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Registro Completo |
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Biblioteca(s): |
Embrapa Pecuária Sudeste. |
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Data corrente: |
04/09/2017 |
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Data da última atualização: |
21/05/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
KASARAPU, P.; PORTO NETO, L. R.; FORTES, M. R. S.; LEHNERT, S. A.; MUDADU, M. de A.; COUTINHO, L. L.; REGITANO, L. C. de A.; GEORGE, A.; REVERTER, A. |
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Afiliação: |
Parthan Kasarapu, Agriculture and Food/CSIRO; Laercio Ribeiro Porto Neto, Agriculture and Food/CSIRO; Marina R. S. Fortes, The University of Queensland; Sigrid A. Lehnert, Agriculture and Food/CSIRO; MAURICIO DE ALVARENGA MUDADU, CNPTIA; Luiz Lehmann Coutinho, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; Andrew George, Agriculture and Food/CSIRO; Antonio Reverter, Agriculture and Food/CSIRO. |
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Título: |
The Bos taurus-Bos indicus balance in fertility and milk related genes. |
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Ano de publicação: |
2017 |
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Fonte/Imprenta: |
PLOS one, v. 12, n. 8, p. 1-20, 2017. |
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DOI: |
https://doi.org/10.1371/journal.pone.0181930 |
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Idioma: |
Inglês |
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Conteúdo: |
Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene?s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility. MenosNumerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene?s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios w... Mostrar Tudo |
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Palavras-Chave: |
Hardy-Weinberg equilibrium. |
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Thesagro: |
Bos Indicus; Bos Taurus. |
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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/163369/1/journal.pone.0181930.pdf
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Marc: |
LEADER 02467naa a2200265 a 4500
001 2074938
005 2019-05-21
008 2017 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1371/journal.pone.0181930$2DOI
100 1 $aKASARAPU, P.
245 $aThe Bos taurus-Bos indicus balance in fertility and milk related genes.$h[electronic resource]
260 $c2017
520 $aNumerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene?s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.
650 $aBos Indicus
650 $aBos Taurus
653 $aHardy-Weinberg equilibrium
700 1 $aPORTO NETO, L. R.
700 1 $aFORTES, M. R. S.
700 1 $aLEHNERT, S. A.
700 1 $aMUDADU, M. de A.
700 1 $aCOUTINHO, L. L.
700 1 $aREGITANO, L. C. de A.
700 1 $aGEORGE, A.
700 1 $aREVERTER, A.
773 $tPLOS one$gv. 12, n. 8, p. 1-20, 2017.
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Registro original: |
Embrapa Pecuária Sudeste (CPPSE) |
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| Registros recuperados : 15 | |
| 1. |  | GRISOLIA, A. B.; D´ANGELO, G. T.; PORTO NETO, L. R.; SIQUEIRA, F.; GARCIA, J. F. Myostatin (GDF8) single nucleotide polymorphisms in Nellore cattle. Genetics and Molecular Research, Ribeirão Preto, v. 8, n. 3, p. 822-830, 2009.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Gado de Corte. |
|    |
| 2. | | KASARAPU, P.; PORTO-NETO, L. R.; FORTES, M. R. S.; LEHNERT, S. A.; MUDADU, M. de A.; COUTINHO, L.; REGITANO, L. C. de A.; GEORGE, A.; REVERTER, A. The Bos taurus-Bos indicus balance in fertility and milk related genes. Plos One, v. 12, n. 8, p. 1-20, 2017. Artigo e0181930. Na publicação: Mauricio A. Mudadu, Luciana Regitano.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 3. | | UTSUNOMIYA, Y. T.; MILANESI, M.; FORTES, M. R. S.; PORTO?NETO, L. R.; UTSUNOMIYA, A. T. H.; SILVA, M. V. G. B.; GARCIA, J. F.; AJMONE-MARSAN, P. Genomic clues of the evolutionary history of Bos indicus cattle. Animal Genetics, v. 50, n. 6, p. 557-568, 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Gado de Leite. |
|  |
| 4. | | PORTO NETO, L. R.; SONSTEGARD, T. S.; LIU, G.; BICKHART, D.; GONDRO, C.; SILVA, M. V. G. B.; UTSUNOMIYA, Y. T.; GARCIA, J. F.; VAN TASSELL, C. P. Genomic divergence of indicine and taurine cattle identified through high-density SNP gebotyping. In: ADSA-ASAS ANNUAL MEETINGS, 2013, Indianápolis, Indiana. Abstracts... Indianápolis: [s.n.], 2013.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 5. | | KASARAPU, P.; PORTO NETO, L. R.; FORTES, M. R. S.; LEHNERT, S. A.; MUDADU, M. de A.; COUTINHO, L. L.; REGITANO, L. C. de A.; GEORGE, A.; REVERTER, A. The Bos taurus-Bos indicus balance in fertility and milk related genes. PLOS one, v. 12, n. 8, p. 1-20, 2017.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 6. | | KIJAS, J. W.; LENSTRA, J. A.; HAYES, B.; BOITARD, S.; PORTO NETO, L. R.; CRISTOBAL, M. S.; SERVIN, B.; MCCULLOCH, R.; WHAN, V.; GIETZEN, K.; PAIVA, S. R.; BARENDSE, W.; CIANI, E.; RAADSMA, H.; MCEWAN, J.; DALRYMPLE, B. Genome-wide analysis of the world's sheep breeds reveals high levels of historic misture and strung recent selection. Plos Biology, v. 10, n. 2, e1001258, 2012. (Open access)| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 7. | | KIJAS, J. W.; LENSTRA, J. A.; HAYES, B.; BOITARD, S.; PORTO NETO, L. R.; CRISTOBAL, M. S.; SERVIN, B.; MCCULLOCH, R.; WHAN, VICKI; GIETZEN, K.; PAIVA, S. R.; BARENDSE, W.; CIANI, E.; RAADSMA, H.; MCEWAN, J.; DALRYMPLE, B. Genome-wide analysis of the world?s sheep breeds reveals high levels of historic mixture and strong recent selection. Plos Biology, v. 10, n. 2, P31, 2012. (Open access)| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 8. | | PORTO-NETO, L. R.; SONSTEGARD, T. S.; LIU, G. E.; BICKHART, D. M.; SILVA, M. V. G. B.; MACHADO, M. A.; UTSUNOMIYA, Y. T.; GARCIA, J. F.; GONDRO, C.; VAN TASSELL, C. P. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics, v. 14, article 876, 2013. Disponível em: http://www.biomedcentral.com/1471-2164/14/876| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 9. | | GOUVEIA, G. C.; RIBEIRO, V. M. P.; FORTES, M. R. S.; RAIDAN, F. S. S.; REVERTER, A.; PORTO-NETO, L. R.; MORAES, M. M. de; GONÇALVES, D. R.; SILVA, M. V. G. B.; TORAL, F. L. B. Unravelling the genetic variability of host resilience to endo and ectoparasites in Nellore commercial herds. Genetics Selection Evolution, v. 55, article 81, 2023.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 10. | | UTSUNOMIYA, Y. T.; CARMO, A. S. do; CARVALHEIRO, R.; NEVES, H. H. R.; MATOS, M. C.; ZAVAREZ, L. B.; O'BRIEN, A. M. P.; SÖLKNER, J.; McEWAN, J. C.; COLE, J. B.; TASSEL, C. P. V.; SCHENKEL, F. S.; SILVA, M. V. G. B.; PORTO NETO, L. R.; SONSTEGARD, T. S.; GARCIA, J. F. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genetics, London, v. 14, article 52, 2013.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 11. | | UTSUNOMIYA, Y. T.; CARMO, A. S.; NEVES, H. H. R.; CARVALHEIRO, R.; MATOS, M. C.; ZAVAREZ, L. B.; ITO, P. K. R. K.; O'BRIEN, A. M. P.; SOLKNER, J.; PORTO-NETO, L. R.; SCHENKEL, F. S.; McEWAN, J.; COLE, J. B.; SILVA, M. V. G. B.; VAN TASSELL, C. P.; SONSTEGARD, T. S.; GARCIA, J. F. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore Cattle. Plos One v. 9, n. 2, p. 1-9, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 12. | | CARDOSO, D. F.; FERNANDES JÚNIOR, G. A.; SCALEZ, D. C. B.; ALVEZ, A. A. C.; MAGALHÃES, A. F. B.; BRESOLIN, T.; VENTURA, R. V.; LI, C.; OLIVEIRA, M. C. de S.; PORTO NETO, L. R.; CARVALHEIRO, R.; OLIVEIRA, H. N. de; TONHATI, H.; ALBUQUERQUE, L. G. Uncovering sub-structure and genomic profiles in across-countries subpopulations of Angus Cattle. Scientific Reports, v. 10, article 8770, 2020. 11 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 13. | | MUDADU, M. de A.; PORTO NETO, L. R.; MOKRY, F. B.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; TULLIO, R. R.; NASSU, R. T.; NICIURA, S. C. M.; THOLON, P.; ALENCAR, M. M. de; HIGA, R. H.; ROSA, A. do N.; FEIJO, G. L. D.; FERRAZ, A. L. J.; SILVA, L. O. C. da; MEDEIROS, S. R. de; LANNA, D. P. D.; NASCIMENTO, M. L. do; CHAVES, A. S.; SOUZA, A. R. D. L.; PACKER, I. U.; TORRES JUNIOR, R. A. de A.; SIQUEIRA, F.; MOURAO, G. B.; COUTINHO, L. L.; REVERTER, A.; REGITANO, L. C. de A. Genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle. BMC Genomics, v. 17, n. 235, p. 1-16, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 14. | | MUDADU, M. de A.; PORTO-NETO, L. R.; MOKRY, F. B.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; TULLIO, R. R.; NASSU, R. T.; NICIURA, S. C. M.; THOLON, P.; ALENCAR, M. M. de; HIGA, R. H.; ROSA, A. do N.; FEIJO, G. L. D.; FERRAZ, A. L. J.; SILVA, L. O. C. da; MEDEIROS, S. R. de; LANNA, D. P.; NASCIMENTO, M. L.; CHAVES, A. S.; SOUZA, A. R. D. L.; PACKER, I. U.; TORRES JUNIOR, R. A. de A.; SIQUEIRA, F.; MOURÃO, G. B.; COUTINHO, L. L.; REVERTER, A.; REGITANO, L. C. de A. Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle. BMC Genomics, London, v. 17, p. 1-16, Mar. 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Gado de Corte. |
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| 15. | | MUDADU, M. de A.; PORTO NETO, L. R.; MOKRY, F. B.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; TULLIO, R. R.; NASSU, R. T.; NICIURA, S. C. M.; THOLON, P.; ALENCAR, M. M. de; HIGA, R. H.; ROSA, A. do N.; FEIJO, G. L. D.; FERRAZ, A. L. J.; SILVA, L. O. C. da; MEDEIROS, S. R. de; LANNA, D. P. D.; NASCIMENTO, M. L. do; CHAVES, A. S.; SOUZA, A. R. D. L.; PACKER, I. U.; TORRES JUNIOR, R. A. de A.; SIQUEIRA, F.; MOURAO, G. B.; COUTINHO, L. L.; REVERTER, A.; REGITANO, L. C. de A. Erratum to: 'Genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle'. BMC Genomics, v. 17, n. 492, p. 1-2, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| Registros recuperados : 15 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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