Use este identificador para citar ou linkar para este item: http://www.alice.cnptia.embrapa.br/alice/handle/doc/908694
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dc.contributor.authorMUDADO, M. de A.pt_BR
dc.contributor.authorREGITANO, L. C. de A.pt_BR
dc.contributor.authorSIQUEIRA, F.pt_BR
dc.contributor.authorROSA, A. do N.pt_BR
dc.contributor.authorHIGA, R.pt_BR
dc.contributor.authorTIZIOTO, P. C.pt_BR
dc.date.accessioned2011-12-06T11:11:11Zpt_BR
dc.date.available2011-12-06T11:11:11Zpt_BR
dc.date.created2011-12-06pt_BR
dc.date.issued2011pt_BR
dc.identifier.citationIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011.pt_BR
dc.identifier.urihttp://www.alice.cnptia.embrapa.br/alice/handle/doc/908694pt_BR
dc.descriptionCattle breeding programs often demand pedigree information to associate the herdability of genetic markers to animal performance, like milk and beef quality or disease predisposition. Paternity mistakes are a common problem in cattle herds and genetic markers have been used in parentage exclusion tests for resolving pedigree disagreements. The most common markers used in these tests are microsatellites and SNPs (Single Nucleotide Polymorphisms). SNPs have also been used in GWAS (Genome Wide Association Studies) based on the novel commercial high density bovine SNP chips. Such platforms possess around 770k SNPs which can be used also as a rich resource for paternity exclusion tests. However genotyping such a large amount of SNPs for individuals of a whole flock to perform paternity exclusion tests is not economically feasible. Furthermore, many of these SNPs are non-informative because of high levels of linkage disequilibrium among them and because of low levels of minimum allele frequency (MAF), call rate and genotyping accuracy (GC score). In this work we devised a method to select a minimal set of SNPs from Nelore cattle samples, which are highly informative and are independent, so they could be used in a small genotyping panel for paternity exclusion tests. Samples from 32 Nelore sires chosen to represent the main genealogies marketed in Brazil and 762 nelore bulls produced by artificial insemination were genotyped. The platform used was Illumina BovineHD Genotyping Beadchip that has ~770k SNPs. The algorithm developed first run a quality control filter that selected, from the starting 770k SNPs, only markers that: i) were in Hardy Weinberg equilibrium, ii) had MAF>0.4, iii) had Illumina's accuracy GC Score > 0.8, iv) had call rate >=0.95 and v) had a D?<0.5 with other marker. 126 pairs of father-sons (151 samples), with the paternity already resolved, were selected to compose the test set. The other 643 animals that were left composed the training set. From the training set, 325 SNPs passed the quality control filter. The selected 325 SNPs were used in the test set to perform paternity tests, following the methodology adapted from Fung et al., 2002. The results show that values of the combined power of exclusion (Q) for all markers, between 0.2 and 0.7, gives the correct paternity answer for all pairs of individuals. We believe that this set of 325 SNPs could be used in a small genotyping chip to perform paternity exclusion tests for Nelore cattle; a low-cost solution to be used by cattle producers to correct paternity disagreements. All procedures were performed using the R language in a local linux server machine.pt_BR
dc.language.isoengeng
dc.rightsopenAccesseng
dc.subjectMarcadores SNPpt_BR
dc.subjectEstudos de genomapt_BR
dc.subjectPolimorfismo de nucleotídeo únicopt_BR
dc.titleFinding a minimal set of SNPs for paternity identification in Nelore cattle.pt_BR
dc.typeResumo em anais e proceedingspt_BR
dc.date.updated2020-01-24T11:11:11Zpt_BR
dc.subject.thesagroGado Nelorept_BR
dc.subject.nalthesaurusCattlept_BR
dc.subject.nalthesaurusNellorept_BR
dc.subject.nalthesaurusSingle nucleotide polymorphismpt_BR
dc.subject.nalthesaurusGenomept_BR
dc.description.notesX-MEETING, 2011.pt_BR
dc.format.extent2Não paginado.pt_BR
riaa.ainfo.id908694pt_BR
riaa.ainfo.lastupdate2020-01-24 -02:00:00pt_BR
dc.contributor.institutionMAURÍCIO DE ALVARENGA MUDADO, CPPSE; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; FABIANE SIQUEIRA, CNPGC; ANTÔNIO DO NASCIMENTO ROSA, CNPGC; ROBERTO HIROSHI HIGA, CNPTIA; POLYANA CRISTINE TIZIOTO, UFSCar.pt_BR
Aparece nas coleções:Resumo em anais de congresso (CNPTIA)

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