Diversidade genética de bovinos Brahman no Brasil por meio da análise de pedigree

The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.O objetivo deste trabalho foi avaliar a diversidade genética de bovinos da raça Brahman no Brasil com análise de pedigree. Registros genealógicos de uma subpopulação foram usados, tendo-se considerado toda a informação de pedigree (Pt) e a informação de pedigree dividida em dois períodos (P1, de 1994 a 2004; e P2, de 2005 a 2012) ou de acordo com sistema de criação (Ppt, animais a pasto; ou Pst, estabulados). Foram obtidas as estimativas de coeficientes médios de endogamia, intervalos de geração (IG), número equivalente de gerações conhecidas (EGC), número de fundadores (Nf), número efetivo de fundadores (fe), número efetivo de ancestrais (fa) e número efetivo de genomas remanescentes (fg). Os coeficientes médios de endogamia foram de 11,97, 7,79, 11,95, 11,74 e 11,31% para Pt, P1, P2, Ppt e Pst, respectivamente. O IG médio foi de 4,4 anos, enquanto o EGC médio foi de 3,18. O fe foi próximo de fa, cujos valores foram maiores que os de fg. As razões fe/fa e fg/fe foram próximas de 1, o que indica ausência de gargalo genético e pequenas perdas por deriva genética. A diversidade genética na raça Brahman no Brasil não está significativamente reduzida

Acurácia da predição genômica para altura do quadril em bovinos Brahman com uso de diferentes matrizes de parentesco

The objective of this work was to evaluate the effects of genomic information on the genetic evaluation of hip height in Brahman cattle using different matrices built from genomic and pedigree data. Hip height measurements from 1,695 animals, genotyped with high-density SNP chip or imputed from 50 K high-density SNP chip, were used. The numerator relationship matrix (NRM) was compared with the H matrix, which incorporated the NRM and genomic relationship (G) matrix simultaneously. The genotypes were used to estimate three versions of G: observed allele frequency (HGOF), average minor allele frequency (HGMF), and frequency of 0.5 for all markers (HG50). For matrix comparisons, animal data were either used in full or divided into calibration (80% older animals) and validation (20% younger animals) datasets. The accuracy values for the NRM, HGOF, and HG50 were 0.776, 0.813, and 0.594, respectively. The NRM and HGOF showed similar minor variances for diagonal and off-diagonal elements, as well as for estimated breeding values. The use of genomic information resulted in relationship estimates similar to those obtained based on pedigree; however, HGOF is the best option for estimating the genomic relationship matrix and results in a higher prediction accuracy. The ranking of the top 20% animals was very similar for all matrices, but the ranking within them varies depending on the method used.O objetivo deste trabalho foi avaliar os efeitos da informação genômica na avaliação genética para altura do quadril em bovinos da raça Brahman, por meio de diferentes matrizes construídas com dados genômicos e de pedigree. Utilizaram-se medidas de altura do quadril de 1.695 animais, genotipados com SNP chip de alta densidade ou imputados do 50 K SNP chip de alta densidade. A matriz de pedigree “numerator relationship matrix” (NRM) foi comparada à matriz H, a qual incorporou as matrizes NRM e de parentesco genômico (G) simultaneamente. Os genótipos foram utilizados para estimar três versões de G: frequência observada dos alelos (HGOF), média da menor frequência alélica (HGMF) e frequência de 0,5 para todos os marcadores (HG50). Para a comparação das matrizes, foram utilizadas informações completas ou divididas em conjuntos de dados de calibração (80% dos animais mais velhos) e de validação (20% dos mais jovens). Os valores de acurácia para NRM, HGOF e HG50 foram 0,776, 0,813 e 0,594, respectivamente. NRM e HGOF foram semelhantes, com menores variâncias para os elementos da diagonal e fora da diagonal, bem como para os valores genéticos estimados. O uso de informações genômicas resultou em estimativas de parentesco semelhantes às obtidas com base em pedigree; entretanto, H­GOF é a melhor opção para estimar a matriz de parentesco genômico e resulta em maiores acurácias de predição. O ranking dos animais top 20% foi muito semelhante para as matrizes, mas a classificação dentro destas varia dependendo do método

Estimativas de parâmetros genéticos para escores visuais e características de crescimento na raça Nelore

O presente trabalho teve dois objetivos. O primeiro foi estimar componentes de (co) variância e parâmetros genéticos dos escores visuais (Estrutura, Precocidade de acabamento e Musculosidade), com características de crescimento, como o peso aos 18 meses, ganho de peso diário e perímetro escrotal na raça Nelore. O segundo foi avaliar a aplicação dos modelos lineares mistos na estimação de parâmetros e predição de valores genéticos, para escores visuais, utilizando dados simulados. Para atingir o primeiro objetivo, foi usada uma base de dados com registros de 7256 machos, participantes de provas de ganho de peso. As estimativas dos componentes de (co) variância foram obtidas usando o método de Máxima Verossimilhança Restrita, com modelo animal. Os efeitos fixos de grupo contemporâneo, idade e peso como covariável (efeito linear) e, o efeito genético aditivo, como aleatório, foram considerados no modelo. Os grupos de contemporâneos foram definidos por animais pertencentes a uma mesma prova de ganho de peso. As estimativas de herdabilidade e os erros padrões foram de 0,30 (0,04) para estrutura corporal; 0,37 (0,04) para precocidade e 0,32 (0,04) para musculosidade. As estimativas de correlações genéticas entre os escores visuais apresentaram-se altas, de 0,76 a 0,95, sendo a correlação entre a precocidade e musculosidade a que apresentou o maior valor. Estas correlações indicam que as características de escores visuais, são controladas, em grande parte, pelo mesmo grupo de genes. As estimativas de correlações genéticas entre os escores visuais e as características de ganho de peso diário, peso aos 18 meses e o perímetro escrotal, apresentaram uma tendência semelhante entre os escores, 0,45 a 0,50 entre os escores visuais e o ganho de peso diário; 0,80 a 0,83 entre os escores...This study had two objectives. The first was to estimate the (co)variance components and genetic parameters of the visual scores (Structure, precocity, and musculature), with growth traits, such as weight at 18 months, average weight gain and scrotal circumference in Nellore cattle. The second was to evaluate the application of linear mixed models in the parameter estimation and prediction of breeding values for visual scores, using simulated data. The first objective was achieved, using records of 7256 male participants in the evidence of weight gain. Estimates of covariance were obtained using the method of Restricted Maximum Likelihood with animal model. The fixed effects of contemporary group, age and weight like a covariate (linear) and the genetic effect like random, were considered in the model. Contemporary groups were defined by animals belonging to the same evidence of weight gain. Heritability estimates and standard errors were 0,30 (0,04) for body structure; 0,37 (0,04) for precocity and 0,32 (0,04) for musculature. Estimates of genetic correlation between visual scores showed up high, from 0,76 to 0,95, and the correlation between precocity and musculature that showed the highest value. These correlations indicate that the characteristics of visual scores are controlled largely by the same group of genes. Estimates of genetic correlations among visual score and average weight gain, weight at 18 months and scrotal circumference showed a similar trend between the scores, from 0,45 to 0,50 between visual scores and average weight gain; 0,80 to 0,83 between visual scores and weight at 18 months and -0,05 to -0,03 between visual scores and scrotal circumference. Estimates indicate that individual selection for structure, musculature or precocity genetic changes will bring the same... (Complete abstract click electronic access below)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Metodologia de atribuição dos escores visuais e estudo de associação genômica para os escores de conformação, precocidade e musculosidade em bovinos Nelore

The visual scores are used as selection criteria in Brazilian cattle and aiming to improve the carcass traits. These traits have the particularity of being attributed depending on relative data and not on absolute references. This property could lead to difficulties in the estimation of genetic parameters and breeding values as well. Considering the importance of the visual scores, two studies were performed with the following objectives: 1) determine if the forms in which these scores are attributed have consequences in the genetic parameters and breeding values estimation, and, 2) identify regions of the genome that are associated with the scores of conformation, finishing precocity and muscling in Nellore cattle. For the first objective, a simulation study was conducted considering populations with and without selection, and three sizes of group attribution scores (10, 40 and 100 animals), these populations were mated for 12 overlapping generations. Genetic parameters and breeding values for each generation were estimated using a threshold model. The results indicate that the estimates of genetic parameters and breeding values are not affected by how the scores are attributed; however, the estimated breeding values are affected by the group size, being recommended the formation of evaluation groups more than 40 animals. For the second objective, a GWAS was conducted using BayesC and Bayesian LASSO models with two types of dependent variable. These variables were the phenotype and the deregressed breeding values (dEBV). In the analyses, a total of 2873 records of males and females from Nellore cattle were used. The animals were genotyped using the chip BovineHD of Illumina, after the quality control, a total of 309,865 SNPs were maintained. The association criterion was the proportion of genetic variance explained by 1 Mb genome windows. After the analyses, the BayesC model was the best fitted the data, as it explained a greater ...Os escores visuais são usados como critério de seleção com o objetivo de melhorar as características de carcaça. Estas características têm a particularidade de serem atribuídas com base em uma referência relativa, e não absoluta, o que pode trazer dificuldades na estimação de parâmetros e valores genéticos. Dada a importância dos escores, dois estudos foram conduzidos com os seguintes objetivos: 1) determinar se a forma de atribuir os escores, tem consequências na estimação de parâmetros e valores genéticos; e 2) identificar as regiões do genoma associadas com os escores de conformação, precocidade e musculosidade em bovinos da raça Nelore. Para o primeiro objetivo foi realizado um estudo de simulação, considerando populações com e sem seleção e três tamanhos de grupo de atribuição dos escores (10, 40 e 100 animais), as populações foram acasaladas ao longo de 12 gerações sobrepostas. A cada geração parâmetros e valores genéticos foram estimados usando um modelo de limiar. Os resultados indicaram que as estimativas de parâmetros e valores genéticos não são afetadas pela forma de atribuir os escores, entretanto os valores genéticos estimados são afetados pelo tamanho do grupo, sendo desejável a formação de grupos de avaliação superiores a 40 animais. Para o segundo objetivo foi realizado um GWAS usando dois modelos, BayesC e LASSO Bayesiano com duas classes de variáveis dependentes, o fenótipo dos escores e os valores genéticos desregredidos (dEBV). Nas análises foram utilizados 2873 registros de machos e fêmeas Nelore. Os animais foram genotipados com o painel BovineHD da Illumina, após o controle de qualidade restaram 309.865 SNPs. O critério de associação foi a porcentagem de variância genética explicada por janelas de 1 Mb de comprimento. Após as análises, o modelo BayesC foi o que se ajustou melhor aos dados, porque explicou uma maior proporção de variância fenotípica para..

Impact of reproductive and productive rates on levels of inbreeding and genetic gain of pigs through data simulation

The objective of this study was to evaluate the impact of farrowing and mortality rates on inbreeding levels and genetic gain through data simulation. Data came from two real populations A and B, composed of Pietrain and Landrace breed pigs, respectively. To generate the simulated populations, a Fortran-language simulator was developed using the (co)variances of the breeding values and productive and reproductive information obtained from populations A and B, as well as restrictions on mating and animals selected per generation. Two data files were created. The first contained the pedigree of the previous 10 years, with 21,906 and 251,343 animals in populations A and B, respectively. The second included the breeding values for age, backfat thickness, and feed conversion, all of which were adjusted for 110 kg live weight, for both populations; longissimus dorsi muscle depth adjusted for 110 kg live weight, for population A only; and number of live piglets at the fifth day of life per farrowing, for population B only. Three scenarios were simulated by varying the farrowing and mortality rates during the lactation period. Ten generations were simulated, with 30 replicates for each generation and scenario. Inbreeding levels in closed production units increase with productive and reproductive losses, and these reduce the variances of breeding values, selection intensity, and genetic gains by reducing the number of animals available for selection. Actions that maximize farrowing rates are more important than those that minimize mortality rates during the lactation period, since a reduction in simulated farrowing resulted in greater losses of genetic gain

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

<div><p>Abstract: The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.</p></div

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals

Estimates of genetic parameters for visual scores and their correlation with production and reproductive traits in Brahman cattle

The objective of this study was to evaluate the association of visual scores of body structure, precocity and muscularity with production (body weight at 18 months and average daily gain) and reproductive (scrotal circumference) traits in Brahman cattle in order to determine the possible use of these scores as selection criteria to improve carcass quality. Covariance components were estimated by the restricted maximum likelihood method using an animal model that included contemporary group as fixed effect. A total of 1,116 observations of body structure, precocity and muscularity were used. Heritability was 0.39, 043 and 0.40 for body structure, precocity and muscularity, respectively. The genetic correlations were 0.79 between body structure and precocity, 0.87 between body structure and muscularity, and 0.91 between precocity and muscularity. The genetic correlations between visual scores and body weight at 18 months were positive (0.77, 0.57 and 0.59 for body structure, precocity and muscularity, respectively). Similar genetic correlations were observed between average daily gain and visual scores (0.60, 0.57 and 0.48, respectively), whereas the genetic correlations between scrotal circumference and these scores were low (0.13, 0.02, and 0.13). The results indicate that visual scores can be used as selection criteria in Brahman breeding programs. Favorable correlated responses should be seen in average daily gain and body weight at 18 months. However, no correlated response is expected for scrotal circumference