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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital. |
Data corrente: |
22/12/2009 |
Data da última atualização: |
15/01/2020 |
Tipo da produção científica: |
Resumo em Anais de Congresso |
Autoria: |
VIEIRA, F. D.; AGOSTINHO, G. C.; REGITANO, L. C. A.; YAMAGISHI, M. E. B. |
Afiliação: |
FABIO DANILO VIEIRA, CNPTIA; GILBERTO CESAR AGOSTINHO, CPPSE; LUCIANA CORREIA ALMEIDA REGITANO, CPPSE; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA. |
Título: |
Database modeling and web interface system: on-line genomic association studies. |
Ano de publicação: |
2009 |
Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. |
Páginas: |
Não paginado. |
Idioma: |
Inglês |
Notas: |
X-Meeting 2009. |
Conteúdo: |
Animal selection is an important phase of any animal breeding program. However, if the selection is not based on easily observable (or measurable) traits, then selection is much tricker. One alternative is to use Marker Assisted Selection (MAS), where genetic markers are positively associated with the desired traits (Duran et al., 2009). MAS has been powered by the advent of large scale SNP genotyping technologies which produces thousands (even millions) of markers in a single chip. However, this huge number of genetic markers brings new challenges to the international scientfic community such as database modeling and the development of association analysis tools capable of dealing with greatly increased volume of information (LaFramboise, 2009). Although no format files are widely accepted as standard and the major commercial SNP chip companies (Affymatrix, Illumina) release their results through flat files, some important whole genome association analysis freeware softwares adopt .PED and .MAP format files as input. In this work, we present a database model and a Web parser system that reads flat files (Illumina, Affymetrix) and generates corresponding .PED and .MAP format files. Furthermore, through the Web interface it is possible to run PLINK (Purcell et al., 2007) routines such as some statistical and association analysis. Noteworthy that the database model was designed in order to speed up all the tasks and turn possible to run online any of the implemented routines. |
Palavras-Chave: |
Bioinformática; Marcadores genéticos; Marker Assisted Selection (MAS); Modelagem de dados; Sistema de interface web. |
Thesaurus Nal: |
Bioinformatics; Genetic markers; Models. |
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
Marc: |
LEADER 02426nam a2200265 a 4500 001 1578783 005 2020-01-15 008 2009 bl uuuu u00u1 u #d 100 1 $aVIEIRA, F. D. 245 $aDatabase modeling and web interface system$bon-line genomic association studies.$h[electronic resource] 260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB$c2009 300 $aNão paginado. 500 $aX-Meeting 2009. 520 $aAnimal selection is an important phase of any animal breeding program. However, if the selection is not based on easily observable (or measurable) traits, then selection is much tricker. One alternative is to use Marker Assisted Selection (MAS), where genetic markers are positively associated with the desired traits (Duran et al., 2009). MAS has been powered by the advent of large scale SNP genotyping technologies which produces thousands (even millions) of markers in a single chip. However, this huge number of genetic markers brings new challenges to the international scientfic community such as database modeling and the development of association analysis tools capable of dealing with greatly increased volume of information (LaFramboise, 2009). Although no format files are widely accepted as standard and the major commercial SNP chip companies (Affymatrix, Illumina) release their results through flat files, some important whole genome association analysis freeware softwares adopt .PED and .MAP format files as input. In this work, we present a database model and a Web parser system that reads flat files (Illumina, Affymetrix) and generates corresponding .PED and .MAP format files. Furthermore, through the Web interface it is possible to run PLINK (Purcell et al., 2007) routines such as some statistical and association analysis. Noteworthy that the database model was designed in order to speed up all the tasks and turn possible to run online any of the implemented routines. 650 $aBioinformatics 650 $aGenetic markers 650 $aModels 653 $aBioinformática 653 $aMarcadores genéticos 653 $aMarker Assisted Selection (MAS) 653 $aModelagem de dados 653 $aSistema de interface web 700 1 $aAGOSTINHO, G. C. 700 1 $aREGITANO, L. C. A. 700 1 $aYAMAGISHI, M. E. B.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
Biblioteca(s): |
Embrapa Café. |
Data corrente: |
06/05/2019 |
Data da última atualização: |
06/05/2019 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Circulação/Nível: |
A - 1 |
Autoria: |
SANT'ANA, G. C.; PEREIRA, L. F. P.; POT, D.; IVAMOTO, S. T.; DOMINGUES, D. S.; FERREIRA, R. V.; PAGIATTO, N. F.; SILVA, B. S. R. da; NOGUEIRA, L. M.; KITZBERGER, C. S. G.; SCHOLZ, M. B. S.; OLIVEIRA, F. F. de; SERA, G. H.; PADILHA, L.; LABOUISSE, J-P.; GUYOT, R.; CHARMETANT, P.; LEROY, T. |
Afiliação: |
Gustavo C. Sant'Ana, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; LUIZ FILIPE PROTASIO PEREIRA, CNPCa; David Pot, CIRAD, UMR AGAP; Suzana T. Ivamoto, Universidade Estadual Paulista/Instituto de Biociências; Douglas S. Domingues, Universidade Estadual Paulista/Instituto de Biociências; Rafaelle V. Ferreira, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Natalia F. Pagiatto, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Bruna S. R. da Silva, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Lívia M. Nogueira, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Cintia S. G. Kitzberger, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Maria B. S. Scholz, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Fernanda F. de Oliveira, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; Gustavo H. Sera, Instituto Agronômico do Paraná - IAPAR/Laboratório de Biotecnologia Vegetal; LILIAN PADILHA, CNPCa; Jean-Pierre Labouisse, AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro; Romain Guyot, IRD, CIRAD, Universit Montpellier; Pierre Charmetant, AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro; Thierry Leroy, AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro. |
Título: |
Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L . |
Ano de publicação: |
2018 |
Fonte/Imprenta: |
Scientific Reports, v. 8, n. 465, p. 1-12, 2018 |
Idioma: |
Inglês |
Conteúdo: |
Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. |
Palavras-Chave: |
Quality of coffee beverages. |
Thesaurus NAL: |
Genome; Genomics; Green beans; Lipids. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/196973/1/Genome-wide-association-study-reveals.pdf
|
Marc: |
LEADER 02458naa a2200385 a 4500 001 2108734 005 2019-05-06 008 2018 bl uuuu u00u1 u #d 100 1 $aSANT'ANA, G. C. 245 $aGenome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L .$h[electronic resource] 260 $c2018 520 $aLipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. 650 $aGenome 650 $aGenomics 650 $aGreen beans 650 $aLipids 653 $aQuality of coffee beverages 700 1 $aPEREIRA, L. F. P. 700 1 $aPOT, D. 700 1 $aIVAMOTO, S. T. 700 1 $aDOMINGUES, D. S. 700 1 $aFERREIRA, R. V. 700 1 $aPAGIATTO, N. F. 700 1 $aSILVA, B. S. R. da 700 1 $aNOGUEIRA, L. M. 700 1 $aKITZBERGER, C. S. G. 700 1 $aSCHOLZ, M. B. S. 700 1 $aOLIVEIRA, F. F. de 700 1 $aSERA, G. H. 700 1 $aPADILHA, L. 700 1 $aLABOUISSE, J-P. 700 1 $aGUYOT, R. 700 1 $aCHARMETANT, P. 700 1 $aLEROY, T. 773 $tScientific Reports$gv. 8, n. 465, p. 1-12, 2018
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