68 results on '"Lopes, Fernando Brito"'
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52. Bayesian estimates of genetic parameters for reproductive traits in Nellore cows raised on pasture in tropical regions.
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Magnabosco, Cláudio Ulhôa, Lopes, Fernando Brito, de Magalhaes Rosa, Guilherme Jordão, and Sainz, Roberto Daniel
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COWS , *PARTURITION grounds , *COVARIANCE matrices , *BAYESIAN analysis , *PREGNANCY in animals - Abstract
Background: Nellore cows are well adapted to tropical conditions, and they have good maternal ability as well as long and prolific reproductive life. Objective: to estimate (co)variances and genetic parameters for calving interval (CI), age at first calving (AFC), gestation length (GL), and days open (DO) in Nellore cows. Methods: covariance components and genetic parameters were estimated using multi-trait Bayesian procedures. Results: three traits had low but statistically significant heritabilities, averaging 0.05, 0.10, and 0.04 for CI, GL, and DO, respectively, whereas age at first calving had a higher heritability (0.36). The permanent environmental effects for CI, GL, and DO were also low, averaging 0.08, 0.07, and 0.15, respectively. The genetic correlations between AFC and CI, AFC and GL, AFC and DO, GL and CI, CI and DO, GL and DO were 0.20, 0.12, 0.11, 0.02, 0.92, and -0.21, respectively. Selection for shorter CI would contribute towards decreasing DO. However, selection for decreased GL could result in a greater number of DO. Despite the favorable genetic correlations, the direct selection responses for these traits would be low. Conclusion: reproductive traits are strongly influenced by environmental effects. Changes in management and environmental factors could rapidly improve reproductive performance of Polled Nellore herds. Genetic selection for these traits should produce a much slower but permanent response. [ABSTRACT FROM AUTHOR]
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- 2016
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53. Índices de seleção para bovinos da raça Nelore participantes de provas de ganho em peso em confinamento
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Marques, Ednira Gleida, primary, Magnabosco, Claudio Ulhoa, additional, and Lopes, Fernando Brito, additional
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- 2012
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54. Breeding goals and selection criteria for intensive and semi-intensive dairy goat system in Brazil
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Lopes, Fernando Brito, primary, Borjas, Arcadio de los Reyes, additional, da Silva, Marcelo Correia, additional, Facó, Olivardo, additional, Lôbo, Raimundo Nonato, additional, Fiorvanti, Maria Clorinda Soares, additional, and McManus, Concepta, additional
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- 2012
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55. Tendência genética para características relacionadas à velocidade de crescimento em bovinos Nelore da região norte do Brasil
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Lopes, Fernando Brito, primary, Santos, Geneíldes Cristina de Jesus, additional, Marques, Ednira Gleida, additional, Silva, Marcelo Corrêa da, additional, and Ferreira, Jorge Luis, additional
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- 2012
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56. Tendência genética para pesos padronizados aos 205, 365 e 550 dias de idade de bovinos Nelore da região norte do Brasil
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Santos, Geneíldes Cristina de Jesus, primary, Lopes, Fernando Brito, additional, Marques, Ednira Gleida, additional, Silva, Marcelo Corrêa da, additional, Cavalcante, Tânia Vasconcelos, additional, and Ferreira, Jorge Luis, additional
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- 2012
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57. Quantitative genetic analysis for meat tenderness trait in Polled Nellore cattle.
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de Castro, Letícia Mendes, Magnabosco, Cláudio Ulhôa, Sainz, Roberto Daniel, de Faria, Carina Ubirajara, and Lopes, Fernando Brito
- Abstract
Copyright of Revista Ciência Agronômica is the property of Revista Ciencia Agronomica and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2014
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58. EFICIÊNCIA DA FERTILIZAÇÃO FOSFATADA E NITROGENADA EM CULTIVARES DE MILHETO.
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DA SILVA, ALZIRA GABRIELA, DE SOUZA FRANÇA, ALDI FERNANDES, MIYAGI, ELIANE SAYURI, DAMBROS, CARLOS EDUARDO, and LOPES, FERNANDO BRITO
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PEARL millet varieties ,PEARL millet yields ,NITROGEN content of plants ,NITROGEN fertilizers ,PHOSPHATE fertilizers ,PEARL millet research - Abstract
Copyright of Ciência Animal Brasileira is the property of Universidade Federal de Goias, Escola de Veterinaria and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2014
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59. Multivariate approach of inter-relationships among growth, consumption and carcass traits in Nellore cattle.
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Magnaboscoz, Cláudio Ulhôa, Lopes, Fernando Brito, Miyagi, Eliane Sayuri, Lôbo, Raysildo Barbosa, and Sainz, Roberto Daniel
- Abstract
Copyright of Revista Ciência Agronômica is the property of Revista Ciencia Agronomica and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2014
60. TENDÊNCIAS GENÉTICAS PARA CARACTERÍSTICAS DE CRESCIMENTO EM REBANHOS NELORE CRIADOS NA REGIÃO DO TRÓPICO ÚMIDO DO BRASIL.
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DE LIRA, THAYMISSON SANTOS, DE SOUSA PEREIRA, LEONARDO, LOPES, FERNANDO BRITO, FERREIRA, JORGE LUIS, LÔBO, RAYSILDO BARBOSA, and DE JESUS SANTOS, GENEÍLDES CRISTINA
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CATTLE genetics ,CATTLE breeding ,HERITABILITY ,CALVES - Abstract
Copyright of Ciência Animal Brasileira is the property of Universidade Federal de Goias, Escola de Veterinaria and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2013
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61. Tendência genética para pesos padronizados aos 205, 365 e 550 dias de idade de bovinos Nelore da região norte do Brasil.
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De Jesus Santos, Geneíldes Cristina, Lopes, Fernando Brito, Marques, Ednira Gleida, Da Silva, Marcelo, Cavalcante, Tânia Vasconcelos, and Ferreira, Jorge Luis
- Abstract
Copyright of Acta Scientiarum: Animal Sciences is the property of Universidade Estadual de Maringa and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2012
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62. Prediction of biological age and evaluation of genome-wide dynamic methylomic changes throughout human aging.
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Roudbar, Mahmoud Amiri, Mousavi, Seyedeh Fatemeh, Ardestani, Siavash Salek, Lopes, Fernando Brito, Momen, Mehdi, Gianola, Daniel, and Khatib, Hasan
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STANDARD deviations , *AGE , *AGING , *DNA methylation , *HILBERT space , *SUBSET selection - Abstract
The use of DNA methylation signatures to predict chronological age and aging rate is of interest in many fields, including disease prevention and treatment, forensics, and anti-aging medicine. Although a large number of methylation markers are significantly associated with age, most age-prediction methods use a few markers selected based on either previously published studies or datasets containing methylation information. Here, we implemented reproducing kernel Hilbert spaces (RKHS) regression and a ridge regression model in a Bayesian framework that utilized phenotypic and methylation profiles simultaneously to predict chronological age. We used over 450,000 CpG sites from the whole blood of a large cohort of 4409 human individuals with a range of 10-101 years of age. Models were fitted using adjusted and un-adjusted methylation measurements for cell heterogeneity. Un-adjusted methylation scores delivered a significantly higher prediction accuracy than adjusted methylation data, with a correlation between age and predicted age of 0.98 and a root mean square error (RMSE) of 3.54 years in un-adjusted data, and 0.90 (correlation) and 7.16 (RMSE) years in adjusted data. Reducing the number of predictors (CpG sites) through subset selection improved predictive power with a correlation of 0.98 and an RMSE of 2.98 years in the RKHS model. We found distinct global methylation patterns, with a significant increase in the proportion of methylated cytosines in CpG islands and a decreased proportion in other CpG types, including CpG shore, shelf, and open sea (P<5e-06). Epigenetic drift seemed to be a widespread phenomenon as more than 97% of the age-associated methylation sites had heteroscedasticity. Apparent methylomic aging rate (AMAR) had a sex-specific pattern, with an increase in AMAR in females with age related to males. [ABSTRACT FROM AUTHOR]
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- 2021
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63. Use of automation to estimate food consumption, live weight and feed efficiency in beef bovine
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Crozara, Adriano Santana, Magnabosco, Cláudio Ulhôa, Eifert, Eduardo da Costa, Costa, Marcos Fernando de Oliveira e, Lopes, Fernando Brito, and Cavalcanti, Luigi Francis Lima
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Residual feed intake ,Nelore ,Balança automatizada ,Guzerá ,Guzera ,Automated balance ,PRODUCAO ANIMAL [ZOOTECNIA] ,Consumo alimentar residual - Abstract
Objetivou-se com o presente estudo verificar a correlação do consumo alimentar residual e variáveis de ganho e peso corporal obtidos por métodos de pesagem tradicional, a cada 14 dias e animais em jejum, e pesagem diária via balança automatizada, em testes de eficiência alimentar, também verificar a viabilidade de redução do tempo de duração do teste utilizando o sistema automatizado, identificando a quantidade de dias mínimos e adequados para mensuração acurada do consumo alimentar residual, ganho em peso, consumo de matéria seca e conversão alimentar. Foram utilizados 28 bovinos da raça Nelore e 16 da raça Guzerá, não castrados, com idade entre 18 e 21 meses. A prova teve duração de 70 dias, com uma pesagem inicial, quatro intermediárias e final. Os animais também foram pesados diariamente por meio de balanças eletrônicas acopladas aos bebedouros. As variáveis mensuradas para gerar as informação de eficiência alimentar (CA, EA e CAR) foram: consumo de matéria seca (CMS; kg/dia); ganho médio diário (GMD, kg/dia); peso vivo (PV; kg); espessura de gordura subcutânea (EG, mm) e, posteriormente, consumo alimentar residual (CAR; kg/dia). Efeitos de raça passaram por análise de variância de medidas repetidas, para a verificação da necessidade de analisa-la separadamente. Foi feito teste de médias para as características de peso inicial e final, GMD, CA e EA para as duas balanças. Para CAR, oriundo via informações da pesagem da balança tradicional e automatizada, foi feita a correlação entre eles, verificando sua magnitude. Foi verificada significância das inclinações das curvas de regressões de peso provindas das duas balanças. Foram feitas as correlações entre os pesos oriundos a partir da balança tradicional e automatizada, levadas em consideração as seis pesagens via balança tradicional no decorrer do teste de eficiência e as pesagens automatizadas inviabilizando os dias de possível interferência no peso devido ao jejum (um dia anterior e outro posterior ao jejum). Para verificação da possível redução de tempo para testes de eficiência alimentar, utilizando o sistema de pesagem automatizado, as variáveis de CAR, PV, GMD e CMS foram agrupadas obtendo valor médio a cada quatro dias. Estes dados sendo representativo para os dias 14, 18, 22, 26, 30, 34, 38, 42, 46, 50, 54, 58, 62 e 66 e 70. Assim, a partir das informações sequenciais das quatro características foram gerados os coeficientes de correlação de Pearson e Spearman em relação a informação final (70º dia) para as mesmas características e suas variações. O momento cuja a correlação foi significativa a 0,1% e diferença entre variâncias abaixo de 1% para cada característica considerou-se como adequado para o momento de conclusão para respectiva característica em teste de eficiência alimentar. Não foram encontradas diferenças entre médias das duas balanças para pesos inicial e final, CA e EA, apenas para GMD. As correlações de Pearson e Spearman do CAR entre os valores oriundos da pesagem via balança tradicional e automatizada foram, respectivamente, 0,75 e 0,76. As inclinações das retas para pesos entre as duas balanças foram estatisticamente semelhantes. Para redução do tempo de teste, levando em considerações a redução das variâncias e os coeficientes de correlação, recomenda-se que para as características de GMD e CA é possível uma redução para 58 dias, para CMS 38 dias e para CAR 34 dias. A utilização das balanças automatizadas pode servir como opção para informação do CAR em testes de eficiência alimentar. Ao conduzi-los utilizando estas é possível reduzir o período de teste de acordo com a característica desejada, ganho médio e conversão alimentar 58 dias, para consumo 38 dias e para consumo alimentar residual 34 dias, obtendo resultados confiáveis. The objective of this study was to verify the correlation of residual feed intake and gain and body weight variables obtained by traditional weighing methods, every 14 days and fasting animals, and daily weighing using an automated scale, in food efficiency tests, also verify the feasibility of reducing the duration of the test using the automated system, identifying the amount of minimum and adequate days for accurate measurement of residual feed intake, weight gain, dry matter intake and ratio conversion. A total of 28 Nellore and 16 Guzera cattle were used, not castrated and aged between 18 and 21 months. The test had a duration of 70 days, with an initial weighing, four intermediate and final weighing. The animals were also weighed daily by means of electronic scales coupled to drinking fountains. The variables measured to generate the food efficiency information (RC, FE and RFI) were: dry matter intake (DMI, kg/day); average daily gain (ADG, kg / day); live weight (LW, kg); subcutaneous fat thickness (mm) and, later, residual feed intake (RFI, kg/day). Cattle effects went through analysis of variance of repeated measures, to verify the need to analyze it separately. Averages test was performed for initial and final weight characteristics, ADG, RC and FE for the two scales. For RFI, originating from traditional and automated weighing information, was made a correlation between them, to verifying their magnitude. Significance of the slopes of the weight regression curves from the two scales was verified. Correlations were made between the weights from the traditional and automated scale, considering the six weighings by the traditional balance during the efficiency test and automated weighing disregarding the days of possible interference in weight due to fasting (one day before and one after the fast). To verify the possible reduction of time for food efficiency tests, using the automated weighing system, the variables of RFI, BW, ADG and DMI were grouped, obtaining an average value every four days. These data are representative for days 14, 18, 22, 26, 30, 34, 38, 42, 46, 50, 54, 58, 62 and 66 and 70. Thus, from the sequential information of the four characteristics, the Pearson and Spearman correlation coefficients were generated in relation to the final information (70th day) for the same characteristics and their variations. The moment when the correlation was significant at 0.1% and difference between variances below 1% for each characteristic was considered as adequate for the conclusion time for respective characteristic in food efficiency test. No differences were found between means of the two scales for initial and final weights, RC and FE, only for ADG. The Pearson and Spearman correlations of the RFI between the values obtained by weighing using the traditional and automated scale were, respectively, 0.75 and 0.76. The slopes of the lines for weights between the two scales were statistically similar. To reduce the test time, considering the reduction of the variances and the correlation coefficients, it is recommended that for the characteristics of ADG and RC it is possible to reduce to 58 days, for DMI 38 days and for RFI 34 days. The use of automated scale can serve as an option for RFI information in food efficiency tests. By conducting them using these it is possible to reduce the test period according to the desired characteristic, average gain and ratio conversion 58 days, for dry matter intake 38 days and for residual feed intake 34 days, obtaining reliable results. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
- Published
- 2018
64. Meta-analytical study of characteristics related to the quality of meat and in carcass bovine
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Cavalcante, Alliny Souza de Assis, Borges, Naida Cristina, Prado, Cristiano Sales, Lopes, Fernando Brito, and Ferreira, Jorge Luis
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Meta-analysis ,Quality of meat ,SAUDE ANIMAL (PROGRAMAS SANITARIOS) [MEDICINA VETERINARIA PREVENTIVA] ,Ultrassonografia ,Carcass ,Meta-análise ,Qualidade de carne ,Carcaça ,Ultrasonography - Abstract
O número do rebanho brasileiro vem crescendo exponencialmente, por este motivo, faz-se necessário alguns ajustes nos sistemas e desempenhos produtivos com objetivo de favorecer o aumento da produção e a oferta de carne no Brasil. Diversos fatores podem afetar de forma direta ou indireta na característica de qualidade da carne bovina, tais como na maciez, gordura e palatabilidade da carne que podem influenciar no preço final do produto. Algumas avaliações são realizadas para evidenciar a composição da carne no animal, são elas AOL, EG, EGP8, peso, PI, PF, PCQ, MAR e maciez. Estas características são realizadas para avaliação da composição da carne e espessura de gordura no animal. Devido ao grande número de pesquisas sobre qualidade de carne o presente trabalho foi conduzido com objetivo de se obter médias combinadas de parâmetros indicadores de qualidade de carne e carcaça, bem como verificar o efeito de determinados fatores sobre estes parâmetros utilizando a meta-análise como ferramenta. Os registros foram identificados através de pesquisa de banco de dados nos sites PubMed e Scielo no período de 2009 a 2016 com base em 49 artigos científicos que continham assuntos relacionados AOL, EG, EGP8 e maciez realizados em bovinos, totalizando uma média de 9.142 animais analisados em relação às características de carcaça e carne. A construção do banco de dados foi baseada em informações relativas ao sexo, idade, raça e peso do animal. Os resultados deste estudo demonstraram que as mensurações realizadas diretamente na carcaça apresentaram médias superiores às realizadas por ultrassonografia. The number of the Brazilian herd has been increasing exponentially, so it is necessary to adjust the production systems and performance with the objective of favoring the increase of production and a supply of meat in Brazil. A pay for the national court is only a live weight and there is no carcass yield of the animals, however with future changes in the scenario. Several factors may directly or indirectly influence the quality of beef, such as softness, fat and palatability of the meat that may influence the final price of the product. Some evaluations are performed to evidence the body composition, no animal, they are EM, BF and IMF. These evaluations are performed for evaluation of the meat composition and fat thickness of no animal. Due to the large number of researches on the quality of the material, the work was conducted with the aim of obtaining combined means of meat and carcass quality indicators, as well as to verify the effect of certain factors on these data using a meta-analysis as tool. The research was performed in the PubMed and Scielo sites from 2009 to 2016 based on 49 scientific papers containing AOL, EG and EGP8 carried out in cattle, totaling an average of 9,142 animals analyzed in relation to the carcass characteristics. Of the database for the purpose of sex, age, breed and weight of the animal. The results of this study demonstrated that the measurements were performed in the carcass, presenting averages higher than those performed by ultrasonography. Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
- Published
- 2017
65. Identification of SNPs and metabolic pathways associated with meat tenderness in polled nellore cattle
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Castro, Letícia Mendes de, Magnabosco, Cláudio Ulhôa, Rosa, Guilherme Jordão de Magalhães, Lopes, Fernando Brito, Magnabosco, Cláudio de Ulhoa, Rey, Fernando Sebastian Baldi, Costa, Marcos Fernando Oliveira e, Reis, Angela Adamski da Silva, and Pádua, João Teodoro de
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Calpastatina ,Calcium ion ,Ontologias gênicas ,GWAS ,Gene ontology ,MEDICINA VETERINARIA [CIENCIAS AGRARIAS] ,Proteína quinase ,Zebu ,Íon cálcio ,Calpastatin ,Protein kinase - Abstract
O Brasil tem um dos maiores rebanhos bovinos comerciais do mundo, mas a qualidade da carne é altamente variável. O rebanho nacional é em grande parte composto de raças Bos indicus, que em geral têm carne menos macia do que o gado Bos taurus, diminuindo o valor do produto. Objetivou-se nesse estudo identificar regiões genômicas e vias biológicas relevantes associadas com a maciez da carne em bovinos da raça Nelore Mocho. Além disso, objetivou-se também avaliar diferentes protocolos de controle de qualidade dos SNPs e as possíveis influências nos resultados de GWAS. Os dados consistiram em valores de WBSF do músculo Longissimus dorsi, após maturação de sete dias, de 427 animais Nelore Mocho. Os animais foram genotipados em marcadores SNP Illumina BovineHD Beadchip (777k) ou Chip GGP-Indicus (77k). Todos os SNPs passaram por um Call Rate de 90% para posterior imputação utilizando o software FImput. Para averiguar os diferentes protocolos de qualidade e suas influências no GWAS foram utilizados 590.915 marcadores. Os efeitos dos diferentes QCs foram verificados utilizando 16 protocolos com três limiares para MAF (MAF < 0,01;< 0,05 e < 0,10) e HWP (p < 0,01; < 0,0001 e < 0,00001) e suas possíveis combinações. Os GWASs foram realizados utilizando método P3D/EMMAx com os marcadores restantes de cada QC. No GWAS realizado para posterior análise das vias utilizou-se 369.007 marcadores após a exclusão de SNPs baseada nos filtros Call Rate < 90%, HWP p < 0,01 e MAF < 0,01. Grupo de abate e sexo foram incluídos no modelo como efeitos fixos. Marcadores significativos (p < 0,0001) foram localizados em todas as análises, e os cromossomos com maior quantidade de SNPs significativos dos diferentes QCs foram 3, 17, 20, 21, 25 e 27. No estudo de vias foram localizados SNPs significativos nos cromossomos 3, 13, 17, 20, 21 e 25, que explicaram maior proporção da variação, indicando que existem QTLs associados à maciez da carne nessas regiões do genoma. As análises dos diferentes QCs evidenciaram efeito do controle de qualidade dos SNPs sobre o GWAS e o filtro para MAF influenciou de maneira mais ampla os resultados. Foi realizada uma análise de enriquecimento de vias baseando-se nos SNPs do GWAS, utilizando o procedimento FatiGO. Apenas os genes com no mínimo um SNP significativo (p < 0,01) foram considerados. Foram utilizados 22.365 genes anotados, incluindo 1.010 genes significativos. Um total de 22 termos GO e duas entradas IP foram consideradas enriquecidas com genes significamente associados com a maciez da carne. Várias dessas categorias funcionais como atividade da proteína tirosina quinase e serina/treonina quinase, ligantes ao íon cálcio e fatores de crescimento, podem estar relacionadas com WBFS em bovinos da raça Nelore Mocho. Estes resultados ajudam elucidar as vias relacionadas com essa característica de extrema importância econômica para o Brasil, já que o Nelore é a raça de gado de corte dominante no país. Brazil has one of the largest commercial cattle herds worldwide, but its meat quality is highly variable. The national herd is largely composed of Bos indicus breeds, which in general have less tender meat than Bos taurus cattle, decreasing the product value. This study was carried out to identify relevant regions and biological pathways associated with meat tenderness in Polled Nellore cattle. It was also aimed to evaluate the effect of different quality control protocols in GWAS for meat tenderness in Polled Nellore cattle. The data consisted of Warner-Bratzler shear force (WBSF) values of Longissimus muscle after 7 days of ageing, from 427 Polled Nellore animals. The animals were genotyped using either the Illumina BovineHD Beadchip (777k) or the GGP-Indicus Chip (77k). SNPs were excluded when Call Rate < 90%, then the imputation from the GGP to the HD Chip was performed using the FImput’s software. To study the different quality control protocols and their influence in GWAS, 590,915 markers were used. The effect of different QCs were verified using 16 protocols with three thresholds for MAF (MAF < 0.01; < 0.05 and < 0.10) and HWP (p < 0.01; < 0.0001 and < 0.00001) and their possible combinations. GWASs were performed using the PD3/EMMAx method with the remaining markers of each QC. For GWAS performed for pathway analysis, 369,007 markers were used after SNPs were excluded when Call rate < 90%, HWP p < 0.01 and MAF < 0.01. Group of slaughter and sex were included as fixed effects. Significant markers (p < 0.0001) were found in all analysis, in which the chromosomes with more significant SNPs of the different QCs were 3, 17, 20, 21, 25 and 27, and in the pathway study were located on chromosomes 3, 13, 17, 20, 21 and 25 explaining great proportion of variation, indicating possible QTLs associated with meat tenderness in those genomic regions. The analyses of different QCs showed that there is an effect of quality control over GWAS, and the filter for MAF influenced the results more broadly. A pathway enrichment analysis based on SNPs from GWAS was performed using FatiGO’s procedure. 22,365 annotated genes, including 1,010 significant genes were used. Thus, 22 GO terms and two IP entries were deemed enriched. Several of these functional categories, such as protein tyrosine and serine/threonine kinase activity, calcium ion binding and growth factors can be related to WBSF in Polled Nellore cattle. These results help to elucidate the metabolic pathways related to this trait, which is of extreme economic and social importance to Brazil as Nellore is the dominant beef cattle breed in the country. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
- Published
- 2016
66. (Quasi) multitask support vector regression with heuristic hyperparameter optimization for whole-genome prediction of complex traits: a case study with carcass traits in broilers.
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Alves AAC, Fernandes AFA, Lopes FB, Breen V, Hawken R, Gianola D, and Rosa GJM
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- Animals, Bayes Theorem, Heuristics, Phenotype, Models, Genetic, Genotype, Multifactorial Inheritance, Chickens genetics
- Abstract
This study investigates nonlinear kernels for multitrait (MT) genomic prediction using support vector regression (SVR) models. We assessed the predictive ability delivered by single-trait (ST) and MT models for 2 carcass traits (CT1 and CT2) measured in purebred broiler chickens. The MT models also included information on indicator traits measured in vivo [Growth and feed efficiency trait (FE)]. We proposed an approach termed (quasi) multitask SVR (QMTSVR), with hyperparameter optimization performed via genetic algorithm. ST and MT Bayesian shrinkage and variable selection models [genomic best linear unbiased predictor (GBLUP), BayesC (BC), and reproducing kernel Hilbert space (RKHS) regression] were employed as benchmarks. MT models were trained using 2 validation designs (CV1 and CV2), which differ if the information on secondary traits is available in the testing set. Models' predictive ability was assessed with prediction accuracy (ACC; i.e. the correlation between predicted and observed values, divided by the square root of phenotype accuracy), standardized root-mean-squared error (RMSE*), and inflation factor (b). To account for potential bias in CV2-style predictions, we also computed a parametric estimate of accuracy (ACCpar). Predictive ability metrics varied according to trait, model, and validation design (CV1 or CV2), ranging from 0.71 to 0.84 for ACC, 0.78 to 0.92 for RMSE*, and between 0.82 and 1.34 for b. The highest ACC and smallest RMSE* were achieved with QMTSVR-CV2 in both traits. We observed that for CT1, model/validation design selection was sensitive to the choice of accuracy metric (ACC or ACCpar). Nonetheless, the higher predictive accuracy of QMTSVR over MTGBLUP and MTBC was replicated across accuracy metrics, besides the similar performance between the proposed method and the MTRKHS model. Results showed that the proposed approach is competitive with conventional MT Bayesian regression models using either Gaussian or spike-slab multivariate priors., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)
- Published
- 2023
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67. Prediction of biological age and evaluation of genome-wide dynamic methylomic changes throughout human aging.
- Author
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Amiri Roudbar M, Mousavi SF, Salek Ardestani S, Lopes FB, Momen M, Gianola D, and Khatib H
- Subjects
- Male, Female, Humans, Child, Preschool, Bayes Theorem, CpG Islands, Epigenesis, Genetic, DNA Methylation genetics, Aging genetics
- Abstract
The use of DNA methylation signatures to predict chronological age and aging rate is of interest in many fields, including disease prevention and treatment, forensics, and anti-aging medicine. Although a large number of methylation markers are significantly associated with age, most age-prediction methods use a few markers selected based on either previously published studies or datasets containing methylation information. Here, we implemented reproducing kernel Hilbert spaces (RKHS) regression and a ridge regression model in a Bayesian framework that utilized phenotypic and methylation profiles simultaneously to predict chronological age. We used over 450,000 CpG sites from the whole blood of a large cohort of 4409 human individuals with a range of 10-101 years of age. Models were fitted using adjusted and un-adjusted methylation measurements for cell heterogeneity. Un-adjusted methylation scores delivered a significantly higher prediction accuracy than adjusted methylation data, with a correlation between age and predicted age of 0.98 and a root mean square error (RMSE) of 3.54 years in un-adjusted data, and 0.90 (correlation) and 7.16 (RMSE) years in adjusted data. Reducing the number of predictors (CpG sites) through subset selection improved predictive power with a correlation of 0.98 and an RMSE of 2.98 years in the RKHS model. We found distinct global methylation patterns, with a significant increase in the proportion of methylated cytosines in CpG islands and a decreased proportion in other CpG types, including CpG shore, shelf, and open sea (P < 5e-06). Epigenetic drift seemed to be a widespread phenomenon as more than 97% of the age-associated methylation sites had heteroscedasticity. Apparent methylomic aging rate (AMAR) had a sex-specific pattern, with an increase in AMAR in females with age related to males., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)
- Published
- 2021
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68. Bayesian and Machine Learning Models for Genomic Prediction of Anterior Cruciate Ligament Rupture in the Canine Model.
- Author
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Baker LA, Momen M, Chan K, Bollig N, Lopes FB, Rosa GJM, Todhunter RJ, Binversie EE, Sample SJ, and Muir P
- Subjects
- Animals, Bayes Theorem, Dogs, Genome-Wide Association Study, Genomics, Machine Learning, Anterior Cruciate Ligament, Anterior Cruciate Ligament Injuries genetics
- Abstract
Anterior cruciate ligament (ACL) rupture is a common, debilitating condition that leads to early-onset osteoarthritis and reduced quality of human life. ACL rupture is a complex disease with both genetic and environmental risk factors. Characterizing the genetic basis of ACL rupture would provide the ability to identify individuals that have high genetic risk and allow the opportunity for preventative management. Spontaneous ACL rupture is also common in dogs and shows a similar clinical presentation and progression. Thus, the dog has emerged as an excellent genomic model for human ACL rupture. Genome-wide association studies (GWAS) in the dog have identified a number of candidate genetic variants, but research in genomic prediction has been limited. In this analysis, we explore several Bayesian and machine learning models for genomic prediction of ACL rupture in the Labrador Retriever dog. Our work demonstrates the feasibility of predicting ACL rupture from SNPs in the Labrador Retriever model with and without consideration of non-genetic risk factors. Genomic prediction including non-genetic risk factors approached clinical relevance using multiple linear Bayesian and non-linear models. This analysis represents the first steps toward development of a predictive algorithm for ACL rupture in the Labrador Retriever model. Future work may extend this algorithm to other high-risk breeds of dog. The ability to accurately predict individual dogs at high risk for ACL rupture would identify candidates for clinical trials that would benefit both veterinary and human medicine., (Copyright © 2020 Baker et al.)
- Published
- 2020
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