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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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Registro Completo
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Biblioteca(s): |
Embrapa Clima Temperado. |
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Data corrente: |
13/01/2020 |
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Data da última atualização: |
23/12/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
LIMA, C. L. R. de; DUPONT, P. B.; PILLON, C. N.; MIOLA, E. C. C. |
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Afiliação: |
CLÁUDIA LIANE RODRIGUES DE LIMA, UFPEL; PATRÍCIA BIANCA DUPONT, UFPEL; CLENIO NAILTO PILLON, CPACT; EZEQUIEL CESAR CARVALHO MIOLA, FURG. |
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Título: |
Least limiting water range, S-index and compressibility of a Udalf under different management systems. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
Scientia Agricola, v. 77, n. 1, e20170224, 2020. |
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Páginas: |
8 p. |
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ISSN: |
1678-992X |
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DOI: |
http://dx.doi.org/10.1590/1678-992X-2017-0224 |
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Idioma: |
Inglês |
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Conteúdo: |
Agricultural areas in the region of Turuçu, on the Southeast Hillside in the state of Rio Grande do Sul (RS), Brazil present many examples of soil physical degradation. Accord-ingly, strategies aimed at evaluating and ameliorating the structural quality of soils should be developed to ensure the sustainable use of these areas. This study aimed to evaluate the least limiting water range (LLWR), S-index, compressibility parameters, organic carbon and the organic matter granulometric fractions of a Udalf under different agricultural uses. Soil samples with disturbed and non-disturbed structure from the 0.00 to 0.10 m layer were collected on farms in the Southeast Hillside, Turuçu region, RS, for analyzing soil under: i) conventional system of corn after tobacco crop, (CT); ii) conventional system of corn after native field (CNF), iii) native field (NF) and iv) native area (NA). Both the CT and the CNF systems had a negative influence on the values of bulk density, soil porosity, least limiting water range, compressibility parameters and total organic carbon, coarse fraction carbon and carbon associated with minerals. |
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Palavras-Chave: |
Faixa de água menos limitante; Least limiting water range; LLWR. |
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Thesagro: |
Física do Solo; Solo. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/208562/1/Artigo-Claudia-Pillon-2019.pdf
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Marc: |
LEADER 01904naa a2200253 a 4500
001 2118599
005 2020-12-23
008 2020 bl uuuu u00u1 u #d
022 $a1678-992X
024 7 $ahttp://dx.doi.org/10.1590/1678-992X-2017-0224$2DOI
100 1 $aLIMA, C. L. R. de
245 $aLeast limiting water range, S-index and compressibility of a Udalf under different management systems.$h[electronic resource]
260 $c2020
300 $a8 p.
520 $aAgricultural areas in the region of Turuçu, on the Southeast Hillside in the state of Rio Grande do Sul (RS), Brazil present many examples of soil physical degradation. Accord-ingly, strategies aimed at evaluating and ameliorating the structural quality of soils should be developed to ensure the sustainable use of these areas. This study aimed to evaluate the least limiting water range (LLWR), S-index, compressibility parameters, organic carbon and the organic matter granulometric fractions of a Udalf under different agricultural uses. Soil samples with disturbed and non-disturbed structure from the 0.00 to 0.10 m layer were collected on farms in the Southeast Hillside, Turuçu region, RS, for analyzing soil under: i) conventional system of corn after tobacco crop, (CT); ii) conventional system of corn after native field (CNF), iii) native field (NF) and iv) native area (NA). Both the CT and the CNF systems had a negative influence on the values of bulk density, soil porosity, least limiting water range, compressibility parameters and total organic carbon, coarse fraction carbon and carbon associated with minerals.
650 $aFísica do Solo
650 $aSolo
653 $aFaixa de água menos limitante
653 $aLeast limiting water range
653 $aLLWR
700 1 $aDUPONT, P. B.
700 1 $aPILLON, C. N.
700 1 $aMIOLA, E. C. C.
773 $tScientia Agricola$gv. 77, n. 1, e20170224, 2020.
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Embrapa Clima Temperado (CPACT) |
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