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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com rosangela.lacerda@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite; Embrapa Pecuária Sudeste. |
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Data corrente: |
17/12/2013 |
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Data da última atualização: |
15/06/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
McCLURE, M. C.; SONSTEGARD, T. S.; WIGGANS, G. R.; EENENNAAM, A. L. V.; WEBER, K. L.; PENEDO, C. T.; BERRY, D. P.; FLYNN, J.; GARCIA, J. F.; CARMO, A. S.; REGITANO, L. C. de A.; ALBUQUERQUE, M.; SILVA, M. V. G. B.; MACHADO, M. A.; COFFEY, M.; MOORE, K.; BOSCHER, M. Y.; GENESTOUT, L.; MAZZA, R.; TAYLOR, J. F.; SCHNABEL, R. D.; SIMPSON, B.; MARQUES, E.; McEWAN, J. C.; CROMIE, A.; COUTINHO, L. L.; KUEHN, L. A.; KEELE, J. W.; PIPER, E. K.; COOK, J.; WILLIAMS, R.; TASSELL, C. P. V. |
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Afiliação: |
MATTHEW C. McCLURE, USDA; TAD S. SONSTEGARD, USDA; GEORGE R. WIGGANS, USDA; ALISON L. VAN EENENNAAM, University of California - Davis; KRISTINA L. WEBER, University of California-Davis; CECILIA T. PENEDO, University of California-Davis; DONAGH P. BERRY, Animal and Grassland Research and Innovation Centre, Ireland; JOHN FLYNN, Weatherbys DNA Laboratory, Ireland; JOSÉ F. GARCIA, UNESP; ADRIANA S. CARMO, Deoxi Biotecnologia, Araçatuba; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; MILLA ALBUQUERQUE, USP; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; MARCO ANTONIO MACHADO, CNPGL; MIKE COFFEY, SRUC, Scotland; KIRSTY MOORE, SRUC, Scotland; MARIE-YVONNE BOSCHER, LABOGENA, France; LUCIE GENESTOUT, LABOGENA, France; RAFFAELE MAZZA, Italian Breeders Association, Roma; JEREMY F. TAYLOR, University of Missouri-Columbia; ROBERT D. SCHNABEL, University of Missouri-Columbia; BARRY SIMPSON, GeneSeek, Neogen Company, Lincoln, USA; ELISA MARQUES, GeneSeek, Neogen Company, Lincoln, USA; JOHN C. McEWAN, AgResearch, Invermay Agricultural Centre, New Zealand; ANDREW CROMIE, Irish Cattle Breeding Federation, Ireland; LUIZ L. COUTINHO, ESALQ/USP; LARRY A. KUEHN, USDA-ARS; JOHN W. KEELE, USDA-ARS; EMILY K. PIPER, University of Queensland, Australia; JIM COOK, University of New England, Australia; ROBERT WILLIAMS, American-International Charolais Association, USA; CURTIS P. VAN TASSELL, USDA. |
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Título: |
Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
Frontiers in Genetics, v. 4, n. 176, 2013. |
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Páginas: |
11 p. |
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Idioma: |
Inglês |
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Conteúdo: |
To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset. MenosTo assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS ... Mostrar Tudo |
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Palavras-Chave: |
Imputation; Microsatellite; Parentage verification; SNP; STR. |
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Categoria do assunto: |
G Melhoramento Genético |
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Marc: |
LEADER 03360naa a2200565 a 4500
001 2154448
005 2023-06-15
008 2013 bl uuuu u00u1 u #d
100 1 $aMcCLURE, M. C.
245 $aImputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds.$h[electronic resource]
260 $c2013
300 $a11 p.
520 $aTo assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
653 $aImputation
653 $aMicrosatellite
653 $aParentage verification
653 $aSNP
653 $aSTR
700 1 $aSONSTEGARD, T. S.
700 1 $aWIGGANS, G. R.
700 1 $aEENENNAAM, A. L. V.
700 1 $aWEBER, K. L.
700 1 $aPENEDO, C. T.
700 1 $aBERRY, D. P.
700 1 $aFLYNN, J.
700 1 $aGARCIA, J. F.
700 1 $aCARMO, A. S.
700 1 $aREGITANO, L. C. de A.
700 1 $aALBUQUERQUE, M.
700 1 $aSILVA, M. V. G. B.
700 1 $aMACHADO, M. A.
700 1 $aCOFFEY, M.
700 1 $aMOORE, K.
700 1 $aBOSCHER, M. Y.
700 1 $aGENESTOUT, L.
700 1 $aMAZZA, R.
700 1 $aTAYLOR, J. F.
700 1 $aSCHNABEL, R. D.
700 1 $aSIMPSON, B.
700 1 $aMARQUES, E.
700 1 $aMcEWAN, J. C.
700 1 $aCROMIE, A.
700 1 $aCOUTINHO, L. L.
700 1 $aKUEHN, L. A.
700 1 $aKEELE, J. W.
700 1 $aPIPER, E. K.
700 1 $aCOOK, J.
700 1 $aWILLIAMS, R.
700 1 $aTASSELL, C. P. V.
773 $tFrontiers in Genetics$gv. 4, n. 176, 2013.
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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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| 4. |  | SANTOS, G. R.; KORNDORFER, G.; RANGEL, P. H. N. Influência de fontes de silício sobre a brusone foliar, brusone das panículas, mancha-dos-grãos e produtividade do arroz irrigado. In: CONGRESSO DA CADEIA PRODUTIVA DE ARROZ, 1.; REUNIÃO NACIONAL DE PESQUISA DE ARROZ - RENAPA, 7., 2002, Florianópolis. Anais... Santo Antônio de Goiás: Embrapa Arroz e Feijão, 2002. p. 480-483. (Embrapa Arroz e Feijão. Documentos, 134).| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 10. | | SANTOS, G. R. dos; SILVA, E. M. R. da; SAGGIN JUNIOR, O. J.; WAGNER, E. R. Multiplicação de fungos micorrízicos arbusculares nativos em sistema on farm. In: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 36., 2017, Belém, PA. Amazônia e seus solos: peculiaridades e potencialidades. Belém, PA: SBCS, 2017.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agrobiologia. |
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| 11. | | BATISTA, A. P. B.; SANTOS, G. R.; MELLO, J. M.; SILVA, K. E. da; KALEITA, A. Geoestatística no R: um estudo comparativo entre dois scripts. In: SIMPÓSIO DE GEOESTATÍSTICA APLICADA EM CIÊNCIAS AGRÁRIAS, 4., 2015, Botucatu. Anais... Botucatu, SP: UNESP, 2015. 5 p.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 12. | | CARLOTTO, H. S.; SANTOS, G. R.; REIS FILHO, J. C. D.; PRABHU, A. S. Efeito do silício, nitrogênio e do tratamento de sementes sobre o controle das principais doenças, produtividade e qualidade dos grãos do arroz irrigado. Fitopatologia Brasileira, v. 26, p. 411, ago. 2001. Suplemento, ref. 545. Edição dos Resumos do XXXIV Congresso Brasileiro de Fitopatologia, São Pedro, ago. 2001.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 13. | | ITUASSÚ, D. R.; SANTOS, G. R. S. dos; ROUBACH, R.; PEREIRA FILHO, M. Desenvolvimento de tambaqui submetido a períodos de privação alimentar. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 39, n. 12, p. 1199-1203, dezembro 2004 Título em inglês: Growth of tambaqui submitted to different feed deprivation periods.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 15. | | WANDERLEY, B. S.; SANTOS, G. R.; RANGEL, P. H. N.; GOMES, J. C. Resistência de diferentes genótipos de arroz irrigado às principais doenças no Projeto Formoso, Tocantins. Fitopatologia Brasileira, v. 26, p. 413, ago. 2001. Suplemento, ref. 553. Edição dos Resumos do XXXIV Congresso Brasileiro de Fitopatologia, São Pedro, ago. 2001.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 16. | | SANTOS, G. R.; RANGEL, P. H. N.; CAMARA, R. K.; SANTIAGO, C. M. Resistência de genótipos de arroz irrigado à queima e mancha das bainhas em condições de campo, no Estado do Tocantins. In: CONGRESSO DA CADEIA PRODUTIVA DE ARROZ, 1.; REUNIÃO NACIONAL DE PESQUISA DE ARROZ - RENAPA, 7., 2002, Florianópolis. Anais... Santo Antônio de Goiás: Embrapa Arroz e Feijão, 2002. p. 289-292. (Embrapa Arroz e Feijão. Documentos, 134).| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 18. | | SANTOS, G. R.; CAFÉ FILHO, A. C. C.; REIS, A.; LOPES, C. A. Progresso do crestamento gomoso do caule da melancia (Didymella bryoniae) em campo comercial. Fitopatologia Brasileira, Brasília, v. 28, p. 226, ago. 2003. Suplemento. Trabalho apresentado no 36º Congresso Brasileiro de Fitopatologia, 2003, Brasília. Resumo.| Biblioteca(s): Embrapa Hortaliças. |
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| 19. | | SANTOS, G. R.; CASTRO, V. C. G.; FERNANDES, P. C. C.; MARTORANO, L. G. Estimativas de presença de gases e conteúdo ruminal em bubalinos suplementados com farelo dendê e óleo de palmiste. In: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA, 19.; SEMINÁRIO DE PÓS-GRADUAÇÃO DA EMBRAPA AMAZÔNIA ORIENTAL, 3., 2015, Belém, PA. Anais. Belém, PA: Embrapa Amazônia Oriental, 2015. p. 86-90.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| Registros recuperados : 103 | |
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