina A, San Primitivo F, Bayón Y Mitochondrial DNA diversity was analysed in 19 Iberian and six foreign sheep breeds. Three mtDNA lineages (B, A and C) were found in the Iberian sheep, with type B clearly predominating over the others. The results were analysed for each of the morphologically determined breed groups in Iberian sheep: Merino, Entrefino, Churro and Iberian trunks. MtDNA lineage C was found only in the Iberian trunk composed of Montesina and Ojalada. These two populations had high mtDNA variability, and in the Iberian sheep only Merino Branco had more variation. The other three Merino types studied showed moderate variability, including the most authentic Merino, the Spanish Merino. These three Merinos clustered closely in a mult... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=352314 Sat, 13 Jan 2007 05:33:02 +0100 352314 http://www.medworm.com/index.php?rid=463151&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17212945%26dopt%3DAbstract In conclusion SDP is a reliable and flexible method for solving contribution problems. PMID: 17212945 [PubMed - indexed for MEDLINE] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=463151 Mon, 01 Jan 2007 05:00:00 +0100 463151 http://www.medworm.com/index.php?rid=300693&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17129560%26dopt%3DAbstract Authors: Damgaard LH, Korsgaard IR Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions.... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=300693 Fri, 01 Dec 2006 07:09:02 +0100 300693 http://www.medworm.com/index.php?rid=300692&cid=s_33034_176_f&fid=33034&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17129561%26dopt%3DAbstract Authors: Jaffrézic F, Meza C, Lavielle M, Foulley JL The analysis of nonlinear function-valued characters is very important in genetic studies, especially for growth traits of agricultural and laboratory species. Inference in nonlinear mixed effects models is, however, quite complex and is usually based on likelihood approximations or Bayesian methods. The aim of this paper was to present an efficient stochastic EM procedure, namely the SAEM algorithm, which is much faster to converge than the classical Monte Carlo EM algorithm and Bayesian estimation procedures, does not require specification of prior distributions and is quite robust to the choice of starting values. The key idea is to recycle the simulated values from one iteration to the next in the EM algorithm, which considerabl... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=300692 Fri, 01 Dec 2006 07:09:02 +0100 300692