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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
28/11/2018 |
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Data da última atualização: |
24/01/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
PERIPOLLI, E.; STAFUZZA, N. B.; MUNARI, D. P.; LIMA, A. L. F.; IRGANG, R.; MACHADO, M. A.; PANETTO, J. C. do C.; VENTURA, R. V.; BALDI, F.; SILVA, M. V. G. B. |
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Afiliação: |
ELISA PERIPOLLI, UNESP; NEDENIA BONVINO STAFUZZA, UNESP; DANÍSIO PRADO MUNARI, UNESP / CNPQ; ANDRÉ LUÍS FERREIRA LIMA, UFSC; RENATO IRGANG, UFSC; MARCO ANTONIO MACHADO, CNPGL; JOAO CLAUDIO DO CARMO PANETTO, CNPGL; RICARDO VIEIRA VENTURA, USP / Beef Improvement Opportunities, Canada / University of Guelph, Canada; FERNANDO BALDI, UNESP; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL. |
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Título: |
Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
BMC Genomics, v. 19, n. 34, 2018. |
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Páginas: |
13 p. |
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DOI: |
10.1186/s12864-017-4365-3 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from -0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. CONCLUSIONS: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. MenosAbstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficient... Mostrar Tudo |
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Palavras-Chave: |
Dairy traits; Inbreeding coefficients; ROH islands. |
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Thesagro: |
Bos Indicus. |
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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/187250/1/Cnpgl-2018-BMC-Gen-Machado-Assessment.pdf
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Marc: |
LEADER 03293naa a2200301 a 4500
001 2100275
005 2023-01-24
008 2018 bl uuuu u00u1 u #d
024 7 $a10.1186/s12864-017-4365-3$2DOI
100 1 $aPERIPOLLI, E.
245 $aAssessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle.$h[electronic resource]
260 $c2018
300 $a13 p.
520 $aAbstract BACKGROUND: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). RESULTS: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1-2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from -0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. CONCLUSIONS: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.
650 $aBos Indicus
653 $aDairy traits
653 $aInbreeding coefficients
653 $aROH islands
700 1 $aSTAFUZZA, N. B.
700 1 $aMUNARI, D. P.
700 1 $aLIMA, A. L. F.
700 1 $aIRGANG, R.
700 1 $aMACHADO, M. A.
700 1 $aPANETTO, J. C. do C.
700 1 $aVENTURA, R. V.
700 1 $aBALDI, F.
700 1 $aSILVA, M. V. G. B.
773 $tBMC Genomics$gv. 19, n. 34, 2018.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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| Registros recuperados : 79 | |
| 2. |  | JULIANO, R. S.; FAGLIARI, J. J.; SILVA, L. A. F.; FIORAVANTI, M. C. S. Proteinograma sérico de bovinos da raça Curraleiro obtido por eletroforese em gel de poliacrilamida. (Serum protein concentration in Curraleiro cattle determined by sodium dodecyl sulphate-polyacrilamide gel.) In: CONGRESSO BRASILEIRO DE BUIATRIA, 7., 2007, Curitiba, [Resumo expandido] Curitiba, PR, 2007. 1 p.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Pantanal. |
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| 3. | | NEIVA, A. C. G. R.; SERENO, J. R. B.; SANTOS, S. A.; FIORAVANTI, M. C. S. Caracterização socioeconômica e cultural da comundiade quilombola Kalunga de Cavalcante, Goiás, Brasil: dados preliminares. In: SIMPÓSIO NACIONAL CERRADO, 9.; SIMPÓSIO INTERNACIONAL SAVANAS TROPICAIS, 2., 2008, Brasília, DF. Desafios e estratégias para o equilíbrio entre sociedade, agronegócio e recursos naturais: anais... Planaltina, DF: Embrapa Cerrados, 2008. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Cerrados. |
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| 4. | | NEIVA, A. C. G. R.; SERENO, J. R. B.; SANTOS, S. A.; FIORAVANTI, M. C. S. Caracterização socioeconômica e cultural da comundiade quilombola Kalunga de Cavalcante, Goiás, Brasil : dados preliminares. In: SIMPÓSIO NACIONAL CERRADO, 9.; SIMPÓSIO INTERNACIONAL SAVANAS TROPICAIS, 2., 2008, Brasília, DF. Desafios e estratégias para o equilíbrio entre sociedade, agronegócio e recursos naturais: anais... Planaltina, DF: Embrapa Cerrados, 2008. 8 p.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Pantanal. |
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| 5. | | FELIX, G. A.; PIOVEZAN, U.; JULIANO, R. S.; SILVA, M. C. da; FIORAVANTI, M. C. S. Potencial de uso de raças bovinas locais brasileiras: Curraleiro Pé-Duro e Pantaneiro. Enciclopédia Biosfera, Centro Científico Conhecer, Goiânia, v. 9, n. 1, p. 1715-1741, 2013. 27 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Pantanal. |
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| 9. | | FELIX, G. A.; PIOVEZAN, U.; JULIANO, R. S.; ALVES, F. V.; SANTOS, D. de C.; FIORAVANTI, M. C. S. Análise morfométrica para identificação de raças bovinas locais Pantaneiro e Caracu - resultados preliminares. In: CONGRESSO BRASILEIRO DE MASTOZOOLOGIA, 7., 2014, Gramado, RS. Caderno de Resumos... Gramado: UFRGS, 2014. SBMZ, 2014. p. 239-240. 2 p.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Pantanal. |
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| 11. | | LOPES, F. B.; SILVA, M. C. da; MIYAGI, E. S.; FIORAVANTI, M. C. S.; FACO, O.; McMANUS, C. Comparison of selection indexes for dairy goats in the tropics. Acta Scientiarum. Animal Sciences, Maringá, v. 35, n. 3, p. 321-328, July/Sept. 2013.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Caprinos e Ovinos. |
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| 12. | | SILVA, M. C. da; PAULINI, F.; LOPES, F. B.; FIORAVANTI, M. C. S.; SERENO, J. R. B. A heterogeneidade dos sistemas de produção agropecuários e da paisagem: um ponto de partida para compreender a conservação de recursos genéticos animais. Enciclopédia Biosfera, Centro Científico Conhecer, Goiânia, v. 9, n. 16, 2013.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Cerrados. |
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| 13. | | ABUD, L. J.; GUIMARÃES, C. O.; COSTA, G. L.; FIORAVANTI, M. C. S.; MARTINS, C. F.; SERENO, J. R. B. Idade, peso e prenhez de novilhas Nelore mocha. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 49., 2012, Brasília. A produção animal no mundo em transformação: anais. Brasília, DF: SBZ, 2012. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Cerrados. |
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| 14. | | FELIX, G. A.; PIOVEZAN, U.; QUADROS, J.; JULIANO, R. S.; ALVES, F. V.; FIORAVANTI, M. C. S. Thricology for identifying mammal species and breeds: its use in research and agriculture. Archivos de Zootecnia, v. 63, n. 1 , p. 107-116, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 2 |
| Biblioteca(s): Embrapa Pantanal. |
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| 17. | | FIORAVANTI, M. C. S.; JULIANO, R. S.; PIOVEZAN, U.; RAMOS, A. F.; ALVES, F. V.; EGITO, A. A. do. Rede Pró-Centro Oeste curraleiro pé-duro e pantaneiro: uma experiência de sucesso na conservação de recursos genéticos animais. In: SIMPOSIO IBEROAMERICANO SOBRE CONSERVACIÓN Y UTILIZACIÓN DE RECURSOS ZOOGENÉTICOS, 16., 2015, Villavicencio, Colombia. Iberoamérica compartirá experiencias y logros científicos: libro de resúmenes... Villavicencio, Colombia: Asocriollanos: Red Conbiand Co-lombia: Universidad Nacional de Colombia Sede Palmira, 2015. p. 57| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 19. | | SILVA, B. P. A.; JULIANO, R. S.; ARNHOLD, E.; FIORAVANTI, M. C. S.; FERRO, D. A. C.; FERRO, R. A. C.; SERENO, J. R. B. Avaliação fenotípica qualitativa como critério para implantação de programas de acasalamentos em rebanhos da raça Curraleiro Pé-Duro. Actas Iberoamericanas de Conservación Animal, v. 7, p. 64-73, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: C - 0 |
| Biblioteca(s): Embrapa Pantanal. |
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| 20. | | SILVA, M. C.; MATIKA, O.; BISHOP, S. C.; PEREIRA, R. M.; MOURA, M. I.; McMANUS, C. M.; FIORAVANTI, M. C. S.; JULIANO, R. S.; SERENO, J. R. B. Autocorrelação espacial e descontinuidades genéticas em bovinos Pantaneiro e Curraleiro Pé-Duro: uma abordagem da genética geográfica com uso de marcadores SNP. In: SIMPOSIO IBEROAMERICANO SOBRE CONSERVACIÓN Y UTILIZACIÓN DE RECURSOS ZOOGENÉTICOS, 16., 2015, Villavicencio, Colombia. Iberoamérica compartirá experiencias y logros científicos: libro de resúmenes. Villavicencio, Colombia: Asocriollanos: Red Conbiand Colombia: Universidad Nacional de Colombia Sede Palmira, 2015. p. 74.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Pantanal. |
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| Registros recuperados : 79 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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