Multiple trait and random regression models using linear splines for genetic evaluation of multiple breed populations.

This study aimed to verify if random regression models using linear splines (RRMLS) are suitable for identifying genetic parameters in multiple-breed populations and also to investigate whether an interaction exists between the breeding value (BV) of sires and their progeny breed group. Ten populations were simulated by crossing 2 breeds with distinct genetic variance and nonzero segregation variance. To obtain the genetic parameters, 2 models were used: a multiple-trait model (MULT), in which the trait was considered distinct when evaluated in each group (1/2P1 + 1/2P2, 5/8P1 + 3/8P2, and 3/4P1 + 1/4P2), and a RRMLS with the spline polynomial knots adjusted to these same groups. The genetic parameters estimated through MULT and RRMLS did not differ from the simulated values. The correlations between BV (simulated and estimated) of animals were high and varied from 0.74 to 0.76, which indicates the efficiency of using MULT and RRMLS for predicting BV. Using field data, the traits age at first calving (AFC), first lactation length (LL), and 305-d milk yield (MY-305) from a multiple-breed population of Holstein-Gyr cattle were analyzed. The BV of animals were modeled through RRMLS with 3, 5, and 7 knots, distributed in accordance with the fraction of Holstein breed in each progeny breed group. It was verified that RRMLS with 7 knots for adjusting mean trajectories and genetic effects, with homogeneous residual variance, best fit AFC and LL. For MY-305, the best fit for mean trajectory and genetic effects was the RRMLS with 5 knots and with homogeneous residual variance. The posterior means of heritability varied from 0.21 to 0.48, 0.21 to 0.38, and 0.10 to 0.33 for AFC, LL, and MY-305, respectively. Estimates from genetic parameters obtained by using RRMLS with field data showed that this model is a useful tool for genetic evaluations of populations formed by a great number of breed groups. An interaction occurred between the BV of sires and their progeny breed group, and the genetic parameters for AFC, LL, and MY-305 traits from a multiple-breed population depend on breed composition of the progeny from which the evaluations are based.

Modelos para avaliação genética da produção de leite no dia do controle nas três primeiras lactações / Models for genetic evaluation of milk yield on the day of control in the three first lactations

Objetivou-se verificar se a utilização do modelo autorregressivo (MAR) é adequada para obtenção de parâmetros genéticos para produção de leite no dia do controle (PLDC) de bovinos leiteiros da raça Gir. Foram analisados 125.191 registros de produções diárias, nas três primeiras lactações, por meio dos modelos de repetibilidade (MREP) e MAR. No MREP, foi considerado o efeito de ambiente de curto prazo; no MAR, foi considerado, também, o efeito de ambiente de longo prazo. Os modelos foram comparados por meio do logaritmo da função de máxima verossimilhança (−2logL) . A herdabilidade estimada pelo MREP foi 0,18; no caso do MAR, as estimativas para primeira, segunda e terceira lactações foram 0,32, 0,28 e 0,26, respectivamente. A estimativa de autocorrelação dos componentes de variância de longo prazo foi próxima de zero, e as de curto prazo foram de alta magnitude para primeira (0,79), segunda (0,79) e terceira (0,81) lactações. Logo, a influência do ambiente de curto prazo dentro de cada lactação não é a mesma. O valor de −2logL mais próximo de zero foi obtido para o MAR (-294.884,7778) em relação ao MREP (-329.266,4810). Assim, o MAR é adequado para obtenção de estimativas de parâmetros genéticos para PLDC nas três primeiras lactações de bovinos leiteiros.(AU)

Aimed to verify if the autoregressive model (MAR) is adequate to obtain genetic parameters for Gyr dairy cattle milk yield on the test day in the three first lactations. Analysis was performed on 125,191 records of daily production of 9,242 cows using repeatability model (MREP) and MAR. On MREP, a long-term environment was considered, on MAR, the short-term environment was also taken into consideration. The models were compared by logarithm of the maximum likelihood function (−2logL) . The heritability estimated using the MREP model was 0.18, while the heritability estimated by MAR for first, second, and third lactations were 0.32, 0.28 and 0.26, respectively. The autocorrelation estimates of the components of long-term variance were close to zero, and those of the short-term were of high magnitude for first (0.79), second (0.79) and third (0.81) lactations. Therefore, the influence of the short-term environment within each lactation is not the same. The value of −2logL closer to zero was obtained for MAR (-294,884.7778) in relation to MREP (-329,266.4810). Thus, MAR is suitable for obtaining genetic parameters estimates for PLDC in the first three lactations of dairy cattle.(AU)

A multivariate approach to determine the factors affecting response level of growth, carcass, and meat quality traits in finishing pigs fed ractopamine.

The effect of ractopamine (RAC) supplementation on growth, carcass, and meat quality traits of finishing pigs was studied using a meta-analytical approach. The database was composed of 57 studies published from 2004 to 2016. The dependent variables extracted for the meta-analysis included final BW, ADG, ADFI, feed:gain ratio, HCW, dressing percentage, carcass length, lean yield, back fat thickness, loin muscle area, loin depth, postmortem pH, meat brightness, redness, and yellowness. The studies were grouped by similarity in 3 clusters (C1, C2, and C3) by hierarchical clustering on principle components. The main differences observed between clusters were those of animal initial weight, which increased from C1 through C3. Linear mixed models were used to analyze the data, where studies were assumed as random effect, whereas the total amount of RAC in the diet, cluster, and sex category were considered fixed effects. The interactions between cluster and sex category (barrows, gilts, and mixed sex) and RAC level were also evaluated. Dietary RAC was effective in improving final weight ( < 0.0001), ADG ( < 0.0001), and feed:gain ratio ( < 0.0001) and had a positive effect on HCW ( < 0.0001), lean yield ( = 0.0081), loin muscle area ( = 0.0190), and loin depth ( < 0.0001). In addition, a relatively limited effect on pork quality was observed in the current study. The RAC supplementation was more effective, mainly when pigs started supplementation with higher initial weight, although different responses were observed according to sex category ( < 0.05). There is ample indication that growth and carcass traits could be improved by dietary RAC supplementation. Ractopamine supplementation did not influence the pork quality.

Modelagem das trajetórias médias do peso vivo e do rendimento de carcaça de tilápias do Nilo (Oreochromis niloticus) por meio de funções B-spline / Modeling the mean trajectories of live body weight and carcass yield of Nile tilapia (Oreochromis niloticus) by B-spline functions

Empregando o método dos quadrados mínimos e polinômios B-spline quadráticos, diferentes modelos estatísticos foram testados para identificar o mais apropriado para modelar as trajetórias médias do peso vivo e do rendimento de carcaça de tilápias do Nilo (Oreochromis niloticus). Dados de peso vivo (8.758) e de rendimento de carcaça (2.042) de tilápias com idades entre 106 e 245 dias foram obtidos de 72 famílias provenientes de 36 machos e 72 fêmeas. As variáveis sexo e tanque de criação foram consideradas como classificatórias, e os coeficientes dos polinômios B-spline quadráticos com dois a cinco intervalos de mesmo tamanho foram utilizados como covariáveis. Segundo a maioria dos critérios de ajuste utilizados, os modelos com polinômio B-spline quadrático com cinco intervalos de mesmo tamanho apresentaram os melhores ajustes. O aumento do número de intervalos do polinômio B-spline melhorou o ajuste dos polinômios aos dados. A inclusão dos efeitos classificatórios de sexo, tanque de criação, interação entre esses efeitos e polinômio B-spline quadrático aninhado a essa interação indicou que, com o decorrer do tempo, cada sexo, cultivado em diferente tanque, apresentou trajetória média diferente, sendo necessária a inclusão do aninhamento do tempo na interação sexo x tanque de criação para que, em programas de melhoramento genético da espécie, os valores genéticos dos candidatos à seleção não sejam sub ou superestimados.

Employing the method of least squares and quadratic B-spline polynomials, different statistical models were tested to identify the most appropriate to model the mean trajectories of live weight and carcass yield of Nile tilapia (Oreochromis niloticus). Data of live weight (8,758) and carcass yield (2,042) of tilapias with ages between 106 and 245 days were obtained from 72 families derived from 36 males and 72 females. The sex and tank variables were considered as classificatory and the coefficients of quadratic polynomials B-spline of two to five intervals of the same size were used as covariables. According to most fit criteria used, the models with quadratic B-spline polynomial with five intervals of the same size presented the best adjustments. The increase in number of intervals of B-spline polynomial improved the fit of the polynomials to the data. The inclusion of classificatory effects from sex, tank, the interaction of these effects and the quadratic polynomial B-spline nested in this interaction indicated that, over time, each sex, grown in different tank, presented different mean trajectory, necessitating the inclusion of nesting time in the interaction sex x tank in order to avoid the under or overestimation of breeding values of the selection candidates in breeding programs of this species.

Genotype × environment interaction in individual performance and progeny tests in beef cattle.

The study reported here evaluated genotype × environment interaction in individual performance and progeny tests in beef cattle. Genetic parameters for final weight (FW), ADG, and scrotal circumference (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 correlated responses relative to production on pasture and based on selection in feedlots were similar to the direct responses, whereas the correlated responses for production in feedlots and based on selection on pasture were lower than the direct responses. When the selection 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 existence 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 genotype × environment interaction in beef cattle.

Probability of pregnancy in beef heifers / Probabilidade de prenhez em novilhas de corte

This study aimed to evaluate the influence of initial weight, initial age, average daily gain in initial weight, average daily gain in total weight and genetic group on the probability of pregnancy in primiparous females of the Nellore, 1/2 Simmental + 1/2 Nellore, and 3/4 Nellore + 1/4 Simmental genetic groups. Data were collected from the livestock file of the Farpal Farm, located in the municipality of Jaíba, Minas Gerais State, Brazil. The pregnancy diagnosis results (success = 1 and failure = 0) were used to determine the probability of pregnancy that was modeled using logistic regression by the Proc Logistic procedure available on SAS (Statistical..., 2004) software, from the regressor variables initial weight, average daily gain in initial weight, average daily gain in total weight, and genetic group. Initial weight (IW) was the most important variable in the probability of pregnancy in heifers, and 1-kg increments in IW allowed for increases of 5.8, 9.8 and 3.4% in the probability of pregnancy in Nellore, 1/2 Simmental + 1/2 Nellore and, 3/4 Nellore + 1/4 Simmental heifers, respectively. The initial age influenced the probability of pregnancy in Nellore heifers. From the estimates of the effects of each variable it was possible to determine the minimum initial weights for each genetic group. This information can be used to monitor the development of heifers until the breeding season and increase the pregnancy rate...

Objetivou-se avaliar a influência do peso inicial, idade inicial, ganho médio diário em peso inicial, ganho médio diário em peso total e grupo genético sobre a probabilidade de prenhez de fêmeas primíparas da raça Nellore, 1/2 Simental + 1/2 Nelore e 3/4 Nelore + 1/4 Simental. Os dados analisados foram do arquivo zootécnico da Fazenda Farpal, localizada no município de Jaíba, Minas Gerais. O resultado do diagnóstico de gestação (sucesso=1 e insucesso=0) foi utilizado para determinar a probabilidade de prenhez que foi modelada por meio de regressão logística pelo procedimento Logistic disponível no SAS, a partir das variáveis regressoras peso inicial, ganho médio diário em peso inicial, ganho médio diário em peso total e grupo genético. O peso inicial foi a variável de maior relevância na probabilidade de prenhez de novilhas e incrementos de 1,0kg no peso inicial possibilitaram acréscimos de 5,8; 9,8 e 3,4% na probabilidade de prenhez de novilhas Nelore, 1/2 Simental + 1/2 Nelore e 3/4 Nelore + 1/4 Simental, respectivamente. Entretanto o ganho médio diário em peso inicial e ganho médio diário em peso total não apresentaram efeito significativo na probabilidade de prenhez das novilhas. A idade inicial influenciou a probabilidade de prenhez das novilhas Nelore. A partir das estimativas dos efeitos de cada variável, foi possível determinar o peso inicial mínimo para cada grupo genético. Essa informação pode ser usada para monitorar o desenvolvimento de novilhas até a estação de monta e aumentar a taxa de prenhez...

Análise genética de características de fertilidade, de crescimento e de produtividade em vacas da raça Canchim / Genetic analysis of fertility, growth and productivity traits of Canchim cows

O objetivo deste trabalho foi estimar herdabilidades e correlações genéticas para idade (IPP), peso (PPP) e escore da condição corporal (EPP) ao primeiro parto, tempo de permanência no rebanho (TPR), número (ND10) e quilograma (QD10) de bezerros desmamados em até dez anos de idade, número (NDT) e quilograma (QDT) de bezerros desmamados durante a permanência no rebanho, quilograma de bezerros desmamados por ano de permanência no rebanho (QTPR), peso adulto (PAD) e parâmetros A e k da curva de crescimento de Bertalanffy de fêmeas de um rebanho da raça Canchim. As distribuições a posteriori dos componentes de (co)variância foram obtidas por inferência bayesiana, em análises bicaráter de IPP, PPP e EPP com as outras características. Os modelos estatísticos incluíram os efeitos aleatórios genético aditivo direto e residual e os efeitos fixos de ano e mês de nascimento ou do parto e idade da vaca ao parto, dependendo da característica. As médias a posteriori das herdabilidades foram 0,12 (IPP); 0,51 (PPP); 0,36 (EPP); 0,22 (TPR); 0,24 (ND10); 0,24 (QD10); 0,25 (NDT); 0,23 (QDT); 0,31 (QTPR); 0,56 (PAD); 0,60 (A) e 0,54 (k), indicando que as características possuem variação genética aditiva suficiente para apresentar boa resposta à seleção massal, com exceção de IPP. As correlações genéticas de TPR (-0,35; -0,23 e -0,02), ND10 (-0,33; -0,40 e -0,02), QD10 (-0,47; -0,29 e 0,00), NDT (-0,43; -0,41 e -0,02), QDT (-0,46; -0,28 e 0,00), QTPR (-0,52; -0,35 e 0,00), PAD (0,19; 0,86 e 0,40), A (0,07; 0,09 e -0,18) e k (-0,21; 0,08 e 0,04) com IPP, PPP e EPP, respectivamente, sugerem que a seleção para reduzir a IPP deve melhorar a longevidade e as características de produtividade das fêmeas; porém, o aumento do PPP poderá prejudicá-las...

The objective of this work was to estimate heritabilities and genetic correlations for age at first calving (AFC), weight at first calving (WFC), body condition score at first calving (SFC), culling age (DIH, days in herd), number (NW10) and kilograms (KW10) of calves weaned up to ten years of age, total number (TNW) and total kilograms (TQW) of calves weaned during herd life, kilograms of calves weaned per year in herd (KYH), adult body weight (ABW) and parameters A and k of the Bertalanffy growth curve of females of a Canchim (5/8 Charolais + 3/8 Zebu) beef cattle herd. The variance and covariance components were obtained by two-trait analyses of AFC, WFC and SFC with the other production traits, using the bayesian inference with statistical models that included the additive direct and residual random effects, and the fixed effects of year and month of birth or of calving and calving age, depending on the trait. The posteriori means of the heritability estimates were 0.12 (AFC), 0.51 (WFC), 0.36 (SFC), 0.22 (DIH), 0.24 (NW10), 0.24 (KW10), 0.25 (TNW), 0.23 (TKW), 0.31 (KYH), 0.56 (ABW), 0.60 (A) and 0.54 (k), indicating that these traits have enough additive genetic variation to show response to mass selection. The genetic correlations for DIH (-0.35, -0.23 and -0.02), NW10 (-0.33, -0.40 and -0.02), KW10 (-0.47, -0.29 and 0.00), TNW (-0.43, -0.41 and -0.02), TKW (-0.46, -0.28 and 0.00), KYH (-0.52, -0.35 and 0.00), ABW (0.19, 0.86 and 0.40), A (0.07, 0.09 and -0.18) and k (-0.21, 0.08 and 0.04) with AFC, WFC and SFC, suggest that selection to reduce age at first calving should improve longevity and productivity traits of females, but the increase in body weight at first calving should reduce these traits...

Polynomials to model the growth of young bulls in performance tests.

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.

Selection criteria for sexual precocity in Guzerat bulls raised under grazing conditions.

The objectives of the present study were to obtain posterior densities of genetic parameters for scrotal circumference (SC), testicular volume (TV), BW, and age at puberty, to determine their correlations, and to evaluate the inclusion of these traits as selection criteria for sexual precocity in Guzerat bulls. Two-trait analyses were performed including records of SC, TV, and BW at 365, 450, 550, 650, 730, 850, and 970 d of age with age at puberty of 1,783 Guzerat bulls born between 2000 and 2011. The (co)variance components were estimated using Bayesian methods. Posterior means of heritability ranged from 0.45 to 0.60 for SC, from 0.35 to 0.55 for TV, and from 0.39 to 0.60 for BW. Posterior means of heritabilities for age at puberty using the two-trait analysis with SC ranged from 0.46 to 0.55, those with TV ranged from 0.49 to 0.57, and those with BW ranged from 0.49 to 0.62. The genetic correlation between age at puberty and SC ranged from -0.52 to -0.85, those between age at puberty and TV ranged from -0.33 to -0.66, and those between age at puberty and BW ranged from -0.38 to -0.72. In general, the same trend was observed for the phenotypic correlation between age at puberty and SC, TV, and BW. The selection of the top 10% of young males for SC, TV, or BW caused a decrease in age at puberty, with the most favorable expected correlated response in age at puberty at 650 d of age (-119.95 ± 15.1 d per generation), 730 d of age (-82.20 ± 20.9), and 850 d of age (-93.68 ± 21.5), respectively. In conclusion, SC, TV, and BW can be used as selection criteria to improve early sexual development in Guzerat bulls, and SC measured at 650 d of age is the most advantageous indicative selection criterion for improvement of age at puberty in Guzerat young bulls.

Use of nonlinear models for describing scrotal circumference growth in Guzerat bulls raised under grazing conditions.

The objective was to use various nonlinear models to describe scrotal circumference (SC) growth in Guzerat bulls on three farms in the state of Minas Gerais, Brazil. The nonlinear models were: Brody, Logistic, Gompertz, Richards, Von Bertalanffy, and Tanaka, where parameter A is the estimated testis size at maturity, B is the integration constant, k is a maturating index and, for the Richards and Tanaka models, m determines the inflection point. In Tanaka, A is an indefinite size of the testis, and B and k adjust the shape and inclination of the curve. A total of 7410 SC records were obtained every 3 months from 1034 bulls with ages varying between 2 and 69 months (<240 days of age = 159; 241-365 days = 451; 366-550 days = 1443; 551-730 days = 1705; and >731 days = 3652 SC measurements). Goodness of fit was evaluated by coefficients of determination (R(2)), error sum of squares, average prediction error (APE), and mean absolute deviation. The Richards model did not reach the convergence criterion. The R(2) were similar for all models (0.68-0.69). The error sum of squares was lowest for the Tanaka model. All models fit the SC data poorly in the early and late periods. Logistic was the model which best estimated SC in the early phase (based on APE and mean absolute deviation). The Tanaka and Logistic models had the lowest APE between 300 and 1600 days of age. The Logistic model was chosen for analysis of the environmental influence on parameters A and k. Based on absolute growth rate, SC increased from 0.019 cm/d, peaking at 0.025 cm/d between 318 and 435 days of age. Farm, year, and season of birth significantly affected size of adult SC and SC growth rate. An increase in SC adult size (parameter A) was accompanied by decreased SC growth rate (parameter k). In conclusion, SC growth in Guzerat bulls was characterized by an accelerated growth phase, followed by decreased growth; this was best represented by the Logistic model. The inflection point occurred at approximately 376 days of age (mean SC of 17.9 cm). We inferred that early selection of testicular size might result in smaller testes at maturity.

Seleção e classificação multivariada de modelos de crescimento não lineares para bovinos Nelore / Selection and multivariate classification of nonlinear growth model for Nelore cattle

Utilizou-se análise de agrupamento para classificar e selecionar modelos não lineares de crescimento de bovinos Nelore, tendo em vista os resultados de diferentes avaliadores de qualidade de ajuste. Ajustaram-se 12 modelos não lineares. A qualidade de ajuste dos modelos foi medida pelo coeficiente de determinação (R²), quadrado médio do erro (QME), critério de informação de Akaike (AIC), critério de informação Bayesiano (BIC), erro quadrático médio de predição (MEP) e coeficiente de determinação de predição (R²p). O modelo Brody foi o que apresentou o melhor ajuste para o conjunto de dados.

This study aimed to evaluate cluster analysis in classifying and selecting non linear models to describe Nelore beef cattle growth based on different goodness of fit criteria tests. A total of 12 non linear models were evaluated based on the following criteria: the determination coefficient (R²), error mean square (QME), Akaike information criterion (AIC), Bayesian information criterion (BIC), mean quadratic error of prediction (MEP) and predicted determination coefficient (R²p). The Brody model showed the best adjustment for the data set.