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A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle. Repositório Alice
SANTANA, M. H. A.; GOMES, R. da C.; BONIN, M. N..
2015
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bos indicus; Candidate genes; Fat thickness; Genomewide association studies; Single nucleotide polymorphisms; Ultrasonography.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1030961
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A lack of association between adiponectin polymorphisms and coronary artery disease in a Chinese population Genet. Mol. Biol.
Zhong,Chen; Zhen,Ding; Qian,Qi; Genshan,Ma.
We investigated the association between two single nucleotide polymorphisms (SNPs) in the adiponectin gene (rs822395 and rs266729) and coronary artery disease (CAD) in a case-control study of 198 unrelated Chinese CAD patients (with ; 70% coronary stenosis or previous myocardial infarction) and 237 non-CAD controls. The ligase reaction was used to detect SNPs rs822395 and rs266729, and the allelic association of these SNPs with the occurrence and severity of CAD was assessed. There were no significant differences in the genotypic or allelic frequencies of the two SNPs between control and CAD individuals. In addition, there was no association between the two SNPs and the severity of CAD based on the number of diseased vessels. The frequencies of alleles C...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Adiponectin gene; Coronary artery disease; Single nucleotide polymorphisms.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000300005
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Análise de associação genômica ampla baseada em conjunto de genes: implementação em R. Repositório Alice
GUERREIRO, A. T.; HIGA, R. H..
O objetivo deste trabalho é a criação de um pacote R (R CORE TEAM, 2014) que implemente quatro diferentes métodos de GSEA no contexto de GWAS, considerando adaptações para aplicação em espécies animais de interesse para a agricultura.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Polimorfismo de nucleotídeo único; Modelos mistos; Genome Wide Association Studies; Random forests; Mixed models; Single nucleotide polymorphisms.
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1009826
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Association of MDR1 gene polymorphisms with the risk of hepatocellular carcinoma in the Chinese Han population BJMBR
Gao,Jian.
The multidrug resistance 1 gene (MDR1) is an important candidate gene for influencing susceptibility to hepatocellular carcinoma (HCC). The objective of the present study was to evaluate the association ofMDR1 polymorphisms with the risk of HCC in the Chinese Han population. A total of 353 HCC patients and 335 healthy subjects were enrolled in the study. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), created restriction site-PCR (CRS-PCR) and DNA sequencing methods were used to identify MDR1 gene polymorphisms. Two allelic variants (c.335T>C and c.3073A>C) were detected. The CC genotype of the c.335T>C polymorphism was associated with an increased risk of developing HCC compared to the TT genotype (OR = 2.161, 95%CI...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Hepatocellular carcinoma; Multidrug resistance 1 gene; Single nucleotide polymorphisms; Susceptibility; Risk factors.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2013000300311
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CHRNA5 polymorphism and susceptibility to lung cancer in a Chinese population BJMBR
Shen,Bo; Zhu,Qun; Zheng,Ma-Qing; Chen,Jia; Shi,Mei-Qi; Feng,Ji-Feng.
Polymorphisms in the nicotinic acetylcholine receptor subunit CHRNA5 gene have been associated with lung cancer positive susceptibility in European and American populations. In the present hospital-based, case-control study, we determined whether polymorphism in rs503464 of CHRNA5 is associated with lung cancer risk in Chinese individuals. A single nucleotide polymorphism in CHRNA5 rs503464, c.-166T>A (hereafter T>A), was identified using TaqMan-MGB probes with sequencing via PCR in 600 lung cancer cases and 600 healthy individuals. Genotype frequencies for rs503464 (T>A) were in Hardy-Weinberg equilibrium for the control population. However, genotype frequencies were significantly different between cases and controls (P < 0.05), while allele...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Lung cancer; Nicotinic acetylcholine receptors; CHRNA5 gene; Single nucleotide polymorphisms.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2013000100079
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Exploratory analysis of single nucleotide polymorphism (SNP) for quantitative traits AgEcon
Cleves, Mario A..
With the decreasing cost and the increasing ability to quickly genotype single nucleotide polymorphisms (SNP) across the human genome, large databases containing possibly hundreds of typed SNPs are becoming common in population-based studies of quantitative traits. Testing for association between individual SNPs and the quantitative trait is an important first step in the discovery of disease susceptibility SNPs. This task, however, could be time-consuming and tedious if a large number of SNPs is involved. In this article, I introduce two new commands designed to facilitate the screening and testing of multiple SNPs for possible association with quantitative traits.
Tipo: Journal Article Palavras-chave: Hwsnp; Qtlsnp; Genetic epidemiology; Genetic linkage; QTL; Biallelic marker; Single nucleotide polymorphisms; Hardy–Weinberg; Research Methods/ Statistical Methods.
Ano: 2005 URL: http://purl.umn.edu/117508
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Genetic improvement of beef cattle through opportunities in genomics R. Bras. Zootec.
Miller,Stephen.
Genomics will improve the efficiency of beef cattle genetic improvement programs through the incorporation of genomic predictions into traditional genetic evaluations. The global dairy cattle breeding industry has been changed considerably in the last year through the implementation of genomic selection. Now proven to work in dairy cattle breeding, the challenge remains for the beef industry to successfully implement this technology. The primary challenge in beef cattle is the required resource population that relates genomic profile to phenotypic performance, which is quite large and its establishment will require collaboration or a significant investment by any one enterprise. Another challenge in beef cattle is the requirement for genomic predictions to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Breeding strategies; DNA; Genomic selection; Phenotype; Recording; Single nucleotide polymorphisms.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982010001300027
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Genetic polymorphisms related to meat traits in purebred and crossbred Nelore cattle. Repositório Alice
CURI, R. A.; FORTES, M. R. S.; CHARDULO, L. A. L.; SILVEIRA, A. C.; DE BENI ARRIGONE, M.; MARTINS, C. L.; ASSUMPÇÃO, M. E. O. d' A.; OLIVEIRA, H. N. de.
Abstract - The objective of this work was to estimate the allelic and genotypic frequencies of CAST/XmnI, a calpastatin gene polymorphism, and CAPN530, a calpain 1 large subunit gene polymorphism, in different beef genetic groups (Nelore and Nelore x Bos taurus), and to investigate associations between these polymorphisms and carcass and meat traits. Three hundred animals ? comprising 114 Nelore, 67 Angus x Nelore, 44 Rubia Gallega x Nelore, 41 Canchim, 19 Brangus three-way cross and 15 Braunvieh three-way cross ? were genotyped by PCR-RFLP and phenotyped for rib-eye area (REA), back-fat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The occurrence of the two alleles of the CAST/XmnI and CAPN530 single...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Calpain gene; Calpastatin gene; Single nucleotide polymorphisms; Bos indicus; Meat tenderness.
Ano: 2009 URL: http://www.alice.cnptia.embrapa.br/handle/doc/662457
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Genetic polymorphisms related to meat traits in purebred and crossbred Nelore cattle PAB
Curi,Rogério Abdallah; Fortes,Marina Rufino Salinas; Chardulo,Luis Artur Loyola; Silveira,Antonio Carlos; Arrigoni,Mário De Beni; Martins,Cyntia Ludovico; Assumpção,Mayra Elena Ortiz D' Avila; Oliveira,Henrique Nunes de.
The objective of this work was to estimate the allelic and genotypic frequencies of CAST/XmnI, a calpastatin gene polymorphism, and CAPN530, a calpain 1 large subunit gene polymorphism, in different beef genetic groups (Nelore and Nelore x Bos taurus), and to investigate associations between these polymorphisms and carcass and meat traits. Three hundred animals - comprising 114 Nelore, 67 Angus x Nelore, 44 Rubia Gallega x Nelore, 41 Canchim, 19 Brangus three-way cross and 15 Braunvieh three-way cross- were genotyped by PCR-RFLP and phenotyped for rib-eye area (REA), back-fat thickness (BT), intramuscular fat (IF), shear force (SF) and myofibrillar fragmentation index (MFI). The occurrence of the two alleles of the CAST/XmnI and CAPN530 single nucleotide...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bos indicus; Calpain gene; Calpastatin gene; Meat tenderness; Single nucleotide polymorphisms.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2009001200015
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Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw. Repositório Alice
VIANA, J. P. G.; SIQUEIRA, M. V. B. M.; ARAUJO, F. L.; GRANDO, C.; SUJII, P. S.; SILVESTRE, E. de A.; NOVELLO, M.; PINHEIRO, J. B.; CAVALLARI, M. M.; BRANCALION, P. H. S.; RODRIGUES, R. R.; SOUZA, A. P. de; CATCHEN, J.; ZUCCHI, M. I..
The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: SNP; Single nucleotide polymorphisms; Floresta Tropical; Casearia Sylvestris; Tropical forests.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1101157
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Genotypic profile of Pantanal creole sheep regarding susceptibility or resistance to scrapie. Repositório Alice
GONÇALVES, A. N. D.; SOARES, C. O.; SANCHES, S. C.; REIS, F. A.; ROSINHA, G. M. S..
The objective of this work was to determine the genotypic profile specific to scrapie in codons 136, 154, and 171 of the PRNP gene of the Pantanal creole sheep. Genomic DNA was extracted from blood samples collected from 66 sheep, and the regions of interest on the DNA strand were amplified by PCR. Five haplotypes were identified: ARR, alanine, arginine, arginine; ARQ, alanine, arginine, glutamine; AHQ, alanine, histidine, glutamine; ARH, alanine, arginine, histidine; and VRQ, valine, arginine, glutamine. The most common genotypes were ARQ/ARQ (27%) and ARR/ARQ (24%). The genotypic profile of the Pantanal creole sheep shows low to moderate susceptibility.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Encefalopatia espongiforme transmissivel; Gene PRNP; Genotipagem; Polimorfismo de nucleotídeo único; Single nucleotide polymorphisms; Transmissible spongiform encephalopathies; Genotyping; Prion diseases.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1050554
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Genotypic profile of Pantanal creole sheep regarding susceptibility or resistance to scrapie PAB
Gonçalves,Aline Najara Domingos; Soares,Cleber Oliveira; Sanches,Simone Camargo; Reis,Fernando Alvarenga; Rosinha,Grácia Maria Soares.
Abstract: The objective of this work was to determine the genotypic profile specific to scrapie in codons 136, 154, and 171 of the PRNP gene of the Pantanal creole sheep. Genomic DNA was extracted from blood samples collected from 66 sheep, and the regions of interest on the DNA strand were amplified by PCR. Five haplotypes were identified: ARR, alanine, arginine, arginine; ARQ, alanine, arginine, glutamine; AHQ, alanine, histidine, glutamine; ARH, alanine, arginine, histidine; and VRQ, valine, arginine, glutamine. The most common genotypes were ARQ/ARQ (27%) and ARR/ARQ (24%). The genotypic profile of the Pantanal creole sheep shows low to moderate susceptibility.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genotyping; PRNP gene; Single nucleotide polymorphisms; Transmissible spongiform encephalopathies..
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2016000500684
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Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance Genet. Mol. Biol.
Vidal,Ramon Oliveira; Nascimento,Leandro Costa do; Maurício Costa Mondego,Jorge; Amarante Guimarães Pereira,Gonçalo; Falsarella Carazzolle,Marcelo.
The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Single nucleotide polymorphisms; Deep sequencing; Drought resistance.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200014
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Initial analysis of copy number variations in canchim beef cattle with extreme phenotypes for ribeye area. Repositório Alice
GIACHETTO, P. F.; PEREIRA, F. C. P.; MOKRY, F. B.; HIGA, R. H.; MUDADU, M. A.; SILVA, M. V.; NICIURA, S. C. M.; CARDOSO, F. F.; ALENCAR, M. M.; MEIRELLES, S. L. C.; LIMA, A. O.; REGITANO, L. C. A..
Genomic structural variation, in the form of large-scale insertions and deletions, as well as inversions and translocations, are referred to as copy number variations (CNVs). Compared to single nucleotide polymorphisms (SNPs), CNVs have potentially greater effects on gene structure, dosage and regulation, being an important source of phenotypic variation. In humans, CNVs are widespread in the genome and have been shown to be associated with complex traits. In livestock species, the characterization of this genetic variation is an important step toward linking genes or genomic regions with phenotypic traits of economic importance. Studies in cattle have revealed some CNVs associated with differences in host parasite resistance and breed-specific differences...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Variação genética; Polimorfismo de nucleotídeo único; Bioinformática; Copy number variations; Genetic variation; Single nucleotide polymorphisms; Bioinformatics.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/974748
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Initial analysis of copy number variations in canchim beef cattle with extreme phenotypes for ribeye area. Repositório Alice
GIACHETTO, P. F.; PEREIRA, F. C. P.; MOKRY, F. B.; HIGA, R. H.; MUDADU, M. A.; SILVA, M. V.; NICIURA, S. C. M.; CARDOSO, F. F.; ALENCAR, M. M.; MEIRELLES, S. L. C.; LIMA, A. O.; REGITANO, L. C. A..
Genomic structural variation, in the form of large-scale insertions and deletions, as well as inversions and translocations, are referred to as copy number variations (CNVs). Compared to single nucleotide polymorphisms (SNPs), CNVs have potentially greater effects on gene structure, dosage and regulation, being an important source of phenotypic variation. In humans, CNVs are widespread in the genome and have been shown to be associated with complex traits. In livestock species, the characterization of this genetic variation is an important step toward linking genes or genomic regions with phenotypic traits of economic importance. Studies in cattle have revealed some CNVs associated with differences in host parasite resistance and breed-specific differences...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Variação genética; Polimorfismo de nucleotídeo único; Bioinformática; Copy number variations; Genetic variation; Single nucleotide polymorphisms; Bioinformatics.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/980708
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Modelagem difusa para suporte à decisão na descoberta de SNPs em sequências de cDNA. Repositório Alice
ARBEX, W.; CARVALHO, L. A. V. de; SILVA, M. V. B. da; YAMAGISHI, M. E. B..
Diferenças pontuais entre pares de bases de diferentes sequências alinhadas são o tipo mais comum de variabilidade genética. Tais diferenças, conhecidas como polimorfismos de base única (single nucleotide polymorphisms ? SNPs), são importantes no estudo davariabilidade das espécies, pois podem provocar alterações funcionais ou fenotípicas, as quais podem implicar em consequências evolutivas ou bioquímicas nos indivíduos das espécies. A descoberta de SNPs por algoritmos computacionais é uma prática bastante difundida e o presente texto apresenta um modelo que se baseia em lógica difusa (fuzzy logic) para, a partir de resultados prévios, auxiliar na tomada de decisão, nos casos em que as informações preliminares sejam divergentes, assim como, na confirmação...
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Modelagem difusa; Inferência difusa; Descoberta de conhecimento; Polimorfismo de base única; Variabilidade genética; Lógica fuzzy; Sequências de cDNA; Descoberta de conhecimento em bases de dados; Suporte à decisão; Single nucleotide polymorphisms; FuzzyMorphic.pl.; Knowledge discovery in database; Decision support.
Ano: 2009 URL: http://www.alice.cnptia.embrapa.br/handle/doc/513035
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Prevalence of IFNL3 gene polymorphism among blood donors and its relation to genomic profile of ancestry in Brazil BJID
Rizzo,Silvia Renata Cornelio Parolin; Gazito,Diana; Pott-Junior,Henrique; Latini,Flavia Roche Moreira; Castelo,Adauto.
ABSTRACT The recent development of interferon-free regimens based on direct-acting antivirals for the treatment of chronic hepatitis C virus infection has benefited many but not all patients. Some patients still experience treatment failure, possibly attributed to unknown host and viral factors, such as IFNL3 gene polymorphism. The present study assessed the prevalence of rs12979860-CC, rs12979860-CT, and rs12979860-TT genotypes of the IFNL3 gene, and its relationship with ancestry informative markers in 949 adult Brazilian healthy blood donors. Race was analyzed using ancestry informative markers as a surrogate for ancestry. IFNL3 gene was genotyped using the ABI TaqMan single nucleotide polymorphisms genotyping assays. The overall frequency of...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Ancestry informative markers; Chronic hepatitis C virus infection; Direct-acting antivirals; Single nucleotide polymorphisms.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702016000600619
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Single nucleotide polymorphisms predisposing to asthma in children of Mauritian Indian and Chinese Han ethnicity BJMBR
Ramphul,K.; Lv,J.; Hua,L.; Liu,Q.H.; Fang,D.Z.; Ji,R.X.; Bao,Y.X..
Our objective was to investigate the distributions of six single nucleotide polymorphisms (SNPs) MS4A2 E237G, MS4A2 C-109T, ADRB2 R16G, IL4RA I75V,IL4 C-590T, and IL13 C1923T in Mauritian Indian and Chinese Han children with asthma. This case-control association study enrolled 382 unrelated Mauritian Indian children, 193 with asthma and 189 healthy controls, and 384 unrelated Chinese Han children, 192 with asthma and 192 healthy controls. The SNP loci were genotyped using polymerase chain reaction (PCR)-restriction fragment length polymorphism for the Chinese Han samples and TaqMan real-time quantitative PCR for the Mauritian Indian samples. In the Mauritian Indian children, there was a significant difference in the distribution of IL13 C1923T between the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Asthma; Single nucleotide polymorphisms; Mauritian Indian; Chinese Han.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2014000500394
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SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment Genet. Mol. Biol.
Labuschagne,Christiaan; Dalton,Desiré L.; Grobler,J. Paul; Kotzé,Antoinette.
Abstract The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros. We found that a combined dataset of SNPs and microsatellites was most informative with the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Single nucleotide polymorphisms; Microsatellite markers; White Rhinoceros; Ceratotherium simum.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000100084
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