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Registro Completo |
Biblioteca(s): |
Embrapa Arroz e Feijão. |
Data corrente: |
26/09/2017 |
Data da última atualização: |
31/10/2017 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
VALDISSER, P. A. M. R.; PEREIRA, W. J.; ALMEIDA FILHO, J. E.; MÜLLER, B. S. F.; COELHO, G. R. C.; MENEZES, I. P. P. de; VIANNA, J. P. G.; ZUCCHI, M. I.; LANNA, A. C.; COELHO, A. S. G.; OLIVEIRA, J. P. de; MORAES, A. da C.; BRONDANI, C.; VIANELLO, R. P. |
Afiliação: |
PAULA ARIELLE M RIBEIRO VALDISSER, CNPAF; WENDELL J. PEREIRA, UNB; JANEO E. ALMEIDA FILHO, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro-; BARBARA S. F. MULLER, UNB; GESIMARIA RIBEIRO COSTA COELHO, CNPAF; IVANDILSON P. P. DE MENEZES, INSTITUTO FEDERAL GOIANO, Urutaí-GO; JOÃO P. G. VIANNA, UNICAMP; MARIA I. ZUCCHI, UNICAMP; ANNA CRISTINA LANNA, CNPAF; ALEXANDRE S. G. COELHO, UFG; JAISON PEREIRA DE OLIVEIRA, CNPAF; ALESSANDRA DA CUNHA MORAES, CNPAF; CLAUDIO BRONDANI, CNPAF; ROSANA PEREIRA VIANELLO, CNPAF. |
Título: |
In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. |
Ano de publicação: |
2017 |
Fonte/Imprenta: |
BMC Genomics, v. 18, Article 423, 30 mai. 2017. |
DOI: |
10.1186/s12864-017-3805-4 |
Idioma: |
Inglês |
Conteúdo: |
Background: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was~88 kbp, while for the Andean gene pool was~395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches. MenosBackground: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 1... Mostrar Tudo |
Palavras-Chave: |
Core collection; Diversity analysis; Diversity arrays technology; Loci under selection. |
Thesagro: |
Feijão; Genética vegetal; Phaseolus vulgaris. |
Thesaurus Nal: |
Genotyping; Linkage disequilibrium; Single nucleotide polymorphism. |
Categoria do assunto: |
S Ciências Biológicas |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/164318/1/CNPAF-2017-bmc.pdf
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Marc: |
LEADER 03492naa a2200409 a 4500 001 2076278 005 2017-10-31 008 2017 bl uuuu u00u1 u #d 024 7 $a10.1186/s12864-017-3805-4$2DOI 100 1 $aVALDISSER, P. A. M. R. 245 $aIn-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping.$h[electronic resource] 260 $c2017 520 $aBackground: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was~88 kbp, while for the Andean gene pool was~395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches. 650 $aGenotyping 650 $aLinkage disequilibrium 650 $aSingle nucleotide polymorphism 650 $aFeijão 650 $aGenética vegetal 650 $aPhaseolus vulgaris 653 $aCore collection 653 $aDiversity analysis 653 $aDiversity arrays technology 653 $aLoci under selection 700 1 $aPEREIRA, W. J. 700 1 $aALMEIDA FILHO, J. E. 700 1 $aMÜLLER, B. S. F. 700 1 $aCOELHO, G. R. C. 700 1 $aMENEZES, I. P. P. de 700 1 $aVIANNA, J. P. G. 700 1 $aZUCCHI, M. I. 700 1 $aLANNA, A. C. 700 1 $aCOELHO, A. S. G. 700 1 $aOLIVEIRA, J. P. de 700 1 $aMORAES, A. da C. 700 1 $aBRONDANI, C. 700 1 $aVIANELLO, R. P. 773 $tBMC Genomics$gv. 18, Article 423, 30 mai. 2017.
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Registro original: |
Embrapa Arroz e Feijão (CNPAF) |
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Biblioteca(s): |
Embrapa Amazônia Oriental. |
Data corrente: |
24/06/1999 |
Data da última atualização: |
16/07/2020 |
Tipo da produção científica: |
Resumo em Anais de Congresso |
Autoria: |
SILVA, L. G. T.; SILVA, B. N. R. da; SILVA, H. M. e; SILVA, J. F. de A.; GATO, R. F.; CARVALHO, R. de A.; COSTA FILHO, P. P.; ALBUQUERQUE, N. I.; VEIGA, J. B. da; GALEÃO, R. R.; KITAMURA, P. C.; FERRAZ, L. F.; IKEDA, F. F.; LOBATO, R. F.; SOUSA SOBRINHO, A. |
Afiliação: |
LUIZ GUILHERME TEIXEIRA SILVA, CPATU; BENEDITO NELSON RODRIGUES DA SILVA, CPATU; HERCULES MARTINS E SILVA, CPATU; JOSE FRANCISCO DE ASSIS F DA SILVA, CPATU; RUBENISE FARIAS GATO, CPATU; RUI DE AMORIM CARVALHO, CPATU; PERMINIO PASCOAL COSTA FILHO, CPATU; NATALIA INAGAKI DE ALBUQUERQUE, CPATU; JONAS BASTOS DA VEIGA, CPATU; RUY RANGEL GALEAO, CPATU; PAULO CHOJI KITAMURA, CNPMA; FCAP; EMATER-PA; EMATER-PA; SECRETARIA MUNICIPAL DE AGRICULTURA DE MOJU. |
Título: |
Diagnóstico agroambiental rápido de propriedades rurais para a região do Moju-PA. Um enfoque sistêmico e a construção de um instrumento de coleta de dados participativo. |
Ano de publicação: |
1998 |
Fonte/Imprenta: |
In: CONGRESSO DE ECOLOGIA DO BRASIL, 4., 1998, Belém, PA. Ecossistemas: com enfoque em seus componentes básicos: resumos. Belém, PA: FCAP: Sociedade de Ecologia do Brasil, 1998. |
Páginas: |
p. 638-639. |
Idioma: |
Português |
Palavras-Chave: |
Alternative agriculture; Brasil; Ecologia agrícola; Moju; Pará; Tipificação. |
Thesagro: |
Propriedade Rural. |
Thesaurus NAL: |
Amazonia; classification; land ownership. |
Categoria do assunto: |
-- |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/205399/1/Diagnostico-agroambiental.pdf
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Marc: |
LEADER 01315nam a2200397 a 4500 001 1399336 005 2020-07-16 008 1998 bl uuuu u00u1 u #d 100 1 $aSILVA, L. G. T. 245 $aDiagnóstico agroambiental rápido de propriedades rurais para a região do Moju-PA. Um enfoque sistêmico e a construção de um instrumento de coleta de dados participativo. 260 $aIn: CONGRESSO DE ECOLOGIA DO BRASIL, 4., 1998, Belém, PA. Ecossistemas: com enfoque em seus componentes básicos: resumos. Belém, PA: FCAP: Sociedade de Ecologia do Brasil$c1998 300 $ap. 638-639. 650 $aAmazonia 650 $aclassification 650 $aland ownership 650 $aPropriedade Rural 653 $aAlternative agriculture 653 $aBrasil 653 $aEcologia agrícola 653 $aMoju 653 $aPará 653 $aTipificação 700 1 $aSILVA, B. N. R. da 700 1 $aSILVA, H. M. e 700 1 $aSILVA, J. F. de A. 700 1 $aGATO, R. F. 700 1 $aCARVALHO, R. de A. 700 1 $aCOSTA FILHO, P. P. 700 1 $aALBUQUERQUE, N. I. 700 1 $aVEIGA, J. B. da 700 1 $aGALEÃO, R. R. 700 1 $aKITAMURA, P. C. 700 1 $aFERRAZ, L. F. 700 1 $aIKEDA, F. F. 700 1 $aLOBATO, R. F. 700 1 $aSOUSA SOBRINHO, A.
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