SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene.

RIBEIRO, I. M.; BORGES, C. C. H.; SILVA, B. Z.; ARBEX, W. A..

Abstract The genome-wide associations studies (GWAS) aims to identify the most influential markers in relation to the phenotype values. One of the substantial challenges is to find a non-linear mapping between genotype and phenotype, also known as epistasis, that usually becomes the process of searching and identifying functional SNPs more complex. Some diseases such as cervical cancer, leukemia and type 2 diabetes have low heritability. The heritability of the sample is directly related to the explanation defined by the genotype, so the lower the heritability the greater the influence of the environmental factors and the less the genotypic explanation. In this work, an algorithm capable of identifying epistatic associations at different levels of...

Tipo: Artigo em periódico indexado (ALICE)

Palavras-chave: GWAS; SNP; Genetic Programming; Random Forest; Computational Modeling; Mathematical Modeling; Bioinformatics.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1102526

Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene

CURI, R.A.; CHARDULO, L.A.L.; SILVEIRA, A.C.; OLIVEIRA, H.N. de..

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR?RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR?RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

Tipo: Artigo em periódico indexado (ALICE)

Palavras-chave: Calpastatin gene; Meat texture; PCR?RFLP; SNP; Gene da calpastatina; Textura da carne.

Ano: 2008

URL: http://www.alice.cnptia.embrapa.br/handle/doc/126257

PAB

Curi,Rogério Abdallah; Chardulo,Luis Artur Loyola; Silveira,Antônio Carlos; Oliveira,Henrique Nunes de.

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

Alternative methodologies for genotyping polymorphisms in the CAST and CAPN1 genes in beef cattle

Palavras-chave: Calpastatin gene; Meat texture; PCR-RFLP; SNP.

Ano: 2008

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2008000500014

Blecha,Isabella Maiumi Zaidan; Sousa,Isadora Inácio; Ferreira,Anna Beatriz Robottom; Feijó,Gelson Luis Dias; Torres Júnior,Roberto Augusto de Almeida; Siqueira,Fabiane.

ABSTRACT The objectives of this study were to genotype single nucleotide polymorphisms (SNP) AF159246:g.2959A>G (CAST/DdeI) and AF248054.2:g.6545C>T (CAPN4751) in beef cattle by PCR-RFLP (Polymerase Chain Reaction - Restriction Fragment Length Polymorphism), using the restriction enzyme DdeI for both SNP, and describe the use of these genotyping methodologies for the first time. For the SNP located in the CAST gene, new primers were designed, and for the SNP of the CAPN1 gene, the same primers previously described in the literature were used. Bonsmara, Caracu, Senepol, Nelore, and Angus bulls were chosen from among the most used bulls in breeding programs according to their genealogy and the lowest possible degree of parentage between them to ensure...

Alternative Transcription of Peroxisome Proliferator-Activated Receptor Gamma in the Liver Is Associated with Fatness of Chickens

Palavras-chave: Animal breeding; Marker-assisted selection; PCR-RFLP; SNP; Tenderness.

Ano: 2019

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982019000100311

Rev. Bras. Ciênc. Avic.

Parada,R; Malewski,T; Jaszczak,K; Kawka,M.

ABSTRACT The expression of four transcription variant of peroxisome proliferator-activated receptor gamma gene (PPARG) (XM_015292931.1; XM_015292932.1; XM_015292933.1 and NM_001001460.1) in the liver of broilers was measured and its correlation with abdominal fat weight and relative abdominal fat content was investigated. The study was conducted with 92 slow-growing crossbred chickens (Cobb males x indigenous Green-legged Partridge female chickens) divided into “fat” and “lean” groups, according to their abdominal fat yield. The NM_001001460.1 transcriptwas upregulated with ratio of means 4.26 (p≤0.01) in the “fat” group in relation to the “lean” group. Expression of this transcript was highly correlated with relative abdominal fat content (0.71, p≤0.01)...

Amplificação de genes da rota metabólica do amido de mandioca para mapeamento associativo.

Palavras-chave: Fat deposition; PPARG; Transcription factor; SNP; Slow-growing chickens.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2018000300447

VASCONCELOS, L. M. de; CARMO, C. D. do; OLIVEIRA, E. J. de.

A mandioca (Manihot esculenta Crantz) é uma espécie que acumula grande quantidade de amido nas raízes, sendo importante alimento para milhões de pessoas ao redor do mundo. O amido de mandioca é constituído basicamente por amilose e amilopectina, com proporção média na maioria das variedades de 1:5.

Análise da diversidade nucleotídica intra e interespecífica de Coffea spp.

Palavras-chave: SNP; Melhoramento; Biossíntese.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1030909

YANAGUI, K.; VIEIRA, L. G. E.; PEREIRA, L. F. P.; POT, D..

2010

Análise de diversidade genética do gene da osteopontina em bovinos da raça girolando

Palavras-chave: SNP; INDEL; Coffea; Marcador; Polimorfismo.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/handle/doc/880434

Mello,Fernanda de; Guimarães,Marta Fonseca Martins; Cobuci,Jaime Araújo; Silva,Marcos Vinícius Gualberto Barbosa da; Braccini Neto,José; Paiva,Daisyléa de Souza.

Objetivou-se obter os índices de diversidade genética para o SNP (single nucleotide polymorphism) do íntron 4 do gene da osteopontina (OPN) para 434 animais (87 touros e 347 vacas) participantes do Teste de Progênie da raça girolando no Brasil. Para a amplificação, foram utilizados primers descritos para a raça holandesa, e a diferenciação dos alelos C/T desse SNP foi obtida por meio da técnica de PCR-RFLP. As frequências genotípicas TT (52,53%), CT (38,71%) e CC (8,76%) e as frequências alélicas de T (71,9%) e C (28,1%) indicam que a população encontra-se em Equilíbrio de Hardy-Weinberg (EHW). Apesar de o loco do gene OPN estar em EHW, a frequência superior do alelo T do SNP nesses animais pode sugerir uma tendência de fixação do alelo T na raça. Não foi...

Analise in silico e in vivo da diversidade nucleotidica em Coffea ssp.

Palavras-chave: Bovinos leiteiros; Polimorfismo; Produção de leite; SNP; SPP1.

Ano: 2011

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982011001100013

Ant colony algorithm for analysis of gene interaction in high-dimensional association data

VIDAL, R.; FERREIRA, L. P.; LANNES, S. D.; VIEIRA, L. G. E.; MONDEGO, J.; CARAZZOLLE, M. F.; PEREIRA, G. A.; POT, D.; PEREIRA, L. F. P..

Polimorfismos de modificações nucleotídicas (SNPs ? Single Nucleotide Polymorphisms, INDELs ? Insertion / Deletions) têm uma alta freqüência nos genomas da maioria dos organismos, incluindo plantas. Eles vêm se tornando a escolha principal de marcador para trabalhos de melhoramento, genotipagem e diagnóstico. A identificação destes polimorfismos irá fornecer marcadores que poderão ser utilizados para o mapeamento genético, estudos de genética de população e de associação. Portanto, os objetivos deste trabalho foram: 1) identificar in silico SNPs e INDELS existentes em seqüências de ESTs disponíveis; e 2) analisar a diversidade nucleotídica em Coffea spp. Um pipeline para identificação de SNPs e INDELs foi desenvolvido utilizando seqüências de ESTs...

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: SNP; INDEL; Mapeamento; Genoma.

Ano: 2009

URL: http://www.alice.cnptia.embrapa.br/handle/doc/903595

Rekaya,Romdhane; Robbins,Kelly.

In recent years there has been much focus on the use of single nucleotide polymorphism (SNP) fine genome mapping to identify causative mutations for traits of interest; however, many studies focus only on the marginal effects of markers, ignoring potential gene interactions. Simulation studies have show that this approach may not be powerful enough to detect important loci when gene interactions are present. While several studies have examined potential gene interaction, they tend to focus on a small number of SNP markers. Given the prohibitive computation cost of modeling interactions in studies involving a large number SNP, methods need to be develop that can account for potential gene interactions in a computationally efficient manner. This study adopts...

Antecedentes y nuevos aportes en el estudio del Cromosoma Y en poblaciones humanas sudamericanas

Palavras-chave: Genome; Simulation; SNP.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982009001300011

JBAG

Bailliet,Graciela; Ramallo,Virginia; Muzzio,Marina; Santos,María R; Motti,Josefina MB; Bianchi,Néstor O; Bravi,Claudio M.

Los avances en el conocimiento del genoma humano han llegado también a una situación comprensiva en relación a la región específica del cromosoma Y humano. En los últimos años se han reconocido al menos 600 polimorfismos bialélicos (SNP), a partir de los cuales se ha construido una sólida filogenia y se ha normalizado la nomenclatura. En el presente trabajo se han estudiado 940 muestras de varones no relacionados de 10 poblaciones aborígenes de Argentina, Chile y Paraguay; y 12 poblaciones urbanas de Argentina. Se han analizado 9 marcadores bialélicos para reconocer los clados mayores de la filogenia. Fue posible distinguir los haplogrupos Q* y Q3 autóctonos, y los haplogrupos AB, DE, F, K, P y R alóctonos. El Fst fue de 0, 17, mostrando un alto nivel de...

URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1852-62332011000100003

Palavras-chave: Linajes paternos; Haplogrupos; SNP; Ancestralidad genética; Poblaciones humanas.

Ano: 2011

Aromatase gene and its effects on growth, reproductive and maternal ability traits in a multibreed sheep population from Brazil

Genet. Mol. Biol.

Lôbo,Ana Maria Bezerra Oliveira; Lôbo,Raimundo Nonato Braga; Paiva,Samuel Rezende.

We determined the polymorphism C242T of the aromatase gene (Cyp19) and its allelic frequency, as well as the effect of the variants on productive and reproductive traits in 71 purebred Santa Inês sheep, 13 purebred Brazilian Somali sheep, nine purebred Poll Dorset sheep, and 18 crossbred 1/2 Dorper sheep. The animals were genotyped using the PCR-RFLP technique. The influence of the animal's genotype on its performance or on the performance of its lambs was analyzed by the least square method. Another factor assessed was the importance of the animal's genotype in analysis models for quantitative breeding value estimates, and whether there were differences among the averages of breeding values of animals with different genotypes for this gene. In the sample...

Associação do receptor da adiponectina com cortes nobres e características relacionadas à deposição de gordura em uma linhagem paterna de frangos de corte.

Palavras-chave: Body weight; Lambing interval; PCR-RFLP; Polymorphism; SNP; Litter weight.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300010

CRUZ, V. A. R. da; IBELLI, A. M. G.; MARCHESI, J. A. P.; PANDOLFI, J. R. C.; PEIXOTO, J. de O.; MUNARI, D. P..

2013

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: SNP; Gordura abdominal; ADIPOR 1; Frango de corte.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/968188

Associação entre polimorfismo no gene BMP4 e características de OPU-PIVE em vacas Gir.

Associação entre variantes cis regulatórias do gene KCNJ11e características econômicas em bovinos Nelore.

VEGA, W. H. O.; QUIRINO, C. R.; AZEVEDO, A. S. de; PACHECO, A.; OLIVEIRA, C. S.; SERAPIÃO, R. V.; BARTHOLAZZI, A. J..

2014

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: OPU-PIVE; SNP; Mutação sinónima.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1008566

OLIVEIRA, K. S. de; LIMA, A. O. de; AFONSO, J.; CARDOSO, T. F.; BRUSCADIN, J. J.; REGITANO, L. C. de A..

Características de produção como eficiência alimentar e de qualidade da carne bovina são de suma importância para o agronegócio, agroindústria e consumidores. Assim, ferramentas biotecnológicas como a genômica podem adicionar informações para identificar potenciais biomarcadores com a finalidade de auxiliar os programas de melhoramento e seleção de bovinos de corte.

Association of KCNJ11 gene variants with tenderness in Nelore breed.

Palavras-chave: SNP; Expressão gênica; Sítio de ligação de fator de transcriçã0; Ilha CpG; Qualidade da carne; Bos Indicus.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115556

TIZIOTO, P. C.; SOUZA, M. M. de; MUDADU, M. de A.; THOLON, P.; MEIRELLES, S. L. C.; TULLIO, R. R.; NASSU, R. T.; ROSA, A. do N.; MEDEIROS, S. R. de; SIQUEIRA, F.; FEIJO, G. L. D.; REGITANO, L. C. de A..

The KCNJ11 (potassium inwardly-rectifying channel, subfamily J, member 11) gene is located in BTA15, near a quantitative trait loci for meat tenderness. In this study, single nucleotide polymorphisms (SNPs) were described in KCNJ11 and associated with Warner ? Bratzler shear force (WBSF) at different aging times: 1 d after slaughter (WBSF0), after 7 d (WBSF7) and 14 d (WBSF14) of aging. Fourteen steers of Nelore breed, characterized as extreme for the distribution of WBSF0 in a half-sib population of 500 progenies from 32 sires, were selected for sequencing.

Association of polymorphisms in the leptin and thyroglobulin genes with meat quality and carcass traits in beef cattle

Palavras-chave: KCNJ11; Gene variants; Nelore breed; Cattle; SNP; Meat.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/951696

Carvalho,Thiago Dutra de; Siqueira,Fabiane; Torres Júnior,Roberto Augusto de Almeida; Medeiros,Sérgio Raposo de; Feijó,Gelson Luís Dias; Souza Junior,Maury Dorta de; Blecha,Isabella Maiumi Zaidan; Soares,Cleber Oliveira.

The objective of the present study was to estimate the allelic and genotypic frequencies of the polymorphisms E2FB (AY138588.1: c.305C> T), located in the leptin gene (LEP), and TG5 (X05380.1:g.-422C>T), located in the thyroglobulin gene (TG), and evaluate the association of these polymorphisms in crossbred cattle of seven distinct genetic groups with the following traits: slaughter weight (SW), hot carcass weight (HCW), hot carcass yield (HCY), carcass fat thickness (CFT), ribeye area (REA), marbling (MARM) and shear force (SF). The animals were genotyped using the PCR-RFLP (Polymorphism Chain Reaction-Restriction Fragment Length Polymorphism) technique, using 201 products obtained from F1 Caracu × Nellore, Angus × Nellore and Valdostana × Nellore...