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Made available in DSpace on 2022-04-29T08:40:10Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-05-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objective of this study was to investigate potential causal relationships among hot carcass weight (HCW), longissimus muscle area (LMA), backfat thickness (BF), Warner-Bratzler shear force (WBSF), and marbling score (MB) traits in Nellore cattle using structural equation models (SEM). The SEM fitted comprises the following links between traits: WBSF → LMA, WBSF → HCW, HCW → LMA, BF → HCW, and BF → MB, where the arrows indicate the causal direction between traits, with structural coefficients posterior means (posterior standard deviation) equal to −0.29 cm2/kg (0.09), 0.43 kg/kg (0.29), 0.10 cm2/kg (0.006), 1.92 kg/mm (0.28), and 0.03 score-grade/mm (0.006), respectively. The final SEM revealed some important putative causal relationships among the traits studied here. The implied causal effects suggest that interventions on meat tenderness and fat content would affect overall growth and muscle deposition. Knowledge regarding potential causal relationships inferred among the traits studied here can have important implications for the genetic selection and management of Nellore cattle for improvement of carcass and meat quality. São Paulo State University (Unesp) School of Agricultural and Veterinarian Science Department of Animal Science, Via de Acesso Prof. Paulo Donato Castellane s/n, SP University of Wisconsin Department of Animal and Dairy Sciences, 436 Animal Science Building, 1675 Observatory Dr. São Paulo State University (Unesp) School of Veterinary Medicine and Animal Science Department of Animal Breeding and Nutrition, Rua Prof. Doutor Walter Mauricio Correa, s/n, SP National Council of Technological and Scientific Development (CNPq) São Paulo State University (Unesp) School of Agricultural and Veterinarian Science Department of Animal Science, Via de Acesso Prof. Paulo Donato Castellane s/n, SP São Paulo State University (Unesp) School of Veterinary Medicine and Animal Science Department of Animal Breeding and Nutrition, Rua Prof. Doutor Walter Mauricio Correa, s/n, SP CAPES: 001 FAPESP: 2009/16118-5 FAPESP: 2016/02366-0 FAPESP: 2017/18779-5

The objective of this study was to estimate genetic parameters for body weight of beef cattle in performance tests. Different random regression models with quadratic B-splines and heterogeneous residual variance were fitted to estimate covariance functions for body weights of Nellore and crossbred Charolais × Nellore bulls. The criteria −2 residual log-likelihood (−2RLL), Akaike Information Criterion (AIC), and consistent AIC (CAIC) were used to choose the most appropriate model. For Nellore bulls, residual variance was modeled with six classes of age, and direct additive genetic and permanent environment effects were modeled with quadratic B-splines with two and one intervals, respectively. For crossbred bulls, quadratic B-splines with one interval fitted direct additive genetic and permanent environment effects and nine classes of age were needed to fit residual variance. Pooling classes of age with up to 40% in difference of residual variances does not compromise the fit of the model. Heritability for body weight in performance tests are moderate (>0.25, for crossbred bulls) to high (>0.5, for Nellore bulls) and genetic correlation between weights over the test are also high (>0.65). Then, selection of young bulls in performance test is an efficient tool to increase body weight in beef cattle. Made available in DSpace on 2019-01-11T23:34:49Z (GMT). No. of bitstreams: 1 RamdomRegressionModels.pdf: 1787275 bytes, checksum: f4f686d9435ae56e7939c6f2edc9520c (MD5) Previous issue date: 2018-10-19

The aim of the present study was to obtain genetic parameters for resistance to ticks, gastrointestinal nematodes (worms) and Eimeria spp. in Nellore cattle, analyze the inclusion of resistance traits in Nellore breeding programs and evaluate genetic selection as a complementary tool in parasite control programs. Counting of ticks, gastrointestinal nematode eggs and Eimeria spp. oocysts per gram of feces totaling 4270; 3872 and 3872 records from 1188; 1142 and 1142 animals, respectively, aged 146 to 597 days were used. The animals were classified as resistant (counts equal to zero) or susceptible (counts above zero) to each parasite. The statistical models included systematics effects of contemporary groups and the mean trajectory. The random effects included additive genetic effects, direct permanent environmental effects and residual. The mean trajectory and random effects were modeled with linear Legendre polynomials for all traits except for the mean trajectory of resistance to Eimeria spp., which employed the cubic polynomial. Heritability estimates were of low to moderate magnitude and ranged from 0.06 to 0.30, 0.06 to 0.33 and 0.04 to 0.33 for resistance to ticks, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of genetic and environmental correlations for the same trait at different ages (205, 365, 450 and 550 days) were favorable at adjacent ages and unfavorable at distant ages. In general, the posterior mean of the genetic and environmental correlations between traits of resistance were low and high-density intervals were large and included zero in many cases. The heritability estimates support the inclusion of resistance to ticks, gastrointestinal nematodes and Eimeria spp. in Nellore breeding programs. Genetic selection can increase the frequency of resistant animals and be used as a complementary tool in parasite control programs.

Resumo: O objetivo deste trabalho foi determinar os parâmetros genéticos para o peso de bovinos Nelore, do nascimento até 1.000 dias de idade, por meio de modelos de regressão aleatória. Utilizaram-se 115.096 registros de peso de 19.417 animais. Os parâmetros genéticos foram obtidos por modelos de regressão aleatória via inferência bayesiana. A trajetória média de crescimento foi ajustada com um polinômio de Legendre quártico. O efeito genético aditivo direto foi ajustado com um polinômio quadrático de Legendre. Os efeitos de ambiente permanente direto e materno foram ajustados com polinômios de Legendre quíntico e quadrático, respectivamente. A variância residual foi modelada com três classes de idades. Os valores genéticos dos pesos, do nascimento até 1.000 dias de idade, foram utilizados para a análise da tendência genética, por meio de superfícies de resposta. As herdabilidades variaram entre 0,16 e 0,47. Os efeitos de ambiente permanente direto e materno foram responsáveis por 5 a 77% e 0,2 a 11% da variância fenotípica, respectivamente. As correlações genéticas dos pesos em diferentes idades foram altas e superiores a 0,40. Os valores genéticos foram crescentes ao longo dos anos, e a tendência genética foi máxima para peso aos 500 dias. Abstract: The objective of this work was to determine the genetic parameters for body weight of Nellore cattle, from birth to 1,000 days of age, by random regression models. Data from 115,096 body weight records of 19,417 animals were used. The genetic parameters were obtained by random regression models and Bayesian inference. The average growth trajectory was fitted by a fourth-order Legendre polynomial. The additive direct effect was fitted by a quadratic Legendre polynomial. Direct and maternal permanent environmental effects were fitted by the fifth- and second-order Legendre polynomials, respectively. Residual variance was modeled by three classes of age. The breeding values of weights obtained from birth to 1,000 days of age were used for the analysis of genetic trend by response surfaces. Heritability ranged from 0.16 to 0.47. The direct and maternal permanent environmental effects explained 5 to 77% and 0.2 to 11% of the phenotypic variance, respectively. The genetic correlations of body weights at different ages were high and above 0.40. Breeding values increased throughout the years, and genetic trend was maximum for body weight at 500 days.

The study reported here evaluated genotype × environment interaction in individual per- formance and progeny tests in beef cattle. Genetic parameters for final weight (FW), ADG, and scrotal cir - cumference (SC) of 33,013 Nellore young bulls tested on pasture or in feedlots were analyzed. The posterior means (and highest posterior density interval with 90% of samples (HPD90)) of heritability for traits measured on pasture-raised and feedlot-raised animals were 0.44 (HPD90 = 0.40 to 0.48) and 0.50 (HPD90 = 0.43 to 0.56) for FW, 0.26 (HPD90 = 0.23 to 0.29) and 0.26 (HPD90 = 0.20 to 0.32) for ADG, and 0.53 (HPD90 = 0.48 to 0.59) and 0.65 (HPD90 = 0.55 to 0.74) for SC, respectively. The posterior means (and HPD90) of genetic correlations for FW, ADG, and SC on pasture and in feedlots were 0.75 (HPD90 = 0.66 to 0.87), 0.49 (HPD90 = 0.31 to 0.66), and 0.89 (HPD90 = 0.83 to 0.97), respectively. When the selection intensity was kept the same for both the environments, the greatest direct responses for FW and ADG were exhibited by the animals reared and selected in feedlots. The cor- related responses relative to production on pasture and based on selection in feedlots were similar to the direct responses, whereas the correlated responses for pro- duction in feedlots and based on selection on pasture were lower than the direct responses. When the selec- tion intensity on pasture was higher than the selection intensity in feedlots, the responses to direct selection were similar for both the environments and correlated responses obtained in feedlots by selection on pasture were similar to the direct responses in feedlots. Analyses of few or poor indicators of genotype × environment interaction result in incorrect interpretations of its exis- tence and implications. The present work demonstrated that traits with lower heritability are more susceptible to genotype × environment interaction and that selection intensity plays an important role in the study of geno- type × environment interaction in beef cattle.

Objetivou-se identificar modelos de regressão aleatória adequados para análises genéticas do peso e resistência a carrapatos, nematoides gastrointestinais e Eimeria spp. em bovinos Nelore, utilizando-se polinômios de Legendre e inferência bayesiana. Foram utilizados 63.880, 4.270, 3.872 e 3.872 dados de peso, contagens de carrapatos, nematoides gastrointestinais e Eimeria spp. de 12.260, 1.188, 1.142 e 1.142 bovinos, respectivamente, com idades entre 146 e 597 dias. A matriz de parentesco foi composta por 15.927 animais. Os modelos consideraram os efeitos fixos de grupo de contemporâneos e a trajetória média para todas as características, e a idade da vaca ao parto (linear e quadrático) e idade do bezerro no dia da coleta (linear) para peso. Os efeitos genético aditivo direto, de ambiente permanente direto e o resíduo foram incluídos nos modelos de todas as características. Na análise do peso também foram incluídos os efeitos genético aditivo materno e de ambiente permanente materno. A variância residual do peso foi modelada com classes de idade, e os modelos foram avaliados com uma, quatro e oito classes. O modelo de melhor ajuste para peso considerou polinômios de Legendre cúbico para a trajetória média de crescimento, quártico para ajuste do efeito aditivo direto, e quíntico para os demais efeitos, bem como oito classes de idade para variância residual. Para as características de resistência, os modelos com melhores ajustes consideraram polinômios lineares para a trajetória média e para os efeitos aleatórios, exceto para a trajetória média da resistência a Eimeria spp., ajustada por um polinômio cúbico. As médias a posteriori da herdabilidade direta foram de baixa a alta magnitude e variaram entre 0,18 a 0,58; 0,07 a 0,30; 0,02 a 0,34 e 0,04 a 0,39, para peso, resistência a carrapatos, nematoides gastrointestinais e Eimeria spp., respectivamente. As médias a posteriori das correlações de todos os efeitos aleatórios do peso nas idades 205, 365 e 550 dias foram positivas e de baixa a alta magnitude. As médias a posteriori das correlações genéticas e ambientais para resistência aos parasitos entre as idades 205, 365, 450 e 550 dias foram favoráveis nas idades próximas e desfavoráveis nas idades mais distantes. Em geral, as médias a posteriori das correlações genéticas e ambientais entre as características de resistência aos diferentes parasitos foram baixas e o intervalo de alta densidade com 95% (HPD95%) das amostras foram amplos, e incluíram o zero na maioria dos casos. Exceto para a correlação genética entre resistência aos nematoides gastrointestinais e Eimeria spp. que foi alta e o HPD95% não incluiu o zero. Existe variabilidade genética aditiva suficiente para todas as características avaliadas, e progressos genéticos podem ser obtidos ao longo das gerações por meio da seleção. This work aimed to identify random regression models for genetic evaluation of weight and resistance to tick, gastrointestinal nematodes and Eimeria spp. in Nellore cattle, using Legendre polynomials and bayesian inference. The databases contained 63,880, 4,270, 3,872 and 3,872 records of body weight and resistance to tick, gastrointestinal nematodes and Eimeria spp. of 12,260, 1,188, 1,142 and 1,142 Nellore calves, respectively, from 146 to 597 days of age. The relationship matrix contained 15,927 animals. The models included the fixed effects of contemporary groups and the population mean trend for each trait, and age of dam at calving (linear and quadratic) and age of calf on weighing (linear) for body weight. The direct genetic additive, permanent environmental and residual effects were included in each model for all traits. In body weight analyses the maternal genetic additive and maternal permanent environment effects were also included. The residual variance for body weight was fitted into classes of age, and the models with one, four and eight classes were assessed. The best-fitting model for weight considered third order polynomial to fit the population mean trend, fourth order polynomial for direct additive, and fifth order polynomials for the remaining random effects, and eight classes of age for residual variance. For resistance traits, the best-fitting models considered linear polynomial for population mean trend and all random effects, except for the population mean trend of resistance to Eimeria spp., which was fitted by a third order polynomial. The posterior mean of direct heritability were low to high and ranged from 0.18 to 0.58, 0.07 to 0.38, 0.02 to 0.34 and from 0.04 to 0.39, for body weight, resistance to tick, gastrointestinal nematodes and Eimeria spp., respectively. The posterior mean of correlations for each random effect for body weight were positive with low to high magnitude between the pair of ages 205, 365 and 550 days. The posterior mean of genetic and environmental correlations between the pair of ages 205, 365, 450 and 550 days for the same resistance trait were favorable for closed ages and unfavorable for distant ages. In general, the posterior mean of genetic and environmental correlations between resistance traits were low and the high density intervals with 95% (HDI95%) of samples were large and included the zero in many cases. Exception for the genetic correlation between resistance to nematodes and Eimeria spp. which were high and the HDI95% did not contain zero. There was enough additive genetic variability for all traits and genetic progress can be achieved over generations through selection.

The use of polynomial functions to describe the average growth trajectory and covariance functions of Nellore and MA (21/32 Charolais+11/32 Nellore) young bulls in performance tests was studied. The average growth trajectories and additive genetic and permanent environmental covariance functions were fit with Legendre (linear through quintic) and quadratic B-spline (with two to four intervals) polynomials. In general, the Legendre and quadratic B-spline models that included more covariance parameters provided a better fit with the data. When comparing models with the same number of parameters, the quadratic B-spline provided a better fit than the Legendre polynomials. The quadratic B-spline with four intervals provided the best fit for the Nellore and MA groups. The fitting of random regression models with different types of polynomials (Legendre polynomials or B-spline) affected neither the genetic parameters estimates nor the ranking of the Nellore young bulls. However, fitting different type of polynomials affected the genetic parameters estimates and the ranking of the MA young bulls. Parsimonious Legendre or quadratic B-spline models could be used for genetic evaluation of body weight of Nellore young bulls in performance tests, whereas these parsimonious models were less efficient for animals of the MA genetic group owing to limited data at the extreme ages.

O objetivo deste trabalho foi determinar os parâmetros genéticos para o peso de bovinos Nelore, do nascimento até 1.000 dias de idade, por meio de modelos de regressão aleatória. Utilizaram-se 115.096 registros de peso de 19.417 animais. Os parâmetros genéticos foram obtidos por modelos de regressão aleatória via inferência bayesiana. A trajetória média de crescimento foi ajustada com um polinômio de Legendre quártico. O efeito genético aditivo direto foi ajustado com um polinômio quadrático de Legendre. Os efeitos de ambiente permanente direto e materno foram ajustados com polinômios de Legendre quíntico e quadrático, espectivamente. A variância residual foi modelada com três classes de idades. Os valores genéticos dos pesos, do nascimento até 1.000 dias de idade, foram utilizados para a análise da tendência genética, por meio de superfícies de resposta. As herdabilidades variaram entre 0,16 e 0,47. Os efeitos de ambiente permanente direto e materno foram responsáveis por 5 a 77% e 0,2 a 11% da variância fenotípica, respectivamente. As correlações genéticas dos pesos em diferentes idades foram altas e superiores a 0,40. Os valores genéticos foram crescentes ao longo dos anos, e a tendência genética foi máxima para peso aos 500 dias. Título em inglês: Genetic analysis of body weight in a Nellore cattle herd.