RESUMO

Several methods have been used for genome-enabled prediction (or genomic selection) of complex traits, for example, multiple regression models describing a target trait with a linear function of a set of genetic markers. Genomic selection studies have been focused mostly on single-trait analyses. However, most profitability traits are genetically correlated, and an increase in prediction accuracy of genomic breeding values for genetically correlated traits is expected when using multiple-trait models. Thus, this study was carried out to assess the accuracy of genomic prediction for carcass and meat quality traits in Nelore cattle, using single- and multiple-trait approaches. The study considered 15 780, 15 784, 15 742 and 526 records of rib eye area (REA, cm2), back fat thickness (BF, mm), rump fat (RF, mm) and Warner-Bratzler shear force (WBSF, kg), respectively, in Nelore cattle, from the Nelore Brazil Breeding Program. Animals were genotyped with a low-density single nucleotide polymorphism (SNP) panel and subsequently imputed to arrays with 54 and 777 k SNPs. Four Bayesian specifications of genomic regression models, namely, Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression; blending methods, BLUP; and single-step genomic best linear unbiased prediction (ssGBLUP) methods were compared in terms of prediction accuracy using a fivefold cross-validation. Estimates of heritability ranged from 0.20 to 0.35 and from 0.21 to 0.46 for RF and WBSF on single- and multiple-trait analyses, respectively. Prediction accuracies for REA, BF, RF and WBSF were all similar using the different specifications of regression models. In addition, this study has shown the impact of genomic information upon genetic evaluations in beef cattle using the multiple-trait model, which was also advantageous compared to the single-trait model because it accounted for the selection process using multiple traits at the same time. The advantage of multi-trait analyses is attributed to the consideration of correlations and genetic influences between the traits, in addition to the non-random association of alleles.

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RESUMO

Utilizaram-se registros de pesos corporais padronizados aos 120, 210, 365 e 450 dias de idade, provenientes de 30.481 animais da raça Nelore, progênies de 211 reprodutores acasalados com 19.229 matrizes, oriundos de rebanhos dos estados de Mato Grosso, Mato Grosso do Sul e Goiás, com o objetivo de avaliar a presença de interação genótipo x ambiente entre os estados. As estimativas de herdabilidade entre os estados variaram de 0,09 a 0,14; 0,11 a 0,17; 0,16 a 0,27 e 0,17 a 0,35, respectivamente, para os pesos 120, 210, 365 e 450 dias de idade. As estimativas de correlação genética aditiva entre a mesma característica para os diferentes estados apresentaram valores inferiores a 0,80. As correlações de Spearman entre os valores genéticos para os pesos corporais se reduziram à medida que se aumentou a intensidade de seleção sobre os reprodutores. A presença de interação genótipo x ambiente causa maior impacto sobre a avaliação genética dos reprodutores sob intensidade de seleção elevada, sendo interessante sua consideração no processo de avaliação genética. Estimativas de tendências genéticas para todos os pesos corporais apresentaram-se crescentes ao longo dos anos nos três estados.(AU)

Data of adjusted alive weights at 120, 210, 365 and 450 days of age of 30,481 records of animals of the Nellore beef cattle breed from herds of states of Mato Grosso, Mato Grosso do Sul, and Goiás were used to study the influence of environment genotype interaction on genetic evaluation of sires. Estimates of heritability between the states ranged from 0.09 to 0.14; 0.11 to 0.17; 0.16 to 0.27 and 0.17 to 0.35, respectively for live weights 120, 210, 365 and 450 days of age. The estimates of additive genetic correlation between the same characteristic for the different states presented values lower than 0.80. Spearman correlations between breeding values obtained from live weights of sires lowered as the intensity of selection on sires increased. The presence of environment genotype interaction has greater impact on the genetic evaluation of breeding under high intensity of selection, being an interesting consideration in the process of genetic evaluation. Estimates of genetic trends for all body weights have been increasing over the years in all three states.(AU)

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RESUMO

Utilizaram-se registros de pesos corporais padronizados aos 120, 210, 365 e 450 dias de idade, provenientes de 30.481 animais da raça Nelore, progênies de 211 reprodutores acasalados com 19.229 matrizes, oriundos de rebanhos dos estados de Mato Grosso, Mato Grosso do Sul e Goiás, com o objetivo de avaliar a presença de interação genótipo x ambiente entre os estados. As estimativas de herdabilidade entre os estados variaram de 0,09 a 0,14; 0,11 a 0,17; 0,16 a 0,27 e 0,17 a 0,35, respectivamente, para os pesos 120, 210, 365 e 450 dias de idade. As estimativas de correlação genética aditiva entre a mesma característica para os diferentes estados apresentaram valores inferiores a 0,80. As correlações de Spearman entre os valores genéticos para os pesos corporais se reduziram à medida que se aumentou a intensidade de seleção sobre os reprodutores. A presença de interação genótipo x ambiente causa maior impacto sobre a avaliação genética dos reprodutores sob intensidade de seleção elevada, sendo interessante sua consideração no processo de avaliação genética. Estimativas de tendências genéticas para todos os pesos corporais apresentaram-se crescentes ao longo dos anos nos três estados.(AU)

Data of adjusted alive weights at 120, 210, 365 and 450 days of age of 30,481 records of animals of the Nellore beef cattle breed from herds of states of Mato Grosso, Mato Grosso do Sul, and Goiás were used to study the influence of environment genotype interaction on genetic evaluation of sires. Estimates of heritability between the states ranged from 0.09 to 0.14; 0.11 to 0.17; 0.16 to 0.27 and 0.17 to 0.35, respectively for live weights 120, 210, 365 and 450 days of age. The estimates of additive genetic correlation between the same characteristic for the different states presented values lower than 0.80. Spearman correlations between breeding values obtained from live weights of sires lowered as the intensity of selection on sires increased. The presence of environment genotype interaction has greater impact on the genetic evaluation of breeding under high intensity of selection, being an interesting consideration in the process of genetic evaluation. Estimates of genetic trends for all body weights have been increasing over the years in all three states.(AU)

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The female reproductive performance, productivity and size are strongly associated with production efficiency of herds raised in a tropical environment. The age at first calving (AFC), accumulated productivity (AP), stayability (STAY) and mature weight (MW) could be used as indicators of these traits. In this study, the genetic parameters and correlations between AFC, AP, STAY and MW measured in Nellore females were estimated, in order to provide support for the beef cattle evaluation programs. In addition, the genetic changes for these traits were obtained. The (co)variance components were estimated by Gibbs sampling by four-trait multivariate analysis, using a threshold animal model for STAY and linear animal model for the other traits (AFC, AP and MW). Heritability of AFC, AP and STAY showed low values, with posterior means of 0.13 ± 0.02, 0.14 ± 0.01 and 0.19 ± 0.03, respectively. On the other hand, for MW were estimated mean heritability of 0.44 ± 0.03 and repeatability of 0.77 ± 0.03, demonstrating the importance of genetic and permanent environmental effects for the expression of beef cows' size. The AFC showed null genetic correlation with AP (-0.06 ± 0.12) and MW (0.01 ± 0.09) and low and negative with STAY (-0.15 ± 0.11). The AP showed high genetic correlation with STAY (0.86 ± 0.03) and weak with MW (0.23 ± 0.09). Positive and moderate genetic association was estimated between STAY and MW (0.66 ± 0.05). Annual direct genetic trends of 0.19 kg, 0.30 units and 0.10 kg were estimated for AP, STAY and MW, respectively, and were significant (P < 0.05) for STAY and MW. For AFC, negative and favorable annual genetic change was estimated (-0.08 months, P < 0.05). In this population, the selection of heifers for an early reproductive age should have little influence, however favorable, in the time that the cows remain in the herd. The use of AP as a selection criterion should result in smaller changes in the females' mature weight when compared to selection based on STAY.

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We assessed whether single nucleotide polymorphisms (SNPs) in the genes beta 1,4- galactosyltransferase (B4GALT1), luteinizing hormone receptor (LHR), follicle-stimulating hormone receptor (FSHR) and insulin-like growth factor 2 (IGF2) could be molecular markers for scrotal circumference (SC) in Nellore bulls. Animals with positive (+, n = 104) and negative (-, n = 74) expected progeny difference for scrotal circumference at 365 days (EPD SC 365) were selected and their SNPs were analyzed by restriction fragment length polymorphism (RFLP). The correlation between EPD SC 365 and expected progeny difference for age at first birth (EPD AFB) was also investigated. The SNPs in B4GALT1 and FSHR was not different between two groups analyzed. The CC genotype for LHR gene was most frequent in animals with EPD SC 365(+), whereas the TT was most frequent in the EPD SC 365(-). For IGF2 the CT and CC were the most frequent genotypes observed in animals with positive and negative EPD SC 365, respectively. The EPD SC 365 was negatively correlated with the EPD AFB (r = 0.23). We suggest that CC and TT genotypes for LHR and IGF2, respectively, could be possible molecular markers for SC selection in Nellore bulls, that can also predict for AFB.

Foram avaliados se polimorfismos de base única (SNPs) presentes nos genes beta-1,4- galactosiltransferase (B4GALT1), receptor de hormônio luteinizante (LHR), receptor de hormônio folículo estimulante (FSHR) e fator de crescimento semelhante à insulina 2 (IGF2) poderiam ser marcadores moleculares para o perímetro escrotal (PE) em touros da raça Nelore. Animais com diferença esperada de progênie positiva (+, n = 104) e negativa (-, n = 74) para PE aos 365 dias (DEP PE 365) foram selecionados e seus SNPs foram analisados utilizando a técnica de polimorfismo de comprimento de fragmentos de restrição (RFLP). A correlação entre DEP PE 365 e idade ao primeiro parto (DEP IPP) também foi investigada. Os SNPs dos genes B4GALT1 e FSHR não apresentaram diferença entre os dois grupos analisados. O genótipo CC para o gene LHR foi mais freqüente em animais com DEP PE 365 (+), enquanto o TT foi mais frequente no grupo com DEP PE 365 (-). Para o gene IGF2, os genótipos CT e CC foram mais freqüentes em animais com DEP PE 365 positiva e negativa, respectivamente. A DEP PE 365 foi negativamente correlacionada com a DEP IPP (r = -0,23). O genótipo CC para o gene LHR e genótipo TT para o gene IGF2 podem ser possíveis marcadores de PE para a seleção assistida em touros da raça Nelore, podendo ser ainda preditores para IPP.

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We assessed whether single nucleotide polymorphisms (SNPs) in the genes beta 1,4- galactosyltransferase (B4GALT1), luteinizing hormone receptor (LHR), follicle-stimulating hormone receptor (FSHR) and insulin-like growth factor 2 (IGF2) could be molecular markers for scrotal circumference (SC) in Nellore bulls. Animals with positive (+, n = 104) and negative (-, n = 74) expected progeny difference for scrotal circumference at 365 days (EPD SC 365) were selected and their SNPs were analyzed by restriction fragment length polymorphism (RFLP). The correlation between EPD SC 365 and expected progeny difference for age at first birth (EPD AFB) was also investigated. The SNPs in B4GALT1 and FSHR was not different between two groups analyzed. The CC genotype for LHR gene was most frequent in animals with EPD SC 365(+), whereas the TT was most frequent in the EPD SC 365(-). For IGF2 the CT and CC were the most frequent genotypes observed in animals with positive and negative EPD SC 365, respectively. The EPD SC 365 was negatively correlated with the EPD AFB (r = 0.23). We suggest that CC and TT genotypes for LHR and IGF2, respectively, could be possible molecular markers for SC selection in Nellore bulls, that can also predict for AFB.(AU)

Foram avaliados se polimorfismos de base única (SNPs) presentes nos genes beta-1,4- galactosiltransferase (B4GALT1), receptor de hormônio luteinizante (LHR), receptor de hormônio folículo estimulante (FSHR) e fator de crescimento semelhante à insulina 2 (IGF2) poderiam ser marcadores moleculares para o perímetro escrotal (PE) em touros da raça Nelore. Animais com diferença esperada de progênie positiva (+, n = 104) e negativa (-, n = 74) para PE aos 365 dias (DEP PE 365) foram selecionados e seus SNPs foram analisados utilizando a técnica de polimorfismo de comprimento de fragmentos de restrição (RFLP). A correlação entre DEP PE 365 e idade ao primeiro parto (DEP IPP) também foi investigada. Os SNPs dos genes B4GALT1 e FSHR não apresentaram diferença entre os dois grupos analisados. O genótipo CC para o gene LHR foi mais freqüente em animais com DEP PE 365 (+), enquanto o TT foi mais frequente no grupo com DEP PE 365 (-). Para o gene IGF2, os genótipos CT e CC foram mais freqüentes em animais com DEP PE 365 positiva e negativa, respectivamente. A DEP PE 365 foi negativamente correlacionada com a DEP IPP (r = -0,23). O genótipo CC para o gene LHR e genótipo TT para o gene IGF2 podem ser possíveis marcadores de PE para a seleção assistida em touros da raça Nelore, podendo ser ainda preditores para IPP.(AU)

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This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal and direct genetic effects). In contrast, W120 should be preferred when the objective is improving the maternal ability of the dams. Furthermore, selection for postWWG can be used if the animals show both heavier weaning weights and high growth rate after weaning because it is possible to shorten the time between weaning and slaughter based on weaning weight, postWWG, and desired weight at the time of slaughter.

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The aim of this study was to estimate genetic parameters for scrotal circumference at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), ribeye area (REA), backfat (BF) thickness, and rump fat (RF) thickness, in order to provide information on potential traits for Nelore cattle breeding program. Genetic parameters were estimated using the Average Information Restricted Maximum Likelihood method in single- and multitrait analyses. Four different animal models were tested for SC365, SC450, REA, BF, and RF in single-trait analyses. For SC365 and SC450, the maternal genetic effect was statistically significant (P < 0.01) and was included for multitrait analyses. The direct heritability estimates for SC365, SC450, AFC, REA, BF, and RF were equal to 0.31, 0.38, 0.24, 0.32, 0.16, and 0.19, respectively. Maternal heritability for SC365 and SC450 was equal to 0.06 and 0.08, respectively. The highest genetic correlations were found among the scrotal circumferences. Testing for the inclusion of maternal effects in genetic parameters estimation for scrotal circumference should be evaluated in the Nelore breeding program, mostly for correctly ranking the animal's estimated breeding values. Similar heritability estimates were observed for scrotal circumference, as well as favorable genetic correlations of this trait with AFC and carcass traits. Thus, scrotal circumference measured at 365 days of age could be a target trait for consideration in the Nelore selection index in order to improve most of the traits herein analyzed.

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The aims of our study were to estimate genetic parameters for body weight and visual scores and to evaluate their inclusion as selection criteria in the Nelore breeding program in Brazil. The traits studied were the body weight adjusted to 210 (W210) and to 450 (W450) days of age and visual scores for body structure, finishing precocity, and muscling evaluated at weaning (BSW, FPW, and MSW) and yearling (BSY, FPY, and MSY) ages. A total of 33,242, 26,259, 23,075, and 26,057 observations were considered to analyze W210, W450, and visual scores at weaning and yearling. The significant (P < 0.05) fixed effects for all traits were farm, birth season, birth year, sex, and management group. Single-trait analyses were performed to define the most fitting model to our data using the average information restricted maximum likelihood algorithm, for weaning traits. Subsequently, these models were used in single- and two-trait analyses considering the Bayesian inference algorithm. Two-trait Bayesian analyses resulted in average direct heritability estimates for BSW, FPW, MSW, W210, BSY, FPY, MSY, and W450 of 0.28, 0.30, 0.27, 0.28, 0.40, 0.44, 0.39, and 0.50, respectively. Genetic correlations varied from 0.40 to 0.96. Benefits to animal performance can best be achieved by considering body structure, finishing precocity, and muscling as selection criteria in the Nelore breeding programs. The decision to use visual scores measured at weaning should be considered in order to decrease generation interval and assist pre-selecting individuals, expecting carcass improvements in the future progeny.

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Foram utilizados 138.976 registros de informações de pesos corporais variando de 60 a 610 dias de idade, provenientes de 27.327 animais da raça Nelore, oriundos de rebanhos do estado do Mato Grosso, com o objetivo de descrever a variabilidade genética e estimar parâmetros genéticos para o peso corporal em diferentes idades, utilizando-se modelos de regressão aleatória. O modelo empregado incluiu efeitos fixos de grupo de contemporâneos e idade da vaca ao parto como covariáveis, além de efeitos aleatórios genético aditivo direto, genético materno, ambiente permanente de animal, ambiente permanente materno e efeito de ambiente temporário. O modelo de regressão aleatória mais adequado foi o que empregou função de covariância com polinômios de quarta ordem para descrição da variabilidade de todos os efeitos e duas classes de variância residual. As estimativas de variância genética aditiva direta e de ambiente permanente de animal aumentaram com a idade dos animais. As variâncias genética materna e de ambiente permanente materno exibiram comportamento semelhante, com maiores valores na fase de aleitamento. Os coeficientes de herdabilidade estimados variam de 0,25 a 0,43, com maiores valores nas idades mais avançadas na trajetória de crescimento dos animais. Esses resultados indicaram presença de variabilidade genética suficiente para obtenção de ganho genético expressivo por meio da seleção, principalmente após desmama. Os resultados encontrados para a correlação genética aditiva direta exibiram baixas correlações entre pesos nas idades iniciais e finais, porém pesos altamente correlacionados entre idades mais próximas. As correlações genéticas estimadas entre os pesos da desmama com os pesos até 610 dias de idade foram altas e positivas e indicam que os genes responsáveis por maiores pesos nesse período, em sua maioria, são os mesmos.

In this study 138,976 records of live weight between 60 to 610 days of age, from 27,327 Nellore cattle breed, from herds in Mato Grosso State were used in order to describe the genetic variability and to estimate genetic parameters for the live weight at different ages, using random regression models. The model included the fixed effects of contemporary group and age of cow at calving as covariate, random effects of direct additive genetic, maternal genetic, animal and maternal permanent environmental and temporary environment effect. The most appropriate random regression model employed the covariance function with fourth order polynomials to describe the variability of all effects and two residual variance classes. Estimates of direct additive genetic variance and animal permanent environment increased with the age of the animals. Maternal genetic variances and maternal permanent environment exhibited similar behavior, with higher values in pre weaning. The estimated heritability coefficients ranged from 0.25 to 0.43, with higher values at older ages in the growth trajectory of the animals. These results showed the presence of sufficient genetic variability to obtain significant genetic gain through selection, especially after weaning. The results for the direct additive genetic correlation exhibited low correlations between weights in initial and final ages, however, highly correlated weights between nearest ages. Genetic correlation estimates between weaning with weights up to 610 days of age were high and positive and indicate that most of the genes responsible for higher weights in this period are the same.

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