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, 09 Feb 2012 09:43:36 +0100 http://www.medworm.com/index.php?rid=5636041&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%3D22273519%26dopt%3DAbstract CONCLUSIONS: The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was achieved. The reference population structure had a limited effect on long-term accuracy and response. Use of a shallow reference population, most closely related to the selection candidates, gave early benefits while in later generations, when marker effects were not updated, the estimation of marker effects based on a deeper reference population did not pay off. PMID: 22273519 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5636041 Tue, 24 Jan 2012 05:00:00 +0100 5636041 http://www.medworm.com/index.php?rid=5636042&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%3D22268922%26dopt%3DAbstract Authors: Case LA, Wood BJ, Miller SP Abstract ABSTRACT: Residual feed intake (RFI) and feed conversion ratio (FCR) can be incorporated into a breeding program as traits to select for feed efficiency. Alternatively, the direct measures used to calculate RFI and FCR can be analyzed to determine the underlying variation in the traits that impact overall efficiency. These constituent traits can then be appropriately weighted in an index to achieve genetic gain. To investigate feed efficiency in the turkey, feed intake and weight gain were measured on male primary breeder line turkeys housed in individual feeding cages from 15 to 19 weeks of age. The FCR and RFI showed moderate heritability values of 0.16 and 0.21, respectively. Feed intake, body weight, and weight gain were also modera... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5636042 Mon, 23 Jan 2012 05:00:00 +0100 5636042 http://www.medworm.com/index.php?rid=5617805&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%3D22252172%26dopt%3DAbstract CONCLUSION: Decorrelated selection indices should not be used because of misleading results and the availability of accurate and fast algorithms for exact multidimensional integration. Genomic selection is the method of choice when maximising the genetic gain per year but genotyping females may not allow for a reduction in overall breeding costs. Furthermore, the economic justifcation of genotyping females remains questionable. PMID: 22252172 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5617805 Tue, 17 Jan 2012 05:00:00 +0100 5617805 http://www.medworm.com/index.php?rid=5523538&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%3D22152008%26dopt%3DAbstract CONCLUSIONS: Genomic selection programs benefit greatly from combining data from several closely related populations into a single large reference population. PMID: 22152008 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5523538 Mon, 12 Dec 2011 05:00:00 +0100 5523538 http://www.medworm.com/index.php?rid=5486907&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%3D22132733%26dopt%3DAbstract CONCLUSIONS: Three separate regions on chromosome 9 gave significant results for litter size and pig mortality. The frequencies of favourable alleles of the significant SNP are moderate in the Finnish Landrace population and these SNP are thus valuable candidates for possible marker-assisted selection. PMID: 22132733 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5486907 Thu, 01 Dec 2011 05:00:00 +0100 5486907 http://www.medworm.com/index.php?rid=5486908&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%3D22128882%26dopt%3DAbstract CONCLUSIONS: The results suggest that when analyzing binary data with extreme case problems, bias in the estimation of variance components could be eliminated, or at least significantly reduced by using a g-prior. PMID: 22128882 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5486908 Wed, 30 Nov 2011 05:00:00 +0100 5486908 http://www.medworm.com/index.php?rid=5486909&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%3D22122853%26dopt%3DAbstract CONCLUSIONS: These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy. PMID: 22122853 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5486909 Mon, 28 Nov 2011 05:00:00 +0100 5486909 http://www.medworm.com/index.php?rid=5486910&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%3D22117894%26dopt%3DAbstract CONCLUSIONS: Penalized maximum likelihood estimation provides the means to `make the most' of limited and precious data and facilitates more stable estimation for multi-dimensional analyses. It should become part of our everyday toolkit for multivariate estimation in quantitative genetics. PMID: 22117894 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5486910 Sun, 27 Nov 2011 05:00:00 +0100 5486910 http://www.medworm.com/index.php?rid=5408584&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%3D22070746%26dopt%3DAbstract CONCLUSIONS: Deregressed EBV is the preferred response variable, whereas the choice of statistical method is less critical for pure-bred pigs. The increase of 18 to 39% in reliability is worthwhile, since the reliabilities of the genomic breeding values directly affect the returns from genomic selection. PMID: 22070746 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5408584 Wed, 09 Nov 2011 05:00:00 +0100 5408584 http://www.medworm.com/index.php?rid=5373394&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%3D22047533%26dopt%3DAbstract CONCLUSIONS: Using cryopreserved semen to redirect selection or to improve genetic diversity should be carried out with caution, by considering the pros and cons of prospective changes in genetic diversity and the value of the selected traits. However, the use of genomic information should lead to more interesting perspectives for choosing which animals to store in a cryobank and for increasing the value of cryobank collections for selected breeds. PMID: 22047533 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5373394 Wed, 02 Nov 2011 04:00:00 +0100 5373394 http://www.medworm.com/index.php?rid=5373393&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%3D22047591%26dopt%3DAbstract CONCLUSIONS: Coupling prior knowledge with the output provided by the IC algorithm allowed further learning regarding phenotypic causal structures when compared to standard mixed effects SEM applications. PMID: 22047591 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5373393 Wed, 02 Nov 2011 04:00:00 +0100 5373393 http://www.medworm.com/index.php?rid=5373395&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%3D22044555%26dopt%3DAbstract In this study, we adopted the Pareto principle to weight available marker loci, i.e., we consider that x% of the loci explain (100-x)% of the total genetic variance. Assuming this principle, it is also possible to define the variances of the prior distribution of the 'big' and 'small' SNP. The relatively few large SNP explain a large proportion of the genetic variance and the majority of the SNP show small effects and explain a minor proportion of the genetic variance. We name this method MixP, where the prior distribution is a mixture of two normal distributions, i.e. one with a big variance and one with a small variance. Simulation results, using a real Norwegian Red cattle pedigree, show that MixP is at least as accurate as the other methods in all studied cases. This method also reduce... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5373395 Tue, 01 Nov 2011 04:00:00 +0100 5373395 http://www.medworm.com/index.php?rid=5356858&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%3D21988752%26dopt%3DAbstract CONCLUSIONS: Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs. PMID: 21988752 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5356858 Tue, 11 Oct 2011 04:00:00 +0100 5356858 http://www.medworm.com/index.php?rid=5272326&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%3D21943113%26dopt%3DAbstract CONCLUSIONS: Genetic parameters from the PC and FA approaches were very similar when the optimal number of principal components or factors was fitted. Over-fitting increased estimation time and standard errors of the estimates but did not affect the estimates of genetic correlations or the predictions of breeding values, whereas fitting too few parameters affected bull rankings in different countries. PMID: 21943113 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5272326 Fri, 23 Sep 2011 04:00:00 +0100 5272326 http://www.medworm.com/index.php?rid=5214615&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%3D21896209%26dopt%3DAbstract CONCLUSIONS: Based on experimental data, the current genetic evaluation model can be improved to better take into account the number of lambs reared. Thus, it would be of interest to evaluate this model on field data and update the genetic evaluation model based on the results obtained. PMID: 21896209 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5214615 Wed, 07 Sep 2011 04:00:00 +0100 5214615 http://www.medworm.com/index.php?rid=5170188&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%3D21864407%26dopt%3DAbstract CONCLUSIONS: The selection pressure of conventional breeding on the allele with the deletion is limited due to the observed dominance (overdominance) effects. Inclusion of molecular information in the national breeding scheme will reduce the frequency of this deletion in the population. PMID: 21864407 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5170188 Tue, 23 Aug 2011 23:00:00 +0100 5170188 http://www.medworm.com/index.php?rid=5147037&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%3D21851619%26dopt%3DAbstract CONCLUSIONS: The proposed method can be easily and quickly implemented in BLUP evaluations at the national level, although some improvement is necessary to more accurately propagate genomic information from genotyped to non-genotyped animals. In addition, it is a convenient method to combine direct genomic, phenotypic and pedigree-based information in a multiple-step procedure. PMID: 21851619 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5147037 Wed, 17 Aug 2011 23:00:00 +0100 5147037 http://www.medworm.com/index.php?rid=5133719&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%3D21819592%26dopt%3DAbstract CONCLUSIONS: Duck and chicken VLDLR genes probably perform similar function in the development of growing oocytes and deposition of yolk lipoprotein. Therefore, VLDLR could be a candidate gene for duck egg performance and be used as a genetic marker to improve egg performance in ducks. PMID: 21819592 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5133719 Thu, 04 Aug 2011 23:00:00 +0100 5133719 http://www.medworm.com/index.php?rid=5086925&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%3D21787428%26dopt%3DAbstract CONCLUSIONS: These results emphasize the relationships between endocrine tissues and plasma metabolites in terms of gene expression. Highly tissue-specific association patterns suggest that candidate genes or gene pathways should be investigated in the context of specific tissues. PMID: 21787428 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5086925 Sun, 24 Jul 2011 23:00:00 +0100 5086925 http://www.medworm.com/index.php?rid=5037360&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%3D21418602%26dopt%3DAbstract Authors: Laenoi W, Uddin MJ, Cinar MU, Grosse-Brinkhaus C, Tesfaye D, Jonas E, Scholz AM, Tholen E, Looft C, Wimmers K, Phatsara C, Juengst H, Sauerwein H, Mielenz M, Schellander K Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs. PMID: 21418602 [PubMed - indexed for MEDLINE] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5037360 Tue, 19 Jul 2011 06:30:02 +0100 5037360 http://www.medworm.com/index.php?rid=5037358&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%3D21749687%26dopt%3DAbstract CONCLUSIONS: Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift. PMID: 21749687 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5037358 Mon, 11 Jul 2011 23:00:00 +0100 5037358 http://www.medworm.com/index.php?rid=5037359&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%3D21729282%26dopt%3DAbstract CONCLUSIONS: When the indicator trait had a genetic correlation lower than 0.5 with the trait of interest in our simulated data, the accuracy was higher if genotypes rather than phenotypes were obtained for the indicator trait. However, when genetic correlations were higher than 0.5, using an indicator trait led to higher accuracies for selection candidates. For different combinations of traits, the level of genetic correlation below which genotyping selection candidates is more effective than obtaining phenotypes for an indicator trait, needs to be derived considering at least the heritabilities and the numbers of animals recorded for the traits involved. PMID: 21729282 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=5037359 Mon, 04 Jul 2011 23:00:00 +0100 5037359 http://www.medworm.com/index.php?rid=4993624&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%3D21703021%26dopt%3DAbstract Conclusions:} Different allele coding methods lead to the same inference in the marker-based and equivalent models when a fixed general mean is included in the model. However, reliabilities of genomic breeding values are affected by the allele coding method used. The centered coding has some numerical advantages when Markov chain Monte Carlo methods are used. \end{abstract} PMID: 21703021 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4993624 Sat, 25 Jun 2011 23:00:00 +0100 4993624 http://www.medworm.com/index.php?rid=4993625&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%3D21702919%26dopt%3DAbstract CONCLUSIONS: The results indicate that the complex expression profiling of pathogen challenged pbMEC sampled from cows inheriting alternative QTL alleles is suitable to study genetically determined molecular mechanisms of mastitis susceptibility in mammary epithelial cells in vitro and to highlight the most likely functional pathways and candidate genes underlying the QTL effect. PMID: 21702919 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4993625 Thu, 23 Jun 2011 23:00:00 +0100 4993625 http://www.medworm.com/index.php?rid=4993627&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%3D21693024%26dopt%3DAbstract CONCLUSION: This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays. PMID: 21693024 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4993627 Mon, 20 Jun 2011 23:00:00 +0100 4993627 http://www.medworm.com/index.php?rid=4993626&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%3D21693035%26dopt%3DAbstract In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding populations. PMID: 21693035 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4993626 Mon, 20 Jun 2011 23:00:00 +0100 4993626 http://www.medworm.com/index.php?rid=4894189&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%3D21609451%26dopt%3DAbstract CONCLUSIONS: In terms of estimation's accuracy, both principal component approaches performed equally well and permitted the use of more parsimonious models through random regression MACE. The advantage of the bottom-up PC approach is that it does not need any previous knowledge on the rank. However, with a predetermined rank, the direct PC approach needs less computing time than the bottom-up PC. PMID: 21609451 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4894189 Mon, 23 May 2011 23:00:00 +0100 4894189 http://www.medworm.com/index.php?rid=4894190&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%3D21605351%26dopt%3DAbstract CONCLUSIONS: The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not. PMID: 21605351 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4894190 Sun, 22 May 2011 23:00:00 +0100 4894190 http://www.medworm.com/index.php?rid=4849138&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%3D21349166%26dopt%3DAbstract Authors: Awad A, Russ I, Förster M, Medugorac I In a previous study in the Fleckvieh dual purpose cattle breed, we mapped a quantitative trait locus (QTL) affecting milk yield (MY1), milk protein yield (PY1) and milk fat yield (FY1) during first lactation to the distal part of bovine chromosome 5 (BTA5), but the confidence interval was too large for positional cloning of the causal gene. Our objective here was to refine the position of this QTL and to define the candidate region for high-throughput sequencing. PMID: 21349166 [PubMed - indexed for MEDLINE] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4849138 Sun, 22 May 2011 00:30:10 +0100 4849138 http://www.medworm.com/index.php?rid=4849084&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%3D21575265%26dopt%3DAbstract CONCLUSIONS: Our results suggest that Bayes B is superior to gBLUP to estimate breeding values from genomic data. The underlying model of genetic variation greatly affects the predictive ability of genomic selection methods, and the superiority of Bayes B over gBLUP is highly dependent on the presence of large QTL effects. The use of SNP sequence data will outperform the less dense marker panels. However, the size and distribution of QTL effects and the size of reference populations still greatly influence the effectiveness of using sequence data for genomic prediction. PMID: 21575265 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4849084 Mon, 16 May 2011 23:00:00 +0100 4849084 http://www.medworm.com/index.php?rid=4849078&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%3D21586131%26dopt%3DAbstract CONCLUSIONS: Genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations. We found that fitting a residual polygenic effect reduced the bias in genome-enhanced breeding values, decreased the correlation between direct genomic values and sire's estimated breeding values and made genome-enhanced breeding values more consistent in mean and variance as is the case for pedigree-based estimated breeding values. PMID: 21586131 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4849078 Mon, 16 May 2011 23:00:00 +0100 4849078 http://www.medworm.com/index.php?rid=4849094&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%3D21569623%26dopt%3DAbstract Authors: Garrick DJ ABSTRACT: Artificial selection has proven to be effective at altering the performance of animal production systems. Nevertheless, selection based upon assessment of the genetic superiority of candidates is suboptimal as a result of errors in the prediction of genetic merit. Conventional breeding programs may extend phenotypic measurements on selection candidates to include correlated indicator traits, or delay selection decisions well beyond puberty so that phenotypic performance can be observed on progeny or other relatives. Extending the generation interval to increase the accuracy of selection reduces annual rates of gain compared to accurate selection and use of parents of the next generation at the immediate time they reach breeding age. Genomic prediction aims... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4849094 Sat, 14 May 2011 23:00:00 +0100 4849094 http://www.medworm.com/index.php?rid=4849130&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%3D21569603%26dopt%3DAbstract CONCLUSIONS: Both threshold linear models and grouped data models can guarantee the goodness-of-fit of the genetic evaluation for carcass conformation and fat cover, but our results highlight the need for specific thresholds by sex and slaughterhouse in order to avoid fitting deficiencies. PMID: 21569603 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4849130 Fri, 13 May 2011 23:00:00 +0100 4849130 http://www.medworm.com/index.php?rid=4795088&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%3D21504607%26dopt%3DAbstract CONCLUSION: This study shows that testicular expression of CYP11A1 is not solely responsible for the QTL influencing boar fat androstenone levels. As a conclusion, we propose to refute the hypothesis that a single mutation located near the centre of the QTL region could control androstenone accumulation in fat by regulating the CYP11A1 expression. PMID: 21504607 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4795088 Mon, 18 Apr 2011 23:00:00 +0100 4795088 http://www.medworm.com/index.php?rid=4628710&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%3D21255418%26dopt%3DAbstract Authors: Wolc A, Stricker C, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Habier D, Fernando R, Garrick DJ, Lamont SJ, Dekkers JC Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line. PMID: 21255418 [PubMed - indexed for MEDLINE] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4628710 Thu, 24 Mar 2011 21:30:09 +0100 4628710 http://www.medworm.com/index.php?rid=4628707&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%3D21418636%26dopt%3DAbstract CONCLUSIONS: For Taura syndrome resistance, endurance and susceptibility are apparently distinct genetic traits. However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure fraction for these data. Using the current testing design, genetic variation in observed survival time and absolute survival at the end of test were most likely dominated by genetic variation in susceptibility. If the aim is to reduce susceptibility, earlier termination of the challenge-test or back-truncation of the follow-up period should be avoided, as this may shift focus of selection towards endurance rather than susceptibility. PMID: 21418636 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4628707 Mon, 21 Mar 2011 00:00:00 +0100 4628707 http://www.medworm.com/index.php?rid=4628708&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%3D21418602%26dopt%3DAbstract CONCLUSIONS: Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs. PMID: 21418602 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4628708 Sun, 20 Mar 2011 00:00:00 +0100 4628708 http://www.medworm.com/index.php?rid=4628709&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%3D21388557%26dopt%3DAbstract CONCLUSIONS: The algorithm and software developed in this study make feasible the routine phasing of high-density SNP chips in large datasets. PMID: 21388557 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4628709 Thu, 10 Mar 2011 00:00:00 +0100 4628709 http://www.medworm.com/index.php?rid=4566724&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%3D21375775%26dopt%3DAbstract CONCLUSIONS: Our results show that two QTL on SSC2p affect backfat thickness. Differences in the pedigree structures and in the number of heterozygous females at the IGF2 locus result in different imprinting statuses in the two pedigrees studied. The spurious effect observed when a maternally allele is present at the IGF2 locus, is in fact due to the presence of a second closely located QTL. This work confirms that pig chromosome 2 is a major region associated with fattening traits. PMID: 21375775 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4566724 Sun, 06 Mar 2011 00:00:00 +0100 4566724 http://www.medworm.com/index.php?rid=4566725&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%3D21366914%26dopt%3DAbstract CONCLUSIONS: Methods to impute genotypes and compute genomic evaluations were affordable with many more markers. Reliabilities for individual animals can be modified to reflect success of imputation. Breeders can improve reliability at lower cost by combining marker densities to increase both the numbers of markers and animals included in genomic evaluation. Larger gains are expected from increasing the number of animals than the number of markers. PMID: 21366914 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4566725 Wed, 02 Mar 2011 00:00:00 +0100 4566725 http://www.medworm.com/index.php?rid=4566726&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%3D21362170%26dopt%3DAbstract CONCLUSIONS: The model provides a general framework and some tools to maximize health and performances of a population under infection. Limits and assumptions of the model are clearly identified so it can be improved for different epidemiological settings. PMID: 21362170 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4566726 Tue, 01 Mar 2011 00:00:00 +0100 4566726 http://www.medworm.com/index.php?rid=4566727&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%3D21349166%26dopt%3DAbstract CONCLUSION: This study demonstrates that targeting families segregating for a less frequent QTL allele is a useful method. It improves the mapping resolution of the QTL, which is due to the division of the mapping population based on the results of the haplotype analysis and to the increased frequency of the minor allele in the families. Consequently, we succeeded in refining the region containing the previously detected QTL to 1 Mb on BTA5. This candidate region contains 27 genes with unknown or partially known function(s) and is small enough for high-throughput sequencing, which will allow future detailed analyses of candidate genes. PMID: 21349166 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4566727 Thu, 24 Feb 2011 00:00:00 +0100 4566727 http://www.medworm.com/index.php?rid=4512677&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%3D21329522%26dopt%3DAbstract CONCLUSIONS: The results of this study suggest that the best method for genome-wide prediction may depend on the genetic basis of the population analyzed. All methods were less accurate at correctly classifying intermediate animals than extreme animals. Among the different alternatives proposed to analyze discrete traits, machine-learning showed some advantages over Bayesian regressions. Boosting with a pseudo Huber loss function showed high accuracy, whereas Random Forest produced more consistent results and an interesting predictive ability. Nonetheless, the best method may be case-dependent and a initial evaluation of different methods is recommended to deal with a particular problem. PMID: 21329522 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4512677 Thu, 17 Feb 2011 00:00:00 +0100 4512677 http://www.medworm.com/index.php?rid=4512678&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%3D21310061%26dopt%3DAbstract Authors: Rosa GJ, Valente BD, de Los Campos G, Wu XL, Gianola D, Silva MA ABSTRACT: Phenotypic traits may exert causal effects between them. For example, on the one hand, high yield in dairy cows may increase the liability to certain diseases and, on the other hand, the incidence of a disease may affect yield negatively. Likewise, the transcriptome may be a function of the reproductive status in mammals and the latter may depend on other physiological variables. Knowledge of phenotype networks describing such interrelationships can be used to predict the behavior of complex systems, e.g. biological pathways underlying complex traits such as diseases, growth and reproduction. Structural Equation Models (SEM) can be used to study recursive and simultaneous relationships among phenotypes ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4512678 Thu, 10 Feb 2011 00:00:00 +0100 4512678 http://www.medworm.com/index.php?rid=4388922&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%3D21208445%26dopt%3DAbstract Authors: Forni S, Aguilar I, Misztal I ABSTRACT: PMID: 21208445 [PubMed - in process] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4388922 Mon, 24 Jan 2011 04:15:03 +0100 4388922 http://www.medworm.com/index.php?rid=4388919&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%3D21251244%26dopt%3DAbstract CONCLUSIONS: The much higher speed of the method presented here extends the use of mate selection and enables implementation in relatively large programs across breeding units. PMID: 21251244 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4388919 Thu, 20 Jan 2011 00:00:00 +0100 4388919 http://www.medworm.com/index.php?rid=4388920&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%3D21241486%26dopt%3DAbstract CONCLUSIONS: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed. PMID: 21241486 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4388920 Mon, 17 Jan 2011 00:00:00 +0100 4388920 http://www.medworm.com/index.php?rid=4388921&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%3D21235756%26dopt%3DAbstract CONCLUSIONS: Our study shows that (1) the Ibar, Lim and Drina Rivers grayling populations are genetically distinct from populations outside of Serbia and thus should be managed as native populations in spite of some introgression in the Drina River population and (2) the Rzav River population is not appropriate for further stocking activities since it originates from stocked Slovenian grayling. However, the Rzav River population does not represent an immediate danger to other populations because it is physically isolated from these. PMID: 21235756 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4388921 Fri, 14 Jan 2011 00:00:00 +0100 4388921 http://www.medworm.com/index.php?rid=4299320&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%3D21176141%26dopt%3DAbstract CONCLUSION: The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes. PMID: 21176141 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4299320 Tue, 21 Dec 2010 00:00:00 +0100 4299320 http://www.medworm.com/index.php?rid=4211955&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%3D21108822%26dopt%3DAbstract CONCLUSIONS: Combining two Meishan x European breeds F2 pedigrees improved the mapping of QTL compared to analysing pedigrees separately. Our work was facilitated by the access to raw phenotypic data and DNA of animals from both pedigrees and the combination of the two designs with the addition of new markers allowed us to fine map QTL without phenotyping additional animals. PMID: 21108822 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4211955 Thu, 25 Nov 2010 00:00:00 +0100 4211955 http://www.medworm.com/index.php?rid=4211956&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%3D21092198%26dopt%3DAbstract CONCLUSIONS: This new selection scheme combines communal rearing of families, pre-selection of candidates, DNA pooling and genomic selection and makes multi-trait selection possible in aquaculture selection schemes without keeping families separately until individual tagging is possible. The new scheme can also be used for other farmed species, for which the cost of genotyping test individuals may be high, e.g. if trait heritability is low. PMID: 21092198 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4211956 Mon, 22 Nov 2010 00:00:00 +0100 4211956 http://www.medworm.com/index.php?rid=4134611&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%3D21040563%26dopt%3DAbstract CONCLUSIONS: The present study showed the strength of analysing three connected F2-crosses jointly. In this experiment, statistical power was high because of the reduced number of estimated parameters and the large number of individuals. The applied model was flexible and was computationally fast. PMID: 21040563 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4134611 Mon, 01 Nov 2010 00:00:00 +0100 4134611 http://www.medworm.com/index.php?rid=4121035&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%3D20977705%26dopt%3DAbstract CONCLUSIONS: Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes. PMID: 20977705 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4121035 Tue, 26 Oct 2010 00:00:00 +0100 4121035 http://www.medworm.com/index.php?rid=4106625&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%3D20969751%26dopt%3DAbstract CONCLUSIONS: Therefore, in animal half-sib designs, modelling linkage disequilibrium evolution using a Wright-Fisher model does not significantly improve the accuracy of the QTL location when compared to a simpler method assuming complete and constant linkage between the QTL and the marker alleles. Finally, given the high marker density available nowadays, the simpler method should be preferred as it gives accurate results in a reasonable computing time. PMID: 20969751 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4106625 Thu, 21 Oct 2010 23:00:00 +0100 4106625 http://www.medworm.com/index.php?rid=4087360&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%3D20950478%26dopt%3DAbstract CONCLUSIONS: Accurate genomic evaluation of the broader bull and cow population can be achieved with a single genotyping assays containing ~ 3,000 to 5,000 evenly spaced SNP. PMID: 20950478 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4087360 Fri, 15 Oct 2010 23:00:00 +0100 4087360 http://www.medworm.com/index.php?rid=4024379&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%3D20846385%26dopt%3DAbstract Authors: Cavanagh CR, Jonas E, Hobbs M, Thomson PC, Tammen I, Raadsma HW ABSTRACT: An (Awassi x Merino) x Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major ... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=4024379 Wed, 15 Sep 2010 23:00:00 +0100 4024379 http://www.medworm.com/index.php?rid=3881333&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%3D20712894%26dopt%3DAbstract CONCLUSIONS: Losing favorable alleles that are in weak linkage disequilibrium with markers is perhaps inevitable when using GS. Placing additional weight on low-frequency favorable alleles, however, may reduce the rate of loss of such alleles to below that of phenotypic selection. Applying such weights at the beginning of GS implementation is important. PMID: 20712894 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3881333 Sun, 15 Aug 2010 23:00:00 +0100 3881333 http://www.medworm.com/index.php?rid=3881334&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%3D20701809%26dopt%3DAbstract CONCLUSIONS: When a quantitative assay is used to estimate copy number alleles, segregation analysis of related individuals can greatly improve the precision of the estimates. Existing software for segregation analysis would require little if any change to accommodate the penetrance function for copy number assay data. PMID: 20701809 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3881334 Wed, 11 Aug 2010 23:00:00 +0100 3881334 http://www.medworm.com/index.php?rid=3881335&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%3D20699012%26dopt%3DAbstract The objective of this study was to quantify the efficiency of including dominance effects and practising mating allocation under a whole-genome evaluation scenario. Four strategies of selection, carried out during five generations, were compared by simulation techniques. In the first scenario (MS), individuals were selected based on their own phenotypic information. In the second (GSA), they were selected based on the prediction generated by the Bayes A method of whole-genome evaluation under an additive model. In the third (GSD), the model was expanded to include dominance effects. These three scenarios used random mating to construct future generations, whereas in the fourth one (GSD+MA), matings were optimized by simulated annealing. The advantage of GSD over GSA ranges from 9 to 14% of... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3881335 Tue, 10 Aug 2010 23:00:00 +0100 3881335 http://www.medworm.com/index.php?rid=3849699&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%3D20691068%26dopt%3DAbstract CONCLUSION: Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations. PMID: 20691068 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3849699 Thu, 05 Aug 2010 23:00:00 +0100 3849699 http://www.medworm.com/index.php?rid=3802789&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%3D20667088%26dopt%3DAbstract CONCLUSIONS: Our results reveal specific and partly new QTL positions across genetically diverse pig crosses. For some of the traits associated with specific enzymes, protein content and cell structure in fat tissue, it is the first time that they are included in a QTL analysis. They provide large-scale information to analyse causative genes and useful data for the pig industry. PMID: 20667088 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3802789 Tue, 27 Jul 2010 23:00:00 +0100 3802789 http://www.medworm.com/index.php?rid=3802790&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%3D20659318%26dopt%3DAbstract CONCLUSIONS: The results suggest that bacteria negative and bacteria positive SCS are genetically different traits. A positive genetic correlation between bacteria negative SCS and liability to infection was found, suggesting that the approach of selecting animals for decreased SCS should help to reduce mastitis prevalence. However, the results show that imperfect diagnosis of infection has an impact on estimated genetic parameters, which may reduce the efficiency of selection strategies aiming at distinguishing between bacteria negative and bacteria positive SCS. PMID: 20659318 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3802790 Sun, 25 Jul 2010 23:00:00 +0100 3802790 http://www.medworm.com/index.php?rid=3784802&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%3D20649962%26dopt%3DAbstract CONCLUSIONS: The new algorithm to estimate genetic parameters via Gibbs sampling solves the bias problems typically occurring in animal threshold model analysis of binary traits with one observation per animal. Furthermore, the method considerably speeds up mixing properties of the Gibbs sampler with respect to genetic parameters, which would be an advantage of any linear or non-linear animal model. PMID: 20649962 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3784802 Wed, 21 Jul 2010 23:00:00 +0100 3784802 http://www.medworm.com/index.php?rid=3758377&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%3D20626845%26dopt%3DAbstract CONCLUSIONS: Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs. PMID: 20626845 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3758377 Mon, 12 Jul 2010 23:00:00 +0100 3758377 http://www.medworm.com/index.php?rid=3741262&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%3D20609233%26dopt%3DAbstract CONCLUSION: It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens. PMID: 20609233 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3741262 Tue, 06 Jul 2010 23:00:00 +0100 3741262 http://www.medworm.com/index.php?rid=3718914&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%3D20591149%26dopt%3DAbstract CONCLUSIONS: Reliable estimates of degrees of freedom were obtained in all simulated heavy-tailed and normal datasets. The predictive log-likelihood was able to distinguish the correct model among the models fitted to heavy-tailed datasets. There was no disadvantage of fitting a heavy-tailed model when the true model was normal. Predictive log-likelihood values indicated that heavy-tailed models with low degrees of freedom values fitted gestation length and birth weight data better than a model with normally distributed residuals. Heavy-tailed and normal models resulted in different estimates of direct and maternal heritabilities, and different sire rankings. Heavy-tailed models may be more appropriate for reliable estimation of genetic parameters from field data. PMID: 20591149 [PubMe... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3718914 Tue, 29 Jun 2010 23:00:00 +0100 3718914 http://www.medworm.com/index.php?rid=3718915&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%3D20584334%26dopt%3DAbstract CONCLUSION: Selection for FCR will improve efficiency of feed utilization but because of the genetic dependence of FCR and its components, selection based on FCR will reduce FI and increase growth rate. However, the correlated responses in both FI and BWG cannot be predicted accurately because of the inherent problem of FCR being a ratio trait. PMID: 20584334 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3718915 Mon, 28 Jun 2010 23:00:00 +0100 3718915 http://www.medworm.com/index.php?rid=3718916&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%3D20584267%26dopt%3DAbstract CONCLUSIONS: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes. PMID: 20584267 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3718916 Sun, 27 Jun 2010 23:00:00 +0100 3718916 http://www.medworm.com/index.php?rid=3700111&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%3D20576168%26dopt%3DAbstract CONCLUSIONS: All the analyzed pig and wild boar populations shared one of the four detected RBP4 haplotypes. This suggests an ancestral origin of the quoted haplotype. The joint use of RBP4-MspI and ESR1-PvuII polymorphisms could be implemented to select for higher prolificacy in the Tai-Zumu line. In this population, the paternal allele of IGF2-intron3-3072A increased litter size from the third parity. The non-additive effects on litter size reported here should be tested before implementation in other pig breeding schemes. PMID: 20576168 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3700111 Thu, 24 Jun 2010 23:00:00 +0100 3700111 http://www.medworm.com/index.php?rid=3688165&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%3D20546624%26dopt%3DAbstract In this study, we constructed genetic covariance structures from whole-genome marker data, and thus used realized relationship matrices to estimate variance components in a heterogenous population of ~ 2200 mice for which four complex traits were investigated. These mice were genotyped for more than 10,000 single nucleotide polymorphisms (SNP) and the variances due to family, cage and genetic effects were estimated by models based on pedigree information only, aggregate SNP information, and model selection for specific SNP effects. Results and conclusions We show that the use of genome-wide SNP information can disentangle confounding factors to estimate genetic variances by separating genetic and non-genetic effects. The estimated variance components using realized relationship were more a... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3688165 Mon, 14 Jun 2010 23:00:00 +0100 3688165 http://www.medworm.com/index.php?rid=3688169&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%3D20540741%26dopt%3DAbstract CONCLUSIONS: Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed. PMID: 20540741 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3688169 Thu, 10 Jun 2010 23:00:00 +0100 3688169 http://www.medworm.com/index.php?rid=3688168&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%3D20540752%26dopt%3DAbstract CONCLUSIONS: Dominance and common environmental variance may be important components of variance in harvest weight in O. kisutch, thus not including them may produce an overestimation of the predicted response; furthermore, genetic evaluation was seen to be partially affected, since the ranking of selected animals changed with the inclusion of non-additive effects in the animal model. PMID: 20540752 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3688168 Thu, 10 Jun 2010 23:00:00 +0100 3688168 http://www.medworm.com/index.php?rid=3688167&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%3D20540758%26dopt%3DAbstract CONCLUSION: The multibreed maternal animal model introduced in this study simplifies the problem of estimating (co)variance components in the framework of a hierarchical Bayes analysis. Using this approach, we obtained for the first time estimates of the full set of genetic (co)variance components. It would be interesting to assess the performance of the procedure with field data, especially when interbreed information is limited. PMID: 20540758 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3688167 Thu, 10 Jun 2010 23:00:00 +0100 3688167 http://www.medworm.com/index.php?rid=3688166&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%3D20540762%26dopt%3DAbstract CONCLUSIONS: In conclusion given a high SNP density, the gene frequency model can be used to map QTL with considerable accuracy even within a 1 cM region. PMID: 20540762 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3688166 Thu, 10 Jun 2010 23:00:00 +0100 3688166 http://www.medworm.com/index.php?rid=3641652&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%3D20525320%26dopt%3DAbstract CONCLUSIONS: A large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth. PMID: 20525320 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3641652 Thu, 03 Jun 2010 23:00:00 +0100 3641652 http://www.medworm.com/index.php?rid=3641653&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%3D20525260%26dopt%3DAbstract CONCLUSIONS: In general, our results show that it is possible to combine QTL detection and introgression even in outbred species. Separating QTL mapping and introgression processes is often thought to be longer and more costly. However, using a combined process saves at least one generation. With respect to the linkage drag and obligatory drag, the results of the combined detection and introgression scheme are very similar to those of traditional introgression schemes. PMID: 20525260 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3641653 Wed, 02 Jun 2010 23:00:00 +0100 3641653 http://www.medworm.com/index.php?rid=3622657&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%3D20509901%26dopt%3DAbstract Authors: Hayes H, Boichard D ABSTRACT: It is now nearly a year and a half since the journal Genetics Selection Evolution (GSE) is published as an open access journal and it is time for an update on its activity and to share some changes on the editorial board. PMID: 20509901 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3622657 Thu, 27 May 2010 23:00:00 +0100 3622657 http://www.medworm.com/index.php?rid=3589297&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%3D20482755%26dopt%3DAbstract CONCLUSION: In conclusion, further selection of ALRR-ALRR animals will not result in an overall increase of AS prevalence in the French sheep population although this genotype is clearly susceptible to AS. However the probability of detecting AS cases in flocks participating in genetic breeding programme against CS should be considered. PMID: 20482755 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3589297 Mon, 17 May 2010 23:00:00 +0100 3589297 http://www.medworm.com/index.php?rid=3568394&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%3D20465803%26dopt%3DAbstract CONCLUSIONS: Heritabilities for length of productive life were similar with continuous time and grouped data models in both breeds. Based on these results and because grouped data models better reflect the economical needs in meat animals, we conclude that grouped data models are more appropriate in pig. PMID: 20465803 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3568394 Wed, 12 May 2010 23:00:00 +0100 3568394 http://www.medworm.com/index.php?rid=3560971&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%3D20459708%26dopt%3DAbstract CONCLUSIONS: Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity. PMID: 20459708 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3560971 Sun, 09 May 2010 23:00:00 +0100 3560971 http://www.medworm.com/index.php?rid=3524598&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%3D20429884%26dopt%3DAbstract This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far. PMID: 20429884 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3524598 Wed, 28 Apr 2010 23:00:00 +0100 3524598 http://www.medworm.com/index.php?rid=3398370&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%3D20302681%26dopt%3DAbstract The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased. The accuracy decreased more when QTL had different variance values than when all QTL had an equal variance. The accuracy of MEBV calculated with PLSR was affected neither by the number of QTL nor by the distribution of QTL variance. Additional simulations and analyses showed that these conclusions were not affected by the number of individuals in th... Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3398370 Mon, 22 Mar 2010 00:00:00 +0100 3398370 http://www.medworm.com/index.php?rid=3398369&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%3D20307301%26dopt%3DAbstract CONCLUSIONS: The proposed method is computationally very efficient and suitable for marker-assisted breeding value estimation in large livestock populations including effects of a number of known QTL. Marker-assisted breeding value estimation using predicted haplotypes increases accuracy especially for traits with low heritability. PMID: 20307301 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3398369 Mon, 22 Mar 2010 00:00:00 +0100 3398369 http://www.medworm.com/index.php?rid=3398378&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%3D20302616%26dopt%3DAbstract CONCLUSIONS: We have shown that variance components in the residual variance part of a linear mixed model can be estimated using a DHGLM approach. The method enables analyses of animal models with large number of observations. An important future development of the DHGLM methodology is to include the genetic correlation between the random effects in the mean and residual variance parts of the model as a parameter of the DHGLM. PMID: 20302616 [PubMed - as supplied by publisher] (Source: Genet Sel Evol) Genet Sel Evol journals http://www.medworm.com/rss/comments.php?id=3398378 Fri, 19 Mar 2010 00:00:00 +0100 3398378 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