Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

ABSTRACT: The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

RESUMO: Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Nonlinear mixed models for characterization of growth trajectory of New Zealand rabbits raised in tropical climate.

OBJECTIVE: The identification of nonlinear mixed models that describe the growth trajectory of New Zealand rabbits was performed based on weight records and carcass measures obtained using ultrasonography. METHODS: Phenotypic records of body weight (BW) and loin eye area (LEA) were collected from 66 animals raised in a didactic-productive module of cuniculture located in the southern Piauí state, Brazil. The following nonlinear models were tested considering fixed parameters: Brody, Gompertz, Logistic, Richards, Meloun 1, modified Michaelis-Menten, Santana, and von Bertalanffy. The coefficient of determination (R2), mean squared error, percentage of convergence of each model (%C), mean absolute deviation of residuals, Akaike information criterion (AIC), and Bayesian information criterion (BIC) were used to determine the best model. The model that best described the growth trajectory for each trait was also used under the context of mixed models, considering two parameters that admit biological interpretation (A and k) with random effects. RESULTS: The von Bertalanffy model was the best fitting model for BW according to the highest value of R2 (0.98) and lowest values of AIC (6,675.30) and BIC (6,691.90). For LEA, the Logistic model was the most appropriate due to the results of R2 (0.52), AIC (783.90), and BIC (798.40) obtained using this model. The absolute growth rates estimated using the von Bertalanffy and Logistic models for BW and LEA were 21.51g/d and 3.16 cm2, respectively. The relative growth rates at the inflection point were 0.028 for BW (von Bertalanffy) and 0.014 for LEA (Logistic). CONCLUSION: The von Bertalanffy and Logistic models with random effect at the asymptotic weight are recommended for analysis of ponderal and carcass growth trajectories in New Zealand rabbits. The inclusion of random effects in the asymptotic weight and maturity rate improves the quality of fit in comparison to fixed models.

Cox-Gompertz model for analysis of the time of stay in an Anglo-Nubian goat herd / Modelo de Cox-Gompertz para análise do tempo de permanência em um rebanho de cabras da raça Anglonubiana

Anglo-Nubian goats are hardy animals able to adapt to tropical environments, where their farming is usually held on pasture. However, climatic conditions in this environment also favor endoparasitism, which implies a negative aspect if sensitivity to worm infections interferes by reducing the reproductive lifespan of females, as their stay in the herd is a trait of great importance for efficient goat farming. In this respect, this study proposes to use the survival analysis methodology with the Cox-Gompertz proportional hazards model to assess the length of stay in the herd by relating the removal of females due to death with worm infection being the main cause to other forms of culling, using information from 101 Anglo-Nubian goats born from2009 to 2013 in an experimental herd from Teresina - PI, Brazil. The Cox-Gompertz proportional hazards model chose body condition score, birth weight and birth season as important covariates (p-value ≤ 10%). Body condition score showed to be a favorable factor for the longer stay of the goats in the herd. Eggs per gram, age at first kidding, birth type and dam age were not significant. The Cox-Gompertz proportional hazards model is suitable for fitting the statistical model to estimate the length of stay in the herd, with censoring related to endoparasitism in Anglo-Nubian goats.

Os caprinos da raça Anglonubiana apresentam-se rústicos com adaptabilidade a ambiente tropical, onde sua exploração ocorre geralmente em pasto. Entretanto, condições climáticas desse ambiente favorecem também o endoparasitismo, implicando num aspecto negativo se a sensibilidade a verminoses interferir reduzindo a duração da vida reprodutiva de fêmeas, pois a permanência delas no rebanho é uma característica de grande importância para a maior eficiência da caprinocultura. Neste contexto, objetiva-se com este estudo utilizar a metodologia de análise de sobrevivência com modelo de riscos proporcionais de Cox-Gompertz para avaliação do tempo permanência no rebanho, relacionando a saída da fêmea por morte tendo a verminose como a principal causa, em relação a outras formas de descarte, utilizando-se informações de 101 cabras da raça Anglonubiana nascidas no período de 2009 a 2013 em rebanho experimental localizado em Teresina-Piauí. O modelo de riscos proporcionais de Cox-Gompertz, elegeu como covariáveis importantes (p-valor ≤ 10%): o escore da condição corporal (ECC), o peso ao nascer(PN) e a estação de nascimento (EN). O ECC se apresentou como fator favorável a maior permanência das cabras no rebanho. Não foram significativos o OPG, idade ao primeiro parto, tipo de nascimento e idade da mãe. O modelo de riscos proporcionais de Cox-Gompertz se mostra adequado no ajuste do modelo estatístico para estimar o tempo de permanência no rebanho, com censura relacionada a endoparasitismo em cabras da raça Anglonubiana.

Cox-Gompertz model for analysis of the time of stay in an Anglo-Nubian goat herd / Modelo de Cox-Gompertz para análise do tempo de permanência em um rebanho de cabras da raça Anglonubiana

Anglo-Nubian goats are hardy animals able to adapt to tropical environments, where their farming is usually held on pasture. However, climatic conditions in this environment also favor endoparasitism, which implies a negative aspect if sensitivity to worm infections interferes by reducing the reproductive lifespan of females, as their stay in the herd is a trait of great importance for efficient goat farming. In this respect, this study proposes to use the survival analysis methodology with the Cox-Gompertz proportional hazards model to assess the length of stay in the herd by relating the removal of females due to death with worm infection being the main cause to other forms of culling, using information from 101 Anglo-Nubian goats born from2009 to 2013 in an experimental herd from Teresina - PI, Brazil. The Cox-Gompertz proportional hazards model chose body condition score, birth weight and birth season as important covariates (p-value ≤ 10%). Body condition score showed to be a favorable factor for the longer stay of the goats in the herd. Eggs per gram, age at first kidding, birth type and dam age were not significant. The Cox-Gompertz proportional hazards model is suitable for fitting the statistical model to estimate the length of stay in the herd, with censoring related to endoparasitism in Anglo-Nubian goats.(AU)

Os caprinos da raça Anglonubiana apresentam-se rústicos com adaptabilidade a ambiente tropical, onde sua exploração ocorre geralmente em pasto. Entretanto, condições climáticas desse ambiente favorecem também o endoparasitismo, implicando num aspecto negativo se a sensibilidade a verminoses interferir reduzindo a duração da vida reprodutiva de fêmeas, pois a permanência delas no rebanho é uma característica de grande importância para a maior eficiência da caprinocultura. Neste contexto, objetiva-se com este estudo utilizar a metodologia de análise de sobrevivência com modelo de riscos proporcionais de Cox-Gompertz para avaliação do tempo permanência no rebanho, relacionando a saída da fêmea por morte tendo a verminose como a principal causa, em relação a outras formas de descarte, utilizando-se informações de 101 cabras da raça Anglonubiana nascidas no período de 2009 a 2013 em rebanho experimental localizado em Teresina-Piauí. O modelo de riscos proporcionais de Cox-Gompertz, elegeu como covariáveis importantes (p-valor ≤ 10%): o escore da condição corporal (ECC), o peso ao nascer(PN) e a estação de nascimento (EN). O ECC se apresentou como fator favorável a maior permanência das cabras no rebanho. Não foram significativos o OPG, idade ao primeiro parto, tipo de nascimento e idade da mãe. O modelo de riscos proporcionais de Cox-Gompertz se mostra adequado no ajuste do modelo estatístico para estimar o tempo de permanência no rebanho, com censura relacionada a endoparasitismo em cabras da raça Anglonubiana.(AU)

Comparison of genetic parameters and estimated breeding values for worm resistance in meat sheep obtained using traditional and genomic models.

Gastrointestinal nematode infections have caused expressive losses in sheep production worldwide. The improvement of host genetic resistance to worms has been used as a strategy to mitigate this problem. In this sense, the inclusion of genomic information has shown potential to increase the accuracy of prediction of breeding values and speed up selection. In this study, we aimed to compare estimates of genetic parameters and breeding values for traits that indicate the resistance to gastrointestinal nematode infection in Santa Inês sheep using the pedigree-based BLUP or including genomic information. There were 1478 animals in the pedigree, of which 271 were genotyped using the OvineSNP50 BeadChip (Illumina, Inc.). The host resistance was assessed using the following traits: fecal nematode egg counts (FEC); FAMACHA score (FAMACHA); and resistance to gastrointestinal nematode infection (RGNI) as a combination of FEC, FAMACHA, body condition score, and hematocrit. The genetic parameters and breeding values were estimated using single- and multi-trait analyses. For RGNI, the heritability estimates ranged from 0.25 using the single-trait genomic model (S-H) to 0.54 using the traditional multi-trait model (M-A). The heritability estimates for FEC ranged from 0.06 to 0.36, using the single-trait pedigree-based model (S-A) and the multi-trait genomic model (M-H), respectively. For FAMACHA, the heritability estimates ranged from 0.46 (M-H) to 0.54 (M-A). Estimates of genetic correlation ranged from 0.22 to 0.69. The inclusion of genomic information provided gain in accuracy for all traits. All estimates of predictive ability obtained using genomic data in a multi-trait setting were higher than those obtained using single-trait models. The estimates of predictive ability ranged from 0.03 (S-A) to 0.46 (M-H). The heritability estimates obtained using genomic information showed that all traits evaluated are suitable for genomic selection. Despite the low accuracies obtained, the use of the genomic model provided more accurate estimates of breeding values in comparison to the pedigree-based model.

Genetic evaluation of sheep for resistance to gastrointestinal nematodes and body size including genomic information.

OBJECTIVE: The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the efficiency of including genomic information in the analyses. METHODS: There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses. RESULTS: The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from -0.65±0.31 to 0.59±0.19, using A, and from -0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses. CONCLUSION: The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses.

Influence of non-genetic factors on the maternal ability of Santa Inês ewes / Influência de fatores não-genéticos na habilidade materna de ovelhas Santa Inês

The aim of this study was to evaluate the influence of different non-genetic effects on indicator traits for maternal ability in Santa Inês ewes. Data included performance records of 100 lambs (males and females) born from 59 dams, from 2009 to 2012. The analyzed traits were birth weight (BW), weaning weight (WW), average daily gain from birth until weaning (ADGBW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). The effects analyzed were the year of birth of the lamb, birth season, dam age at lambing, dam weight at lambing, sex of the lamb, lamb birth type, interaction between sex and birth type, and interaction between sex and birth season. SAS® software (SAS University Edition, USA) was used for calculation of the analysis of variance, means, and Pearson correlation coefficients. With the exception of the birth season, all the other environmental effects evaluated had a significant influence on at least one of the studied traits. The correlation estimates ranged from low to high and were either positive or negative. Birth weight was negatively correlated with the birth type and influenced positively all the other performance traits evaluated. The maternal ability of Santa Inês ewes was more clearly influenced by the age and weight of the dam at lambing, and the lamb birth type.(AU)

O objetivo deste estudo foi avaliar a influência de diferentes efeitos não-genéticos sobre características indicadoras de habilidade materna em ovelhas da raça Santa Inês. Os dados utilizados incluíram registros de desempenho de 100 cordeiros (machos e fêmeas) filhos de 59 ovelhas, nascidos de 2009 a 2012. As características analisadas foram peso ao nascimento (PN), peso ao desmame (PD), ganho médio diário do nascimento ao desmame (GMND), peso total das crias ao nascer (PTCN) e peso total das crias ao desmame (PTCD). Os efeitos analisados foram ano de nascimento da cria, estação de nascimento, idade da mãe ao parto, peso da mãe ao parto, sexo da cria, tipo de nascimento da cria, interação entre sexo e tipo de nascimento, e interação entre sexo e estação de nascimento. O programa SAS (SAS University Edition, EUA) foi utilizado para o cálculo de análise de variância, médias e coeficientes de correlação de Pearson. Com exceção da estação de nascimento, os demais efeitos avaliados exerceram influência significativa sobre pelo menos uma das características estudadas. As estimativas de correlação variaram de baixa a alta magnitude e foram tanto positivas quanto negativas. O peso da cria ao nascimento foi negativamente correlacionado com o tipo de nascimento e influenciou positivamente todas as outras características de desempenho avaliadas. A habilidade materna de ovelhas Santa Inês foi mais claramente influenciada pela idade e peso da mãe ao parto e pelo tipo de nascimento da cria.(AU)

Non-hierarchical cluster analysis for determination of resistance to worm infection in meat sheep.

The aim of this study was to determine the resistance to worm infection in Santa Inês sheep by combining different sets of gastrointestinal parasite resistance indicator traits, using the k-means algorithm. Records from 221 animals reared in the Mid-North sub-region of Brazil were used. The following phenotypes were used: hematocrit (HCT); white blood cell count; red blood cell count (RBC); hemoglobin (HGB); platelets; mean corpuscular hemoglobin; mean corpuscular volume; mean corpuscular hemoglobin concentration; fecal egg count (FEC); coloration of the ocular mucosa (FAMACHA score); body condition score (BCS); withers height; and rump height. Two files with phenotypic information of animals were edited: complete, including all traits, and reduced, in which only FAMACHA score, HCT, FEC, and BCS were used. For determination of worm resistance, three groups were formed using the k-means non-hierarchical clustering by combining the traits of the complete and reduced analyses. The animals of the group in which individuals had the lowest values for FEC and FAMACHA score, as well as the highest values for HCT, RBC, HGB, and BCS were classified as resistant. In the group with opposite values for the aforementioned traits, the animals were classified as sensitive. The animals of the group with values between the other two groups were classified as moderately resistant. The results obtained in complete and reduced analyses were equivalent. Thus, it is possible to identify animals of the Santa Inês sheep breed according to their status of resistance to worm infection based on a reduced trait set.

WITHDRAWN: Genetic structure and diversity of Santa Inês sheep flocks in Brazilian Mid-North.

Ahead of Print article withdrawn by publisher.

Genetic parameters for marbling and body score in Anglonubian goats using Bayesian inference via threshold and linear models.

OBJECTIVE: The aim of this study was to estimate (co) variance components and genetic parameters for categorical carcass traits using Bayesian inference via mixed linear and threshold animal models in Anglonubian goats. METHODS: Data were obtained from Anglonubian goats reared in the Brazilian Mid-North region. The traits in study were body condition score, marbling in the rib eye, ribeye area, fat thickness of the sternum, hip height, leg perimeter, and body weight. The numerator relationship matrix contained information from 793 animals. The single- and two-trait analyses were performed to estimate (co) variance components and genetic parameters via linear and threshold animal models. For estimation of genetic parameters, chains with 2 and 4 million cycles were tested. An 1,000,000-cycle initial burn-in was considered with values taken every 250 cycles, in a total of 4,000 samples. Convergence was monitored by Geweke criteria and Monte Carlo error chain. RESULTS: Threshold model best fits categorical data since it is more efficient to detect genetic variability. In two-trait analysis the contribution of the increase in information and the correlations between traits contributed to increase the estimated values for (co) variance components and heritability, in comparison to single-trait analysis. Heritability estimates for the study traits were from low to moderate magnitude. CONCLUSION: Direct selection of the continuous distribution of traits such as thickness sternal fat and hip height allows obtaining the indirect selection for marbling of ribeye.

Behavioral and thermoregulatory characteristics of Dorper sheep

The objective of this study was to evaluate the behavioral and thermoregulatory characteristics of Dorper sheep. The experiment involved 12 adult females in which the respiratory frequency (RF), heart rate (HR), and rectal temperature (RT) were measured and the following behavioral activities were evaluated: Idling while standing, Idling while lying, Drinking, Ruminating while standing, Ruminating while lying, Defecating, Urinating, Walking, Vocalizing, Biting, Coughing, Playing, Fighting, Rubbing, Self-cleaning, and Sleeping. The physical analysis of the thermal environment in the facility was obtained at the meteorological station of the Technical School of Teresina, where the air temperature (AT) and air relative humidity (ARH) were recorded. The black globe humidity index was obtained using a thermometer inserted in a black globe. A significant difference was detected for AT and ARH, especially the former, which had a higher value in the afternoon period (36.5 ºC). A significant effect was observed for the physiological variables, for which the highest values were found in the afternoon period, as follows: 85.30 mov./min, 93.11 beats/min, and 39.51 ºC (RF, HR, and RT, respectively). Air temperature had positive correlations of 0.572, 0.516, and 0.165 with all thermoregulatory characteristics (RF, HR, and RT, respectively). There was a significant difference for the ‘Idling while standing, ‘Idling while lying, ‘Ruminating while lying, ‘Vocalizing, ‘Eating, ‘Playing, and ‘Sleeping behaviors in relation to the evaluated periods of the day. The animals showed a certain level of thermal discomfort, especially in the afternoon period.(AU)

Behavioral and thermoregulatory characteristics of Dorper sheep

The objective of this study was to evaluate the behavioral and thermoregulatory characteristics of Dorper sheep. The experiment involved 12 adult females in which the respiratory frequency (RF), heart rate (HR), and rectal temperature (RT) were measured and the following behavioral activities were evaluated: Idling while standing, Idling while lying, Drinking, Ruminating while standing, Ruminating while lying, Defecating, Urinating, Walking, Vocalizing, Biting, Coughing, Playing, Fighting, Rubbing, Self-cleaning, and Sleeping. The physical analysis of the thermal environment in the facility was obtained at the meteorological station of the Technical School of Teresina, where the air temperature (AT) and air relative humidity (ARH) were recorded. The black globe humidity index was obtained using a thermometer inserted in a black globe. A significant difference was detected for AT and ARH, especially the former, which had a higher value in the afternoon period (36.5 ºC). A significant effect was observed for the physiological variables, for which the highest values were found in the afternoon period, as follows: 85.30 mov./min, 93.11 beats/min, and 39.51 ºC (RF, HR, and RT, respectively). Air temperature had positive correlations of 0.572, 0.516, and 0.165 with all thermoregulatory characteristics (RF, HR, and RT, respectively). There was a significant difference for the ‘Idling while standing’, ‘Idling while lying’, ‘Ruminating while lying’, ‘Vocalizing’, ‘Eating’, ‘Playing’, and ‘Sleeping’ behaviors in relation to the evaluated periods of the day. The animals showed a certain level of thermal discomfort, especially in the afternoon period.

Estimate of genetic parameters for carcass traits and visual scores inmeat sheep using Bayesian inference via threshold and linear models / Estimativa de parâmetros genéticos para características de carcaça e escore corporal em ovinos de corte usando Inferência Bayesiana e modelos de limiar e linear

The aim of this study was to estimate the variance components and genetic parameters for marbling in the ribeye area (MRA) and body condition score (BCS) using Bayesian inference via mixed linear and threshold animal models. Data were obtained from Santa Ines breed sheep reared in the Brazilian Mid-North region. Analyses considering the Monte Carlo methods were performed with Markov chains from 500000 cycles onward. A 200000-cycle initial burn-in was considered with values taken at every 250 cycles, in a total of 1200 samples. The Monte Carlo Error deviations were low for the means heritability in all chains by both linear and threshold models. Additive variances estimated by threshold model were higher than those estimated by the linear model. Marble meat from the ribeye area and body condition score can be used as selection criteria to obtain genetic progress in Santa Inês sheep.

O objetivo deste estudo foi estimar componentes de variância e parâmetros genéticos para marmoreio na área de olho de lombo (MOL) e escore de condição corporal (ECC) usando Inferência Bayesiana por meio dos modelos animais linear misto e de limiar. Os dados foram obtidos em rebanhos de ovinos da raça Santa Inês criados no Meio-Norte do Brasil. As análises, considerando os métodos de Monte Carlo, foram realizadas com cadeias de Markov a partir de 500000 ciclos. Considerou-se burn-in inicial de 200000 ciclos com valores tomados a cada 250 ciclos, obtendo-se 1200 amostras. Os desvios do erro de Monte Carlo foram baixos para as herdabilidades médias em todas as cadeias, tanto pelo modelo linear quanto de limiar. As variâncias aditivas, estimadas pelo modelo de limiar, foram maiores que aquelas obtidas pelo modelo linear. O marmoreio na área de olho de lombo e o escore da condição corporal podem ser usados como critérios de seleção para obter progresso genético em ovinos da raça Santa Inês.

Estimate of genetic parameters for carcass traits and visual scores inmeat sheep using Bayesian inference via threshold and linear models / Estimativa de parâmetros genéticos para características de carcaça e escore corporal em ovinos de corte usando Inferência Bayesiana e modelos de limiar e linear

The aim of this study was to estimate the variance components and genetic parameters for marbling in the ribeye area (MRA) and body condition score (BCS) using Bayesian inference via mixed linear and threshold animal models. Data were obtained from Santa Ines breed sheep reared in the Brazilian Mid-North region. Analyses considering the Monte Carlo methods were performed with Markov chains from 500000 cycles onward. A 200000-cycle initial burn-in was considered with values taken at every 250 cycles, in a total of 1200 samples. The Monte Carlo Error deviations were low for the means heritability in all chains by both linear and threshold models. Additive variances estimated by threshold model were higher than those estimated by the linear model. Marble meat from the ribeye area and body condition score can be used as selection criteria to obtain genetic progress in Santa Inês sheep. (AU)

O objetivo deste estudo foi estimar componentes de variância e parâmetros genéticos para marmoreio na área de olho de lombo (MOL) e escore de condição corporal (ECC) usando Inferência Bayesiana por meio dos modelos animais linear misto e de limiar. Os dados foram obtidos em rebanhos de ovinos da raça Santa Inês criados no Meio-Norte do Brasil. As análises, considerando os métodos de Monte Carlo, foram realizadas com cadeias de Markov a partir de 500000 ciclos. Considerou-se burn-in inicial de 200000 ciclos com valores tomados a cada 250 ciclos, obtendo-se 1200 amostras. Os desvios do erro de Monte Carlo foram baixos para as herdabilidades médias em todas as cadeias, tanto pelo modelo linear quanto de limiar. As variâncias aditivas, estimadas pelo modelo de limiar, foram maiores que aquelas obtidas pelo modelo linear. O marmoreio na área de olho de lombo e o escore da condição corporal podem ser usados como critérios de seleção para obter progresso genético em ovinos da raça Santa Inês. (AU)

Genetic parameters for carcass traits and body size of meat sheep / Parâmetros genéticos para características de carcaça e tamanho corporal em ovinos de corte

The present study aimed to estimate variance components and heritability coefficients (h2) in Santa Inês sheep by single- and two-trait analyses for the traits loin eye area (LEA), length (LEL) and maximum depth (LED), in the longissimus dorsi muscle, subcutaneous fat thickness (SFT), fat thickness over the biceps femoris muscle (FTBF), croup height (CH), thoracic circumference (TC), thoracic depth (TD), body length (BL), and adult live weight (ALW). The restricted maximum likelihood (REML) was used to estimate variance components in an animal model. In both types of analyses, we estimated moderate heritability for all traits, with the exception of SFT, CH, TC, BL, and ALW (all of which yielded low h2 estimates). In two-trait analysis for body size, only TD yielded a lower h2 estimate, when compared to single-trait analysis. On the other hand, CH, TC, and BL yielded higher h2 estimates. Most estimates for variance components and h2 in two-trait analysis were higher than those in single-trait analysis. This finding suggests the possibility of a moderate response to selection for improvement in the carcass of meat sheep using the specific carcass traits evaluated (except SFT), highlighting LEA. The fat thickness over the biceps femoris muscle showed higher potential for response to direct selection for fat deposition than SFT. Thoracic depth showed higher potential for response...(AU)

Objetivou-se com esta pesquisa estimar componentes de variância e coeficientes de herdabilidade (h2) por análises uni e bicaracterística para as características área (AOL), comprimento (COL) e profundidade máxima (POL) de olho de lombo, no músculo longissimus dorsi, espessura de gordura subcutânea (EGS), espessura de gordura do músculo biceps femoris (EGBF), altura da garupa (AG), circunferência torácica (CT), profundidade torácica (PT), comprimento corporal (CC) e peso vivo à idade adulta (PA), em ovinos Santa Inês. Foi utilizado modelo animal pela metodologia da máxima verossimilhança restrita (REML). Estimou-se herdabilidade moderada para as características, nos dois tipos de análise, exceto para EGS, AG, CT, CC e PA, para as quais as estimativas foram de baixa magnitude. Nas análises bicaracterísticas para tamanho corporal, apenas PT apresentou menor estimativa de h2, quando comparado com a análise unicaracterística, enquanto que AG, CT e CC apresentaram valores maiores. Nas análises bicaracterísticas, a maioria das estimativas de componentes de variância e h2 foram superiores àquelas obtidas nas análises unicaracterística, o que evidencia a possibilidade de resposta moderada à seleção para melhoria da carcaça em ovinos de corte usando as características de carcaça avaliadas, com exceção de EGS e com destaque para área de olho de lombo. A espessura de gordura do músculo...(AU)

Genetic parameters for carcass traits and body size of meat sheep / Parâmetros genéticos para características de carcaça e tamanho corporal em ovinos de corte

The present study aimed to estimate variance components and heritability coefficients (h2) in Santa Inês sheep by single- and two-trait analyses for the traits loin eye area (LEA), length (LEL) and maximum depth (LED), in the longissimus dorsi muscle, subcutaneous fat thickness (SFT), fat thickness over the biceps femoris muscle (FTBF), croup height (CH), thoracic circumference (TC), thoracic depth (TD), body length (BL), and adult live weight (ALW). The restricted maximum likelihood (REML) was used to estimate variance components in an animal model. In both types of analyses, we estimated moderate heritability for all traits, with the exception of SFT, CH, TC, BL, and ALW (all of which yielded low h2 estimates). In two-trait analysis for body size, only TD yielded a lower h2 estimate, when compared to single-trait analysis. On the other hand, CH, TC, and BL yielded higher h2 estimates. Most estimates for variance components and h2 in two-trait analysis were higher than those in single-trait analysis. This finding suggests the possibility of a moderate response to selection for improvement in the carcass of meat sheep using the specific carcass traits evaluated (except SFT), highlighting LEA. The fat thickness over the biceps femoris muscle showed higher potential for response to direct selection for fat deposition than SFT. Thoracic depth showed higher potential for response...

Objetivou-se com esta pesquisa estimar componentes de variância e coeficientes de herdabilidade (h2) por análises uni e bicaracterística para as características área (AOL), comprimento (COL) e profundidade máxima (POL) de olho de lombo, no músculo longissimus dorsi, espessura de gordura subcutânea (EGS), espessura de gordura do músculo biceps femoris (EGBF), altura da garupa (AG), circunferência torácica (CT), profundidade torácica (PT), comprimento corporal (CC) e peso vivo à idade adulta (PA), em ovinos Santa Inês. Foi utilizado modelo animal pela metodologia da máxima verossimilhança restrita (REML). Estimou-se herdabilidade moderada para as características, nos dois tipos de análise, exceto para EGS, AG, CT, CC e PA, para as quais as estimativas foram de baixa magnitude. Nas análises bicaracterísticas para tamanho corporal, apenas PT apresentou menor estimativa de h2, quando comparado com a análise unicaracterística, enquanto que AG, CT e CC apresentaram valores maiores. Nas análises bicaracterísticas, a maioria das estimativas de componentes de variância e h2 foram superiores àquelas obtidas nas análises unicaracterística, o que evidencia a possibilidade de resposta moderada à seleção para melhoria da carcaça em ovinos de corte usando as características de carcaça avaliadas, com exceção de EGS e com destaque para área de olho de lombo. A espessura de gordura do músculo...

Covariance structure for carcass and body size traits with repeated measures in sheep from different genetic groups / Estrutura de covariância para características de carcaça e tamanho corporal com medidas repetidas em ovinos de diferentes grupos genéticos

The purpose of this study was to evaluate the influence of environmental effects on body measurements, weight and carcass quality traits with structure of repeated measurements over time in sheep from different genetic groups. Collections were carried out from lamb in until 180 days of age, during the years 2012 and 2013, in 92 lambs from three genetic groups 29from Santa Inês breed, 43 crossbred Dorper x Santa Inês, and 20 crossbred Dorper x Morada Nova belonging to two flocks. Loin eye area, loin depth, subcutaneous fat thickness, height at withers, body length, thoracic depth, and body weight were measured. The effects of collection period, type of birth, sex, flock, genetic group, age of the animal at the time of measurement as a covariate in linear and quadratic effects, and interactions between the different effects were considered in the statistical model. Different structures were tested for modeling the residual (co) variance matrix. The structure that best fit the data was the Composed Symmetry. The interaction between genetic group and age as linear and quadratic effect was significantly important for modeling the traits studied. The environmental effects of the flock, type of birth, genetic group, and collection period influenced carcass traits, body measurements and weight.

Objetivou-se avaliar a influência de efeitos ambientais sobre medidas corporais, peso e características de qualidade de carcaça, com estrutura de mensurações repetidas no tempo, em ovinos de diferentes grupos genéticos. Foram realizadas coletas do nascimento aos 180 dias de idade, durante os anos de 2012 e 2013, em 92 cordeiros de 3 grupos genéticos, sendo 29 da raça Santa Inês, 43 mestiços Dorper x Santa Inês e 20 mestiços Dorper x Morada Nova, pertencentes a dois rebanhos. Foram mensuradas área e profundidade de olho de lombo, espessura de gordura subcutânea, altura da cernelha, comprimento corporal, profundidade torácica e peso corporal. O modelo estatístico considerou os efeitos de período de coleta, tipo de nascimento, sexo, rebanho, grupo genético, idade do animal no momento da mensuração como covariável, em efeitos linear e quadrático, e as interações entre os diferentes efeitos. Foram testadas diferentes estruturas para modelar a matriz de (co) variância residual. A estrutura que melhor se ajustou aos dados foi a Simetria Composta. A interação entre grupo genético e idade como efeito linear e quadrático foi significativamente importante para modelar as características estudadas. Os efeitos ambientais de propriedade, tipo de nascimento, grupo genético e período da mensuração influenciaram as características de carcaça, medidas corporais e peso.

Covariance structure for carcass and body size traits with repeated measures in sheep from different genetic groups / Estrutura de covariância para características de carcaça e tamanho corporal com medidas repetidas em ovinos de diferentes grupos genéticos

The purpose of this study was to evaluate the influence of environmental effects on body measurements, weight and carcass quality traits with structure of repeated measurements over time in sheep from different genetic groups. Collections were carried out from lamb in until 180 days of age, during the years 2012 and 2013, in 92 lambs from three genetic groups 29from Santa Inês breed, 43 crossbred Dorper x Santa Inês, and 20 crossbred Dorper x Morada Nova belonging to two flocks. Loin eye area, loin depth, subcutaneous fat thickness, height at withers, body length, thoracic depth, and body weight were measured. The effects of collection period, type of birth, sex, flock, genetic group, age of the animal at the time of measurement as a covariate in linear and quadratic effects, and interactions between the different effects were considered in the statistical model. Different structures were tested for modeling the residual (co) variance matrix. The structure that best fit the data was the Composed Symmetry. The interaction between genetic group and age as linear and quadratic effect was significantly important for modeling the traits studied. The environmental effects of the flock, type of birth, genetic group, and collection period influenced carcass traits, body measurements and weight.(AU)

Objetivou-se avaliar a influência de efeitos ambientais sobre medidas corporais, peso e características de qualidade de carcaça, com estrutura de mensurações repetidas no tempo, em ovinos de diferentes grupos genéticos. Foram realizadas coletas do nascimento aos 180 dias de idade, durante os anos de 2012 e 2013, em 92 cordeiros de 3 grupos genéticos, sendo 29 da raça Santa Inês, 43 mestiços Dorper x Santa Inês e 20 mestiços Dorper x Morada Nova, pertencentes a dois rebanhos. Foram mensuradas área e profundidade de olho de lombo, espessura de gordura subcutânea, altura da cernelha, comprimento corporal, profundidade torácica e peso corporal. O modelo estatístico considerou os efeitos de período de coleta, tipo de nascimento, sexo, rebanho, grupo genético, idade do animal no momento da mensuração como covariável, em efeitos linear e quadrático, e as interações entre os diferentes efeitos. Foram testadas diferentes estruturas para modelar a matriz de (co) variância residual. A estrutura que melhor se ajustou aos dados foi a Simetria Composta. A interação entre grupo genético e idade como efeito linear e quadrático foi significativamente importante para modelar as características estudadas. Os efeitos ambientais de propriedade, tipo de nascimento, grupo genético e período da mensuração influenciaram as características de carcaça, medidas corporais e peso.(AU)

Environmental effects on reproductive traits in Santa Ines sheep / Efeitos ambientais sobre características reprodutivas em ovinos Santa Inês

In this research we aimed to study environmental effects about litter size and weaning rate in Santa Ines sheep by means of generalized linear models. We used the data from experimental sheep herd of Santa Ines, of the Federal University of Piaui, Campus Professora Cinobelina Elvas, in Bom Jesus-PI, during 2008-2010. The environmental effects studied were: mating year, mating station, birth season, birth type, offspring sex, ewe age at birth, ewe weight at birth and birth weight as covariate. For statistical analysis we used the GENMOD procedure contained in SAS. Mean values for litter size and weaning rates were 1.36 and 68.18% respectively. The effect of ewe weight was significant about the litter size. There was no significant effect of birth season on the weaning rate. Correlations between productive and reproductive traits ranged from negative to positive low magnitude. The effects of ewe weight at birth and birth weight were important sources of variation for litter size and weaning rates, which reflects the need to consider these effects in models of genetic and phenotypic evaluation.

O objetivo com esta pesquisa foi estudar efeitos ambientais sobre a prolificidade e a taxa de desmame em ovinos Santa Inês, por meio de modelos lineares generalizados. Foram utilizados dados do rebanho experimental de ovinos da raça Santa Inês, da Universidade Federal do Piauí, Campus Universitário Professora Cinobelina Elvas, em Bom Jesus-PI, no período de 2008 a 2010. Os efeitos ambientais estudados foram: ano de cobertura, Período de cobertura, Período de nascimento, tipo de nascimento, sexo da cria, idade da mãe ao parto, peso da mãe ao parto e peso ao nascer como covariável. Para análise estatística foi utilizado o procedimento GENMOD contido no programa SAS. Os valores médios de prolificidade e taxa de desmame foram respectivamente 1,36 e 68,18%. O efeito do peso da mãe ao parto foi significativo sobre a prolificidade. Observou-se efeito significativo de Período de nascimento sobre a taxa de desmame. As correlações entre características produtivas e reprodutivas variaram de negativas a positivas de baixa magnitude. Os efeitos de peso da mãe ao parto e peso ao nascer mostraram-se importantes fontes de variação para prolificidade e taxa de desmame, o que reflete a necessidade de considerar estes efeitos em modelos de avaliação genética e fenotípica.