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Registro Completo |
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
07/04/2004 |
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Data da última atualização: |
27/07/2007 |
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Autoria: |
BINNECK, E.; SILVA, J. F. V.; NEUMAIER, N.; FARIAS, J. R. B.; ARIAS, C. A. A.; ALMEIDA, A. M. R.; MARIN, S. R. R.; WENDLAND, A.; SILVEIRA, C. A. da; MOLINA, J. C.; LEMOS, N. G.; FUGANTI, R.; STOLF, R.; NEPOMUCENO, A. L. |
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Título: |
Bioinformatics tools for sequence analysis and annotation applied to soybean functional genome. |
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Ano de publicação: |
2004 |
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Fonte/Imprenta: |
In: WORLD SOYBEAN RESEARCH CONFERENCE, 7.; INTERNATIONAL SOYBEAN PROCESSING AND UTILIZATION CONFERENCE, 4.; CONGRESSO BRASILEIRO DE SOJA, 3., 2004, Foz do Iguassu. Abstracts of contributed papers and posters. Londrina: Embrapa Soybean, 2004. |
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Páginas: |
p. 248-249. |
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Série: |
(Embrapa Soja. Documentos, 228). |
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Idioma: |
Inglês |
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Notas: |
Editado por Flávio Moscardi, Clara Beatriz Hoffmann-Campo, Odilon Ferreira Saraiva, Paulo Roberto Galerani, Francisco Carlos Krzyzanowski, Mercedes Concordia Carrão-Panizzi. |
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Conteúdo: |
Worldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches linked to key words, data insertion, update, and generation of intuitive reports describing the results. These tools are helping to direct our work on identification, cloning and characterization of genes and regulatory sequences potentially useful in the improvement of soybean through genetic engineering. As results nearly 8,000 ESTs was obtained form cDNA clones derived from soybean roots in drought stress and nematode infection conditions. Consensus sequences are being functionally annotated and used to construct cDNA microarrays that will be useful for analyze gene expression under a broad variety of conditions. Initially we are studying drought stress and nematode infection conditions. Analysis of interactions of soybean roots with this defiance conditions will be used do identify new possible sources of resistance and tolerance. Candidate genes will be deeply studied and can be used on the production of transgenic plants. This work was supported by grants from CNPq, PRODETAB, Jircas and Embrapa. MenosWorldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches li... Mostrar Tudo |
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Categoria do assunto: |
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Marc: |
LEADER 03743naa a2200313 a 4500
001 1466823
005 2007-07-27
008 2004 bl uuuu u00u1 u #d
100 1 $aBINNECK, E.
245 $aBioinformatics tools for sequence analysis and annotation applied to soybean functional genome.
260 $c2004
300 $ap. 248-249.
490 $a(Embrapa Soja. Documentos, 228).
500 $aEditado por Flávio Moscardi, Clara Beatriz Hoffmann-Campo, Odilon Ferreira Saraiva, Paulo Roberto Galerani, Francisco Carlos Krzyzanowski, Mercedes Concordia Carrão-Panizzi.
520 $aWorldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches linked to key words, data insertion, update, and generation of intuitive reports describing the results. These tools are helping to direct our work on identification, cloning and characterization of genes and regulatory sequences potentially useful in the improvement of soybean through genetic engineering. As results nearly 8,000 ESTs was obtained form cDNA clones derived from soybean roots in drought stress and nematode infection conditions. Consensus sequences are being functionally annotated and used to construct cDNA microarrays that will be useful for analyze gene expression under a broad variety of conditions. Initially we are studying drought stress and nematode infection conditions. Analysis of interactions of soybean roots with this defiance conditions will be used do identify new possible sources of resistance and tolerance. Candidate genes will be deeply studied and can be used on the production of transgenic plants. This work was supported by grants from CNPq, PRODETAB, Jircas and Embrapa.
700 1 $aSILVA, J. F. V.
700 1 $aNEUMAIER, N.
700 1 $aFARIAS, J. R. B.
700 1 $aARIAS, C. A. A.
700 1 $aALMEIDA, A. M. R.
700 1 $aMARIN, S. R. R.
700 1 $aWENDLAND, A.
700 1 $aSILVEIRA, C. A. da
700 1 $aMOLINA, J. C.
700 1 $aLEMOS, N. G.
700 1 $aFUGANTI, R.
700 1 $aSTOLF, R.
700 1 $aNEPOMUCENO, A. L.
773 $tIn: WORLD SOYBEAN RESEARCH CONFERENCE, 7.; INTERNATIONAL SOYBEAN PROCESSING AND UTILIZATION CONFERENCE, 4.; CONGRESSO BRASILEIRO DE SOJA, 3., 2004, Foz do Iguassu. Abstracts of contributed papers and posters. Londrina: Embrapa Soybean, 2004.
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Registro original: |
Embrapa Soja (CNPSO) |
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Biblioteca(s): |
Embrapa Suínos e Aves. |
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Data corrente: |
11/07/2018 |
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Data da última atualização: |
12/07/2018 |
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Tipo da produção científica: |
Artigo em Anais de Congresso |
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Autoria: |
ONO, R. K.; IBELLI, A. M. G.; CANTAO, M. E.; PEIXOTO, J. de O.; SOLLERO, B. P.; SUREK, D.; MOREIRA, G. C. M.; GODOY, T. F.; COUTINHO, L. L.; LEDUR, M. C. |
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Afiliação: |
RAFAEL KEITH ONO; ADRIANA MERCIA GUARATINI IBELLI, CNPSA; MAURICIO EGIDIO CANTAO, CNPSA; JANE DE OLIVEIRA PEIXOTO, CNPSA; BRUNA PENA SOLLERO, CPPSUL; DIEGO SUREK, CNPSA; GABRIEL COSTA MONTEIRO MOREIRA, ESALQ; THAÍS FERNANDA GODOY, ESALQ; LUIZ LEHMMAN COUTINHO, ESALQ; MONICA CORREA LEDUR, CNPSA. |
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Título: |
Genome-wide association study for femur-related traits in broilers. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
In: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 11., 2018, Auckland, New Zealand. Proceedings... Massey University, 2018. Digital Archive. |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract: Due to the intense selection for heavier and faster growing broilers, metabolic disorders such as skeletal problems became a worldwide concern. Advances in genome-wide association study (GWAS) methodologies increased the possibility of elucidating the genetic architecture controlling bone integrity traits. Therefore, the aim of this study was to perform a GWAS to identify potential genetic markers and candidate genes associated with femur traits in a paternal broiler line developed by Embrapa. To this, three femur bone-related traits were evaluated in 1,433 chickens: dry matter (FDM), ash content (FAC) and breaking strength (FBS). Chickens were genotyped using the 600K Affymetrix® Axiom® HD panel. A total of 16 regions associated to FAC, being a significant SNP in the GGA19 (rs317696422) and 15 suggestive SNPs in the GGA1, GGA2, GGA3, GGA5, GGA8, GGA13, GGA19 and GGA24. For FDM, only one SNP (GGA1) was significantly associated and was located in the DSCAM gene. For the FBS, two suggestive regions (GGA12 and GGA15) were found and no QTLs were described for this trait in these regions. According to the results, new candidate genes and miRNAs related to ossification, such as TPVR2, gga-mir-146a and PCP4 were associated to important femur traits in the broiler line under study. Resumo:Devido à intensa seleção de frangos de corte mais pesados e de crescimento mais rápido, distúrbios metabólicos, como problemas esqueléticos, tornaram-se uma preocupação mundial. Avanços em metodologias de estudo de associação genômica ampla (GWAS) aumentaram a possibilidade de elucidar a arquitetura genética controlando características de integridade óssea. Portanto, o objetivo deste estudo foi realizar um GWAS para identificar potenciais marcadores genéticos e genes candidatos associados às características do fêmur em uma linhagem de frangos de corte paterna desenvolvida pela Embrapa. Para isso, três características relacionadas ao osso do fêmur foram avaliadas em 1.433 aves: matéria seca (FDM), teor de cinzas (FAC) e resistência à ruptura (FBS). As galinhas foram genotipadas usando o painel 600y Affymetrix® Axiom® HD. Um total de 16 regiões associadas ao FAC, sendo um significativo SNP no GGA19 (rs317696422) e 15 SNPs sugestivos no GGA1, GGA2, GGA3, GGA5, GGA8, GGA13, GGA19 e GGA24. Para FDM, apenas um SNP (GGA1) foi significativamente associado e foi localizado no gene DSCAM. Para o FBS, duas regiões sugestivas (GGA12 e GGA15) foram encontradas e não foram descritos QTLs para essa característica nessas regiões. De acordo com os resultados, novos genes candidatos e miRNAs relacionados à ossificação, como TPVR2, gga-mir-146a e PCP4, foram associados a importantes características do fêmur na linha de frangos em estudo. MenosAbstract: Due to the intense selection for heavier and faster growing broilers, metabolic disorders such as skeletal problems became a worldwide concern. Advances in genome-wide association study (GWAS) methodologies increased the possibility of elucidating the genetic architecture controlling bone integrity traits. Therefore, the aim of this study was to perform a GWAS to identify potential genetic markers and candidate genes associated with femur traits in a paternal broiler line developed by Embrapa. To this, three femur bone-related traits were evaluated in 1,433 chickens: dry matter (FDM), ash content (FAC) and breaking strength (FBS). Chickens were genotyped using the 600K Affymetrix® Axiom® HD panel. A total of 16 regions associated to FAC, being a significant SNP in the GGA19 (rs317696422) and 15 suggestive SNPs in the GGA1, GGA2, GGA3, GGA5, GGA8, GGA13, GGA19 and GGA24. For FDM, only one SNP (GGA1) was significantly associated and was located in the DSCAM gene. For the FBS, two suggestive regions (GGA12 and GGA15) were found and no QTLs were described for this trait in these regions. According to the results, new candidate genes and miRNAs related to ossification, such as TPVR2, gga-mir-146a and PCP4 were associated to important femur traits in the broiler line under study. Resumo:Devido à intensa seleção de frangos de corte mais pesados e de crescimento mais rápido, distúrbios metabólicos, como problemas esqueléticos, tornaram-se uma preocupação mund... Mostrar Tudo |
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Palavras-Chave: |
Associação genômica; Características do fêmur; Integridade óssea; QTLs. |
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Thesagro: |
Fêmur; Formação Óssea; Frango de Corte; Melhoramento Genético Animal. |
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Thesaurus NAL: |
Animal genetic resources; Bone metabolism; Broiler chickens; Quantitative trait loci. |
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Categoria do assunto: |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/179661/1/final8692.pdf
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Marc: |
LEADER 03955nam a2200361 a 4500
001 2093205
005 2018-07-12
008 2018 bl uuuu u00u1 u #d
100 1 $aONO, R. K.
245 $aGenome-wide association study for femur-related traits in broilers.$h[electronic resource]
260 $aIn: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 11., 2018, Auckland, New Zealand. Proceedings... Massey University, 2018. Digital Archive.$c2018
520 $aAbstract: Due to the intense selection for heavier and faster growing broilers, metabolic disorders such as skeletal problems became a worldwide concern. Advances in genome-wide association study (GWAS) methodologies increased the possibility of elucidating the genetic architecture controlling bone integrity traits. Therefore, the aim of this study was to perform a GWAS to identify potential genetic markers and candidate genes associated with femur traits in a paternal broiler line developed by Embrapa. To this, three femur bone-related traits were evaluated in 1,433 chickens: dry matter (FDM), ash content (FAC) and breaking strength (FBS). Chickens were genotyped using the 600K Affymetrix® Axiom® HD panel. A total of 16 regions associated to FAC, being a significant SNP in the GGA19 (rs317696422) and 15 suggestive SNPs in the GGA1, GGA2, GGA3, GGA5, GGA8, GGA13, GGA19 and GGA24. For FDM, only one SNP (GGA1) was significantly associated and was located in the DSCAM gene. For the FBS, two suggestive regions (GGA12 and GGA15) were found and no QTLs were described for this trait in these regions. According to the results, new candidate genes and miRNAs related to ossification, such as TPVR2, gga-mir-146a and PCP4 were associated to important femur traits in the broiler line under study. Resumo:Devido à intensa seleção de frangos de corte mais pesados e de crescimento mais rápido, distúrbios metabólicos, como problemas esqueléticos, tornaram-se uma preocupação mundial. Avanços em metodologias de estudo de associação genômica ampla (GWAS) aumentaram a possibilidade de elucidar a arquitetura genética controlando características de integridade óssea. Portanto, o objetivo deste estudo foi realizar um GWAS para identificar potenciais marcadores genéticos e genes candidatos associados às características do fêmur em uma linhagem de frangos de corte paterna desenvolvida pela Embrapa. Para isso, três características relacionadas ao osso do fêmur foram avaliadas em 1.433 aves: matéria seca (FDM), teor de cinzas (FAC) e resistência à ruptura (FBS). As galinhas foram genotipadas usando o painel 600y Affymetrix® Axiom® HD. Um total de 16 regiões associadas ao FAC, sendo um significativo SNP no GGA19 (rs317696422) e 15 SNPs sugestivos no GGA1, GGA2, GGA3, GGA5, GGA8, GGA13, GGA19 e GGA24. Para FDM, apenas um SNP (GGA1) foi significativamente associado e foi localizado no gene DSCAM. Para o FBS, duas regiões sugestivas (GGA12 e GGA15) foram encontradas e não foram descritos QTLs para essa característica nessas regiões. De acordo com os resultados, novos genes candidatos e miRNAs relacionados à ossificação, como TPVR2, gga-mir-146a e PCP4, foram associados a importantes características do fêmur na linha de frangos em estudo.
650 $aAnimal genetic resources
650 $aBone metabolism
650 $aBroiler chickens
650 $aQuantitative trait loci
650 $aFêmur
650 $aFormação Óssea
650 $aFrango de Corte
650 $aMelhoramento Genético Animal
653 $aAssociação genômica
653 $aCaracterísticas do fêmur
653 $aIntegridade óssea
653 $aQTLs
700 1 $aIBELLI, A. M. G.
700 1 $aCANTAO, M. E.
700 1 $aPEIXOTO, J. de O.
700 1 $aSOLLERO, B. P.
700 1 $aSUREK, D.
700 1 $aMOREIRA, G. C. M.
700 1 $aGODOY, T. F.
700 1 $aCOUTINHO, L. L.
700 1 $aLEDUR, M. C.
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