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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
01/02/2018 |
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Data da última atualização: |
30/12/2020 |
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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.; REGITANO, L. C. de A.; GEORGE, A.; REVERTER, A. |
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Afiliação: |
PARTHAN KASARAPU, CSIRO; LAERCIO RIBEIRO PORTO-NETO, CSIRO; MARINA R. S. FORTES, University of Queensland; SIGRID A. LEHNER, CSIRO; MAURICIO DE ALVARENGA MUDADU, CNPTIA; LUIZ COUTINHO, Esalq/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; ANDREW GEORGE, CSIRO; ANTONIO REVERTER, 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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Notas: |
Artigo e0181930. Na publicação: Mauricio A. Mudadu, Luciana Regitano. |
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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: |
Bioinformática; Hardy-Weinberg equilibrium; Polimorfismo de nucleotídeo único. |
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Thesagro: |
Bos indicus; Bos taurus. |
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Thesaurus Nal: |
Bioinformatics; Single nucleotide polymorphism. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/171999/1/AP-Bostaurus-PlosOne.pdf
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Marc: |
LEADER 02714naa a2200325 a 4500
001 2086886
005 2020-12-30
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
500 $aArtigo e0181930. Na publicação: Mauricio A. Mudadu, Luciana Regitano.
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 $aBioinformatics
650 $aSingle nucleotide polymorphism
650 $aBos indicus
650 $aBos taurus
653 $aBioinformática
653 $aHardy-Weinberg equilibrium
653 $aPolimorfismo de nucleotídeo único
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.
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 Agricultura Digital (CNPTIA) |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Café. Para informações adicionais entre em contato com biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Café. |
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Data corrente: |
04/03/2011 |
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Data da última atualização: |
04/03/2011 |
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Tipo da produção científica: |
Artigo em Anais de Congresso |
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Autoria: |
SANTOS, T. B.; MARUR, C. J.; PETKOWICZ, C. L. O.; REICHER, F.; PEREIRA, L. F. P.; VIEIRA, L. G. E. |
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Afiliação: |
IAPAR; IAPAR; UFPR; UFPR; LUIZ FILIPE PROTASIO PEREIRA, SAPC. |
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Título: |
Galactinol synthase expression by heat stress in Coffea arabica L. |
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Ano de publicação: |
2008 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE ON COFFEE SCIENCE, 22., 2008, Campinas. |
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Idioma: |
Inglês |
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Conteúdo: |
Plants in nature encounter a combination of environmental conditions that may include stresses such as drought or heat shock. The response of plants to a combination the stress abiotc induction of a large number of defense genes, and changes in genes involved in sugar metabolism. Galactinol synthase (GolS) is a key enzyme in the raffinose and stachyose biosynthetic pathway (RFOs family). This protein functions a galactosyl transferase, which catalyses the key regulatory reaction utilizing UDP-galactose and myo-inositol as substrates to form galactinol and UDP. GolS genes have often been identified as stress responsive genes in many plant species. To study the function of different isoforms of GolS during heat stress in Coffea arabica, this work was carried out with the objective to characterize the expression of three Galactinol synthase isoforms: CaGolS1, CaGolS2 and CaGolS3. |
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Palavras-Chave: |
Plant in nature. |
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Thesagro: |
Coffea Arábica. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 01479nam a2200193 a 4500
001 1880072
005 2011-03-04
008 2008 bl uuuu u00u1 u #d
100 1 $aSANTOS, T. B.
245 $aGalactinol synthase expression by heat stress in Coffea arabica L.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE ON COFFEE SCIENCE, 22., 2008, Campinas.$c2008
520 $aPlants in nature encounter a combination of environmental conditions that may include stresses such as drought or heat shock. The response of plants to a combination the stress abiotc induction of a large number of defense genes, and changes in genes involved in sugar metabolism. Galactinol synthase (GolS) is a key enzyme in the raffinose and stachyose biosynthetic pathway (RFOs family). This protein functions a galactosyl transferase, which catalyses the key regulatory reaction utilizing UDP-galactose and myo-inositol as substrates to form galactinol and UDP. GolS genes have often been identified as stress responsive genes in many plant species. To study the function of different isoforms of GolS during heat stress in Coffea arabica, this work was carried out with the objective to characterize the expression of three Galactinol synthase isoforms: CaGolS1, CaGolS2 and CaGolS3.
650 $aCoffea Arábica
653 $aPlant in nature
700 1 $aMARUR, C. J.
700 1 $aPETKOWICZ, C. L. O.
700 1 $aREICHER, F.
700 1 $aPEREIRA, L. F. P.
700 1 $aVIEIRA, L. G. E.
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