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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com cnpgl.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Corte; Embrapa Gado de Leite. |
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Data corrente: |
29/08/2024 |
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Data da última atualização: |
07/01/2025 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
BITTENCOURT, A.; EGITO, A. A. do; SUNIGA, P. A. P.; SANTIAGO, G. G.; SANTOS, R. M. dos; CARDOSO, E. P.; VERARDO, L. L.; SILVA, M. V. G. B.; TORAL, F. L. B. |
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Afiliação: |
ANGELA BITTENCOURT, UNIVERSIDADE FEDERAL DO MATO GROSSO DO SUL; ANDREA ALVES DO EGITO, CNPGC; PAULA ADAS PEREIRA SUNIGA, UNIVERSIDADE FEDERAL DO MATO GROSSO DO SUL; GUSTAVO GARCIA SANTIAGO, UNIVERSIDADE FEDERAL DO MATO GROSSO DO SUL; RAFAEL MONTEIRO DOS SANTOS, UNIVERSIDADE FEDERAL DE MINAS GERAIS; EDUARDO PENTEADO CARDOSO, FAZENDA MUNDO NOVO; LUCAS LIMA VERARDO, UNIVERSIDADE FEDERAL DOS VALES DO JEQUITINHONHA E MUCURI; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; FABIO LUIZ BURANELO TORAL, UNIVERSIDADE FEDERAL DE MINAS GERAIS. |
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Título: |
Genome-wide assessment of runs of homozygosity to estimate inbreeding in a closed Nellore herd. |
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Ano de publicação: |
2024 |
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Fonte/Imprenta: |
Livestock Science, v. 288, 105547, 2024. |
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DOI: |
https://doi.org/10.1016/j.livsci.2024.105547 |
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Idioma: |
Inglês |
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Conteúdo: |
The objective of this study was to compare the inbreeding coefficients estimated from pedigree data (FPED), traditionally used for internal monitoring by herds and breeding programs, with genomic estimates through the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Besides, we used the genotype data to obtain the linkage disequilibrium (LD), population effective size (Ne), runs of homozygosity (ROH) islands and functional analysis of the genes presented in ROH islands. Male calves and sires from a closed Nellore herd (Lemgruber line) were genotyped with the Z-chip v2 (Neogen, Lincoln, Nebraska, USA) that contains approximately 30 thousand SNP markers. After quality control, 1088 animals and 21,351 SNPs remained for analysis. Runs of homozygosity (ROH) segments were identified in all analyzed animals, with an average number of 57.93 and average length of 2.95 Mb. We observed a higher occurrence of ROH up to 9 Mb, suggesting a proper mating scheme, which corroborate with LD and Ne analysis results. Estimates of FPED, FGRM and FROH ranged from 0 to 0.2856, from 0.0705 to 0.3686 and from 0.0229 to 0.2762, respectively. Low to moderate correlations were observed between FPED and FGRM (0.17, P < 0.001); FPED and FROH (0.20, P < 0.001) and FGRM and FROH (0.92, P < 0.001). Nevertheless, considering our results we were successful in use runs of homozygosity for estimating autozygosity in a closed Nellore herd. Besides, from ROH islands, we were able to identify a candidate gene (HTR1A) for docility in this Nellore herd. MenosThe objective of this study was to compare the inbreeding coefficients estimated from pedigree data (FPED), traditionally used for internal monitoring by herds and breeding programs, with genomic estimates through the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Besides, we used the genotype data to obtain the linkage disequilibrium (LD), population effective size (Ne), runs of homozygosity (ROH) islands and functional analysis of the genes presented in ROH islands. Male calves and sires from a closed Nellore herd (Lemgruber line) were genotyped with the Z-chip v2 (Neogen, Lincoln, Nebraska, USA) that contains approximately 30 thousand SNP markers. After quality control, 1088 animals and 21,351 SNPs remained for analysis. Runs of homozygosity (ROH) segments were identified in all analyzed animals, with an average number of 57.93 and average length of 2.95 Mb. We observed a higher occurrence of ROH up to 9 Mb, suggesting a proper mating scheme, which corroborate with LD and Ne analysis results. Estimates of FPED, FGRM and FROH ranged from 0 to 0.2856, from 0.0705 to 0.3686 and from 0.0229 to 0.2762, respectively. Low to moderate correlations were observed between FPED and FGRM (0.17, P < 0.001); FPED and FROH (0.20, P < 0.001) and FGRM and FROH (0.92, P < 0.001). Nevertheless, considering our results we were successful in use runs of homozygosity for estimating autozygosity in a closed Nellore herd. Besides, from ROH islands, we were able to identify a ... Mostrar Tudo |
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Palavras-Chave: |
Autozygosity; Inbreeding coefficients; Inbreeding Genomic; SNP. |
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Thesagro: |
Bos Indicus; Bovino. |
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Categoria do assunto: |
L Ciência Animal e Produtos de Origem Animal |
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Marc: |
LEADER 02447naa a2200301 a 4500
001 2171265
005 2025-01-07
008 2024 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1016/j.livsci.2024.105547$2DOI
100 1 $aBITTENCOURT, A.
245 $aGenome-wide assessment of runs of homozygosity to estimate inbreeding in a closed Nellore herd.$h[electronic resource]
260 $c2024
520 $aThe objective of this study was to compare the inbreeding coefficients estimated from pedigree data (FPED), traditionally used for internal monitoring by herds and breeding programs, with genomic estimates through the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Besides, we used the genotype data to obtain the linkage disequilibrium (LD), population effective size (Ne), runs of homozygosity (ROH) islands and functional analysis of the genes presented in ROH islands. Male calves and sires from a closed Nellore herd (Lemgruber line) were genotyped with the Z-chip v2 (Neogen, Lincoln, Nebraska, USA) that contains approximately 30 thousand SNP markers. After quality control, 1088 animals and 21,351 SNPs remained for analysis. Runs of homozygosity (ROH) segments were identified in all analyzed animals, with an average number of 57.93 and average length of 2.95 Mb. We observed a higher occurrence of ROH up to 9 Mb, suggesting a proper mating scheme, which corroborate with LD and Ne analysis results. Estimates of FPED, FGRM and FROH ranged from 0 to 0.2856, from 0.0705 to 0.3686 and from 0.0229 to 0.2762, respectively. Low to moderate correlations were observed between FPED and FGRM (0.17, P < 0.001); FPED and FROH (0.20, P < 0.001) and FGRM and FROH (0.92, P < 0.001). Nevertheless, considering our results we were successful in use runs of homozygosity for estimating autozygosity in a closed Nellore herd. Besides, from ROH islands, we were able to identify a candidate gene (HTR1A) for docility in this Nellore herd.
650 $aBos Indicus
650 $aBovino
653 $aAutozygosity
653 $aInbreeding coefficients
653 $aInbreeding Genomic
653 $aSNP
700 1 $aEGITO, A. A. do
700 1 $aSUNIGA, P. A. P.
700 1 $aSANTIAGO, G. G.
700 1 $aSANTOS, R. M. dos
700 1 $aCARDOSO, E. P.
700 1 $aVERARDO, L. L.
700 1 $aSILVA, M. V. G. B.
700 1 $aTORAL, F. L. B.
773 $tLivestock Science$gv. 288, 105547, 2024.
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Embrapa Gado de Corte (CNPGC) |
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| 1. |  | ALVES, L.; RECH, D. V.; GRITTI, D.; ESTEVES, W. T. C.; THOMÉ, J. D. S.; DUQUE, S. S.; FILGUEIRAS, A. A. L.; VAZ, C. S. L. Avaliação de métodos de produção de atmosfera de microaerofilia para isolamento de Campylobacter termófilos em fezes de galinhas. In: CONFERÊNCIA FACTA, 2010, Santos. Anais [dos] trabalhos de pesquisa José Maria Lamas da Silva Santos: FACTA, 2010. 1 CD-ROM. Projeto/Plano de Ação: 03.08.60.400-03.| Tipo: Artigo em Anais de Congresso |
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