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Registro Completo |
Biblioteca(s): |
Embrapa Gado de Corte. |
Data corrente: |
03/03/2017 |
Data da última atualização: |
03/03/2017 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
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. |
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. |
Título: |
Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. |
Ano de publicação: |
2016 |
Fonte/Imprenta: |
Journal of Applied Gentics, v. 57, n. 4, p. 495-504, 2016 |
Idioma: |
Inglês |
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 |
Palavras-Chave: |
GWAS; Nellore cattle. |
Thesaurus Nal: |
Cattle; Cucumber necrosis virus; Feed conversion; Genomics; Single nucleotide polymorphism. |
Categoria do assunto: |
-- |
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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Biblioteca(s): |
Embrapa Milho e Sorgo. |
Data corrente: |
28/10/2016 |
Data da última atualização: |
11/01/2017 |
Tipo da produção científica: |
Artigo em Anais de Congresso |
Autoria: |
GUIMARAES, E. A.; SILVA, D. D. da; PFENNING, L. H.; COTA, L. V.; LANZA, F. E.; AGUIAR, F. M.; GOMES, G. R.; MENEZES, C. B. de. |
Afiliação: |
ELAINE APARECIDA GUIMARES, UFLA, Lavras, MG.; DAGMA DIONISIA DA SILVA, CNPMS; LUDWIG HEINRICH PFENNING, UFLA, Lavras, MG.; LUCIANO VIANA COTA, CNPMS; FABRICIO EUSTAQUIO LANZA, Bolsista.; FREDERICK MENDES AGUIAR, Bolsista.; GALUCIO REGINALDO GOMES, Faculdade Sato Agostinho, Sete Lagoas, MG.; CICERO BESERRA DE MENEZES, CNPMS. |
Título: |
Patogenicidade de isolados de Fusarium em colmos milho, sorgo e milheto. |
Ano de publicação: |
2016 |
Fonte/Imprenta: |
In: CONGRESSO NACIONAL DE MILHO E SORGO, 31., 2016, Bento Gonçalves. Milho e sorgo: inovações, mercados e segurança alimentar: anais. Sete Lagoas: Associação Brasileira de Milho e Sorgo, 2016. |
Idioma: |
Português |
Thesagro: |
Doença de planta; Fusarium; Gramínea; Podridão; Podridão do Colmo. |
Thesaurus NAL: |
Plant diseases and disorders; Stem rot. |
Categoria do assunto: |
H Saúde e Patologia |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/149818/1/Patogenicidade-isolados.pdf
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Marc: |
LEADER 00911nam a2200265 a 4500 001 2055543 005 2017-01-11 008 2016 bl uuuu u00u1 u #d 100 1 $aGUIMARAES, E. A. 245 $aPatogenicidade de isolados de Fusarium em colmos milho, sorgo e milheto.$h[electronic resource] 260 $aIn: CONGRESSO NACIONAL DE MILHO E SORGO, 31., 2016, Bento Gonçalves. Milho e sorgo: inovações, mercados e segurança alimentar: anais. Sete Lagoas: Associação Brasileira de Milho e Sorgo$c2016 650 $aPlant diseases and disorders 650 $aStem rot 650 $aDoença de planta 650 $aFusarium 650 $aGramínea 650 $aPodridão 650 $aPodridão do Colmo 700 1 $aSILVA, D. D. da 700 1 $aPFENNING, L. H. 700 1 $aCOTA, L. V. 700 1 $aLANZA, F. E. 700 1 $aAGUIAR, F. M. 700 1 $aGOMES, G. R. 700 1 $aMENEZES, C. B. de
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Embrapa Milho e Sorgo (CNPMS) |
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