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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Gado de Corte. |
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Data corrente: |
06/12/2011 |
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Data da última atualização: |
24/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
MUDADO, M. de A.; REGITANO, L. C. de A.; SIQUEIRA, F.; ROSA, A. do N.; HIGA, R.; TIZIOTO, P. C. |
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Afiliação: |
MAURÍCIO 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. |
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Título: |
Finding a minimal set of SNPs for paternity identification in Nelore cattle. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
In: 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. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês |
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Notas: |
X-MEETING, 2011. |
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Conteúdo: |
Cattle 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. MenosCattle 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 Beadc... Mostrar Tudo |
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Palavras-Chave: |
Estudos de genoma; Marcadores SNP; Polimorfismo de nucleotídeo único. |
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Thesagro: |
Gado Nelore. |
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Thesaurus Nal: |
Cattle; Genome; Nellore; Single nucleotide polymorphism. |
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Categoria do assunto: |
--
L Ciência Animal e Produtos de Origem Animal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/49431/1/SNPpaternity.pdf
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Marc: |
LEADER 03772nam a2200289 a 4500
001 1908694
005 2020-01-24
008 2011 bl uuuu u00u1 u #d
100 1 $aMUDADO, M. de A.
245 $aFinding a minimal set of SNPs for paternity identification in Nelore cattle.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional$c2011
300 $aNão paginado.
500 $aX-MEETING, 2011.
520 $aCattle 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.
650 $aCattle
650 $aGenome
650 $aNellore
650 $aSingle nucleotide polymorphism
650 $aGado Nelore
653 $aEstudos de genoma
653 $aMarcadores SNP
653 $aPolimorfismo de nucleotídeo único
700 1 $aREGITANO, L. C. de A.
700 1 $aSIQUEIRA, F.
700 1 $aROSA, A. do N.
700 1 $aHIGA, R.
700 1 $aTIZIOTO, P. C.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 56 | |
| 1. |  | BARRETO, J. R.; BERENGUER, E.; FERREIRA, J. N.; JOLY, C. A.; MALHI, Y.; SEIXAS, M. M. M. de; BARLOW, J. Assessing invertebrate herbivory in human-modified tropical forest canopies. Ecology and Evolution, v. 11, n. 9, p. 4012-4022, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
|    |
| 2. | | MORAIS, T. M. O. de; BERENGUER, E.; BARLOW, J.; FRANÇA, F.; LENNOX, G. D.; MALHI, Y.; ROSSI, L. C.; SEIXAS, M. M. M. de; FERREIRA, J. N. Leaf-litter production in human-modified Amazonian forests following the El Niño-mediated drought and fires of 2015-2016. Forest Ecology and Management, v. 496, Article 119441, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
|  |
| 3. | | BERENGUER, E.; MALHI, Y.; BRANDO, P.; CORDEIRO, A. C. N.; FERREIRA, J. N.; FRANÇA, F.; ROSSI, L. C.; SEIXAS, M. M. M. de; BARLOW, J. Tree growth and stem carbon accumulation in human-modified Amazonian forests following drought and fire. Philosophical Transactions of the Royal Society B, v. 373, n. 1760, p. 1-8, Nov. 2018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
| |
| 4. | | ANDRADE, V. S.; COSTA, J. N.; COSTA, A. L.; FERREIRA, W. M.; SILVA, M. A.; GONÇALVES, P. H.; ATAYDES JUNIOR, J.; MALHI, Y. Variação do dióxido de carbono no interior de um manguezal na Amazônia legal. In: CONFERÊNCIA CIENTÍFICA INTERNACIONAL AMAZÔNIA EM PERSPECTIVA, 2008, Manaus. ciência integrada para um futuro sustentável: conference abstracts. Manaus: LBA/GEOMA/PPBIo, 2008.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Milho e Sorgo. |
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| 5. | | WITHEY, K.; BERENGUER, E.; PALMEIRA, A. F.; ESPÍRITO-SANTO, F. D. B.; LENNOX, G. D.; SILVA, C. V. J.; ARAGÃO, L. E. O. C.; FERREIRA, J. N.; FRANÇA, F.; MALHI, Y.; ROSSI, L. C.; BARLOW, J. Quantifying immediate carbon emissions from El Ninõ-mediated wildfires in humid tropical forests. Philosophical Transactions of the Royal Society B, v. 373, n. 1760, p. 1-11, Nov. 2018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 6. | | WU, J.; CHAVANA-BRYANT, C.; PROHASKA, N.; SERBIN, S. P.; GUAN, K.; ALBERT, L. P.; YANG, X.; LEEUWEN, W. J. D. van; GARNELLO, A. J.; MARTINS, G.; MALHI, Y.; GERARD, F.; OLIVEIRA JUNIOR, R. C. de; SALESKA, S. R. Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests. New Phytologist, v. 214, n. 3, p. 1033-1048, May 2017.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 7. | | MALHI, Y.; MELACK, J.; GATTI, L. V.; OMETTO, J.; KESSELMEIER, J.; WOLFF, S.; ARAGÃO, L. E. O.; COSTA, M.; SALESKA, S.; PANGALA, S. R.; BASSO, L. S.; RIZZO, L.; ARAUJO, A. C. de; RESTREPO-COUPE, N. Biogeochemical cycles of the Amazon. In: SCIENCE panel for the Amazon: Amazon assessment report 2021: part I: The Amazon as a regional entity of the Earth system. New York, NY: United Nations Sustainable Development Solutions Network, 2021. Cap. 6, pag. irregular.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 8. | | RESTREPO-COUPE, N.; LEVINE, N. M.; CHRISTOFFERSEN, B. O.; ALBERT, L. P.; WU, J.; COSTA, M. H.; GALBRAITH, D.; IMBUZEIRO, H.; MARTINS, G.; ARAUJO, A. C. da; MALHI, Y. S.; ZENG, X.; MOORCROFT, P.; SALESKA, S. R. Do dynamic global vegetation models capture the seasonality of carbon fluxes in the Amazon basin? A data-model intercomparison. Global Change Biology, v. 23, n. 1, p. 191-208, Jan. 2017.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 9. | | LEWIS, S. L.; PHILLIPS, O. L.; BAKER, T. R.; LLOYD, J.; MALHI, Y.; ALMEIDA, S.; HIGUCHI, N.; LAURANCE, W. F.; NEILL, D. A.; SILVA, J. N. M.; TERBORGH, J.; LEZAMA, A. T.; VÁSQUEZ MARTÍNEZ, R.; BROWN, S.; CHAVE, J.; KUEBLER, C.; NÚÑEZ VARGAS, P.; VINCETI, B. Concerted changes in tropical forest structure and dynamics: evidence from 50 South American long-term plots. Philippine Transactions of Royal Society of London, B, v. 359, n. 1443, p. 421-436, 2004.| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 10. | | ALVALA, R. C. S.; MANZI, A. O.; SA, L. D. A; MURTY, P. R. V. K.; GIELOW, R.; ARLINO, P. R. A.; ALVALA, P. C.; LIMA, I. D. T.; MARQUES FILHO, E. P. M.; SAMBATTI, S. B. M.; RANDOW, C. von; SOUZA, A. de S; KASSAR, E.; MALHI, Y. S.; KRUIJT, B.; MEIRELLES, M. L. Projeto interdisciplinar do Pantanal - fase umida (IPE - 1). In: CONGRESSO BRASILEIRO DE METEOROLOGIA, 10.; CONGRESSO DA FLISMET, 8., 1998, Brasilia, DF. [Anais]. [S.l.: s.n., 1998?]. n.p.| Biblioteca(s): Embrapa Cerrados. |
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| 11. | | POWELL, T. I.; GALBRAITH, D. R.; CHRISTOFFERSEN, B. O.; HARPER, A.; IMBUZEIRO, H. M. A.; ROWLAND, L.; ALMEIDA, S.; BRANDO, P. M.; COSTA, A. C. L. da; COSTA, M. H.; LEVINE, N. M.; MALHI, Y.; SALESKA, S. R.; SOTTA, E.; WILLIAMS, M.; MEIR, P.; MOORCROFT, P. R. Confronting model predictions of carbon fluxes with measurements of Amazon forests subjected to experimental drought. New Phytologist, Cambridge, Jul. 2013.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amapá. |
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| 12. | | COSTA, A. C. L. da; ALMEIDA, S. S. de; CARVALHO, C. R.; MEIR, P.; MALHI, Y.; COSTA, R. F. da; SILVA JUNIOR, J. de A. da; COSTA, M. C. da; TANAKA, B. T.; FISHER, R. A.; SOTTA, E. D.; OLIVEIRA, L. L.; GONÇALVES, P. H. L.; BRAGA, A. P.; BARRETO, P. N. Experimento Esecaflor-LBA em Caxiuanã. In: LISBOA, P. L. B. (Org.). Caxiuanã: desafios para a conservação de uma Floresta Nacional na Amazônia. Belém, PA: Museu Paraense Emílio Goedi, 2009. p. 45-90.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Amapá; Embrapa Amazônia Oriental. |
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| 13. | | ROWLAND, L.; COSTA, A. C. L. da; GALBRAITH, D. R.; OLIVEIRA, R. S.; BINKS, O. J.; OLIVEIRA, A. A. R.; PULLEN, A. M.; DOUGHTY, C. E.; METCALFE, D. B.; VASCONCELOS, S. S.; FERREIRA, L. V.; MALHI, Y.; GRACE, J.; MENCUCCINI, M.; MEIR, P. Death from drought in tropical forests is triggered by hydraulics not carbon starvation. Nature, v. 528, N. 7580, p. 119-122, 3 Dec. 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 14. | | BAKER, T. R.; PHILLIPS, O. L.; MALHI, Y.; ALMEIDA, S.; ARROYO, L.; DI FIORE, A.; ERWIN, T.; HIGUCHI, N.; KILLEEN, T. J.; LAURENCE, S. G.; LAURENCE, W. F.; LEWIS, S. L.; MONTEAGUDO, A.; NEILL, D. A.; NÚNEZ VARGAS, P.; PITMAN, N. C. A.; SILVA, J. N. M.; VÁSQUEZ MARTÍNEZ, R. Increasing biomass in Amazonian forest plots. Philosophical Transactions of the Royal Society of London. B, v. 359, n. 1443, p. 353-365, Mar. 2004. il.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 15. | | BERENGUER, E.; LENNOX, G. D.; FERREIRA, J. N.; MALHI, Y.; ARAGÃO, L. E. O. C.; BARRETO, J. R.; ESPÍRITO-SANTO, F. del B.; FIGUEIREDO, A. E. S.; FRANÇA, F.; GARDNER, T. A.; JOLY, C. A.; PALMEIRA, A. F.; QUESADA, C. A.; ROSSI, L. C.; SEIXAS, M. M. M. de; SMITH, C. C.; WITHEY, K.; BARLOW, J. Tracking the impacts of El Niño drought and fire in human-modified Amazonian forests. PNAS, v. 118, n. 30, e201937711, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 16. | | ESPÍRITO-SANTO, F. D. B.; GLOOR, M.; KELLER, M.; MALHI, Y.; SAATCHI, S.; NELSON, B.; OLIVEIRA JUNIOR, R.; PEREIRA, C.; LLOYD, J.; FROLKING, S.; PALACE, M.; SHIMABUKURO, Y.; DUARTE, V.; MENDONZA, A.; LOPEZ-GONZALEZ, G.; BAKER, T. R.; FELDPAUSCH, T.; ASNER, G.; BOYD, D.; PHILLIPS, O. The spectrum of natural forest disturbances and the Amazon forest carbon balance. In: AGU FALL MEETING, 2014, San Francisco. [Proceedings]. [San Francisco]: AGU, 2014.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 17. | | ESPÍRITO-SANTO, F. D. B.; GLOOR, M.; KELLER, M.; MALHI, Y.; SAATCHI, S.; NELSON, B.; OLIVEIRA JUNIOR, R. C.; PEREIRA, C.; LLOYD, J.; FROLKING, S.; PALACE, M.; SHIMABUKURO, Y. E.; DUARTE, V.; MONTEAGUDO MENDOZA, A.; LÓPEZ-GONZÁLEZ, G.; BAKER, T. R.; FELDPAUSCH, T. R.; BRIENEN, R. J. W.; ASNER, G. P.; BOYD, D. S.; PHILLIPS, O. L. Size and frequency of natural forest disturbances and the Amazon forest carbon balance. Nature Communications, v. 5, art. n. 3434, 18 Mar. 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental; Embrapa Territorial. |
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| 18. | | RESTREPO-COUPE, N.; ALBERT, L. P.; LONGO, M.; BAKER, I.; LEVINE, N. M.; MERCADO, L. M.; ARAUJO, A. C. de; CHRISTOFFERSEN, B. O.; COSTA, M. H.; FITZJARRALD, D. R.; GALBRAITH, D.; IMBUZEIRO, H.; MALHI, Y.; RANDOW, C. von; ZENG, X.; MOORCROFT, P.; SALESKA, S. R. Understanding water and energy fluxes in the Amazonia: Lessons from an observation-model intercomparison. Global Change Biology, v. 27, n. 9, p. 1802-1819, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 19. | | MALHI, Y.; WOOD, D.; BAKER, T. R.; WRIGHT, J.; PHILLIPS, O. L.; COCHRANE, T.; MEIR, P.; CHAVE, J.; ALMEIDA, S.; ARROYO, L.; HIGUCHI, N.; KILLEEN, T. J.; LAURANCE, S. G.; LEWIS, S. L.; MONTEAGUDO, A.; NEILL, D. A.; VARGAS, P. N.; PITMAN, N. C. A.; QUESADA, C. A.; SALOMÃO, R.; SILVA, J. N. M.; LEZAMA, A. T.; TERBORGH, J.; MARTÍNEZ, R. V.; VINCETI, B. The regional variation of aboveground live biomass in old-growth Amazonian forests. Global Change Biology, v. 12, n. 7, p. 1107-1138, July 2006.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 20. | | BAKER, T. R.; PHILLIPS, O. L.; MALHI, Y.; ALMEIDA, S.; ARROYO, L.; DI FIORE, A.; ERWIN, T.; KILLEEN, T. J.; LAURANCE, S. G.; LAURANCE, W. F.; LEWIS, S. L.; LLOYD, J.; MONTEAGUDO, A.; NEILL, D. A.; PATIÑO, S.; PITMAN, N. C. A.; SILVA, J. N. M.; MARTÍNEZ, R. V. Variation in wood density determines spatial patterns in Amazonian forest biomass. Global Change Biology, v. 10, p. 545-562, 2004. il.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| Registros recuperados : 56 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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