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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
03/03/2017 |
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Data da última atualização: |
03/03/2017 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SANTANA, M. H. de A.; OLIVEIRA JUNIOR, G. A.; CESAR, A. S. M.; FREUA, M. C.; GOMES, R. da C.; SILVA, S. da L.; LEME, P. R.; FUKUMASU, H.; CARVALHO, M. E.; VENTURA, R. V.; COUTINHO, L. L.; KADARMIDEEN, H. N.; FERRAZ, J. B. S. |
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Afiliação: |
MIGUEL HENRIQUE DE ALMEIDA SANTANA; GERSON ANTÔNIO OLIVEIRA JUNIOR; ALINE SILVA MELLO CESAR; MATEUS CASTELANI FREUA; RODRIGO DA COSTA GOMES, CNPGC; SAULO DA LUZ E SILVA; PAULO ROBERTO LEME; HEIDGE FUKUMASU; MINOS ESPERÂNDIO CARVALHO; RICARDO VIEIRA VENTURA; LUIZ LEHMANN COUTINHO; HAJA N. KADARMIDEEN; JOSÉ BENTO STERMAN FERRAZ. |
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Título: |
Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
Journal of Applied Gentics, v. 57, n. 4, p. 495-504, 2016 |
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Idioma: |
Inglês |
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Conteúdo: |
The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR. MenosThe use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid,... Mostrar Tudo |
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Palavras-Chave: |
GWAS; Nellore cattle. |
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Thesaurus Nal: |
Cattle; Cucumber necrosis virus; Feed conversion; Genomics; Single nucleotide polymorphism. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/157039/1/Copy-number-variations-and-genome-wide.pdf
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Marc: |
LEADER 03009naa a2200349 a 4500
001 2066092
005 2017-03-03
008 2016 bl uuuu u00u1 u #d
100 1 $aSANTANA, M. H. de A.
245 $aCopy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle.$h[electronic resource]
260 $c2016
520 $aThe use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.
650 $aCattle
650 $aCucumber necrosis virus
650 $aFeed conversion
650 $aGenomics
650 $aSingle nucleotide polymorphism
653 $aGWAS
653 $aNellore cattle
700 1 $aOLIVEIRA JUNIOR, G. A.
700 1 $aCESAR, A. S. M.
700 1 $aFREUA, M. C.
700 1 $aGOMES, R. da C.
700 1 $aSILVA, S. da L.
700 1 $aLEME, P. R.
700 1 $aFUKUMASU, H.
700 1 $aCARVALHO, M. E.
700 1 $aVENTURA, R. V.
700 1 $aCOUTINHO, L. L.
700 1 $aKADARMIDEEN, H. N.
700 1 $aFERRAZ, J. B. S.
773 $tJournal of Applied Gentics$gv. 57, n. 4, p. 495-504, 2016
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Registro original: |
Embrapa Gado de Corte (CNPGC) |
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Registro |
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Registro Completo
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Biblioteca(s): |
Embrapa Semiárido. |
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Data corrente: |
18/10/2011 |
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Data da última atualização: |
02/03/2023 |
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Tipo da produção científica: |
Artigo em Anais de Congresso |
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Autoria: |
NUNES, F. C.; SILVA, E. F. da; CUNHA, T. J. F.; VILAS BOAS, G. da S.; CARVALHO, J. J. S.; ANGELI, A. |
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Afiliação: |
FÁBIO CARVALHO NUNES, UNEB; ENIO FRAGA DA SILVA, CNPS; TONY JARBAS FERREIRA CUNHA, CPATSA; GERALDO DA SILVA VILAS BOAS, UFBA; JOSÉ JORGE SOUSA CARVALHO; ALINE ANGELI. |
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Título: |
Solos com horizontes coesos desenvolvidos sobre diferentes litofácies do grupo Barreiras no Litoral Norte da Bahia. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
In: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 33., 2011, Uberlândia. Solos nos biomas brasileiros: sustentabilidade e mudanças climáticas: anais. Uberlândia: SBCS: UFU: ICIAG, 2011. |
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Descrição Física: |
1 CD-ROM. |
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Idioma: |
Português |
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Conteúdo: |
Foram estudados solos coesos desenvolvidos sobre diferentes litofácies do Grupo Barreiras, através de análises morfológicas, micromorfológicas, físicas e químicas, concluindo-se que diferentes litofácies geraram solos com horizontes coesos distintos, a saber: a) solos oriundos de diamictitos ferruginosos originam inicialmente horizontes moderadamente coesos e, com o avanço da degradação do plasma dos horizontes superficiais, avanço da iluviação e xantização da cobertura evoluem para solos fortemente coesos, enquanto que aqueles desenvolvidos sobre sedimentos areno-lamosos originam solos moderadamente coesos e não ficam mais coesos com o aumento do gradiente textual e diminuição dos teores de ferro livre; b) a boa distribuição granulométrica dos materiais de origem favorece o adensamento, contudo estudos quantitativos utilizando outros métodos devem ser realizados. |
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Palavras-Chave: |
Bahia; Grupo Barreiras; Horizontes Coesos; Litofácies; Solos. |
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Thesagro: |
Solo. |
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Thesaurus NAL: |
Soil. |
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Categoria do assunto: |
P Recursos Naturais, Ciências Ambientais e da Terra |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/43654/1/Tony11-2011.PDF
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Marc: |
LEADER 01770nam a2200265 a 4500
001 1903354
005 2023-03-02
008 2011 bl uuuu u00u1 u #d
100 1 $aNUNES, F. C.
245 $aSolos com horizontes coesos desenvolvidos sobre diferentes litofácies do grupo Barreiras no Litoral Norte da Bahia.
260 $aIn: CONGRESSO BRASILEIRO DE CIÊNCIA DO SOLO, 33., 2011, Uberlândia. Solos nos biomas brasileiros: sustentabilidade e mudanças climáticas: anais. Uberlândia: SBCS: UFU: ICIAG$c2011
300 $c1 CD-ROM.
520 $aForam estudados solos coesos desenvolvidos sobre diferentes litofácies do Grupo Barreiras, através de análises morfológicas, micromorfológicas, físicas e químicas, concluindo-se que diferentes litofácies geraram solos com horizontes coesos distintos, a saber: a) solos oriundos de diamictitos ferruginosos originam inicialmente horizontes moderadamente coesos e, com o avanço da degradação do plasma dos horizontes superficiais, avanço da iluviação e xantização da cobertura evoluem para solos fortemente coesos, enquanto que aqueles desenvolvidos sobre sedimentos areno-lamosos originam solos moderadamente coesos e não ficam mais coesos com o aumento do gradiente textual e diminuição dos teores de ferro livre; b) a boa distribuição granulométrica dos materiais de origem favorece o adensamento, contudo estudos quantitativos utilizando outros métodos devem ser realizados.
650 $aSoil
650 $aSolo
653 $aBahia
653 $aGrupo Barreiras
653 $aHorizontes Coesos
653 $aLitofácies
653 $aSolos
700 1 $aSILVA, E. F. da
700 1 $aCUNHA, T. J. F.
700 1 $aVILAS BOAS, G. da S.
700 1 $aCARVALHO, J. J. S.
700 1 $aANGELI, A.
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Embrapa Semiárido (CPATSA) |
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