Genetic principal components for reproductive and productive traits in dual-purpose buffaloes in Colombia

ABSTRACT: A multitrait model (MC) and 5 reduced- rank models with principal component structure (components PC1, PC1:2, PC1:3, PC1:4, and PC1:5) were compared. The objectives were to determine the most appropriate model for estimating genetic parameters and to evaluate the genetic progress of dual-purpose buffaloes in Colombia using that mod- el. The traits evaluated were weaning weight (WW), yearling weight (W12), weight at 18 mo of age (W18), weight at 2 yr of age (W24), age at first calving (AFC), and milk yield at 270 d of first lactation (MY270). Genealogy and productive information from 34,326 buffaloes born in Colombia between 1997 and 2014 were used. Colombian Association of Buffalo Breeders (ACB) provided the data. Direct additive genetic and residual random effects were included for all the traits. In addition, the maternal additive genetic effect and permanent environmental random effect were included for WW, while a maternal additive genetic effect was included for W12. The fixed effects were contempo- rary group (farm, year, and calving season: January to April, May to August, or September to December; for all traits) and sex (for WW, W12, W18, and W24). Additionally, parity was included as a fixed effect for WW and W12. Age at weighing was used as a covariate for WW, W12, W18, and W24. Genetic progress of all traits was analyzed using a generalized smooth model (GAM). According to the Akaike information criteria (AIC), the best model was the one with reduced rank and first 3 principal components (PC1:3). This model maintained 100% of the original variance. Genetic parameters estimated with this model were similar to those estimated by MC, but with smaller standard errors. Heritability for weight-related traits ranged between 0.23 and 0.44. Heritabilities for AFC and MY270 were 0.14 and 0.24, respectively. The genetic correlations obtained between all weights (WW, W12, W18, and W24) were positive and high. Correlations between all weights with AFC were negative and mod- erate. Correlations between all weights with MY270 were positive and moderate, and between MY270 with AFC were negative and low

Associação de polimorfismos de nucleotídeo único com características de crescimento e reprodutivas em bovinos Canchim

Recentes avanços tecnológicos possibilitaram a utilização de dados genômicos na avaliação de animais de produção. Os marcadores do tipo SNP (“Single Nucleotide Polymorphism”) estão entre os mais utilizados para estudos do genoma bovino, pois estão presentes em grande quantidade e podem estar associados a regiões do genoma que atuam em características de interesse econômico. Fatores como a redução dos custos de genotipagem e a alta densidade dos painéis de marcadores possibilitaram que esta tecnologia seja utilizada em larga escala. Os objetivos deste trabalho foram avaliar o desequilíbrio de ligação (DL) e a conservação da fase do desequilíbrio de ligação (FDL) entre animais da raça Canchim e do grupo genético MA; e aplicar a metodologia “Generalized Quase- Likelihood Score” para estudo de associações genômica entre SNPs e características de peso corporal ao nascimento (PN), ao desmame (PD) e ao sobreano (PS); perímetro escrotal ao desmame (PED) e ao sobreano (PES); e idade ao primeiro (IPP) e segundo (ISP) parto nestes mesmos animais. Foram utilizados 285 animais da raça Canchim (proporção Charolês-Zebu igual a 62,5 % e 37,5%) e 114 animais do grupo genético MA (proporção aproximada Charolês-Zebu igual a 65,6% e 34,4%) genotipados para o painel de alta densidade BovineHD - Illumina® bead chip (777k). Para o estudo de DL e FDL as informações dos genótipos de alta densidade foram concatenadas com o mapa de genótipos de menor densidade (BovineSNP50 v2 bead chip) que possui aproximadamente 50 mil SNPs (50k), realizando assim a redução da densidade dos marcadores. Foram realizadas análises para animais Canchim, MA e Canchim + MA. O painel de 777k mostrou-se mais eficiente para estudo do DL e FDL quando comparado ao painel de 50k, pois apresentou elevada conservação de FDL (acima de 0,80)...Recent technological advances have enabled to use genomic data in livestock evaluation. Single nucleotide polymorphism (SNP) are one of the most widely used genetic markers because they are widely spread along the genome and also could be associated with traits of economic interest. High-throughput panels are becoming interesting for the producers as the cost of genotyping reduces. The objectives of this study were to evaluate the extent of linkage disequilibrium (LD) and the phase of linkage disequilibrium (PLD) between Canchim animals and MA genetic group; and to apply the Generalized Quasi-Likelihood Score method to perform a genome wide association study with birth weight (BW), weaning weight (WW), yearling weight (YW), scrotal circumference at weaning (SCW), scrotal circumference at yearling (SCY), age at first calving (AFC), and age at second calving (ASC). Analyses considered 285 Canchim animals (Charolais-Zebu proportion of 62.5% - 37.5%) and 114 animals of the MA genetic group (Charolais-Zebu proportion of 65.6% - 34.4%) genotyped with the BovineHD - Illumina Bead® chip (777k). Two marker densities were used for the LD and PLD analyses; one considered the 777k panel while the other considered a reduced panel which was resulted from a combined information of the high-throughput panel and the BovineSNP50 chip bead v2 map from Illumina®. These analyses were carried out for Canchim, MA, and Canchim + MA animals. PLD conservation was high in both panels, but only the 777k panel had higher mean r2 (LD measure) equal to 0.38, 0.34, and 0.31 at distances from 0.00 to 0.0025 Mb, 0.0025 to 0.0050 Mb, and 0.0050 to 0.0075 Mb in the Canchim + MA analysis. After this step, genome wide associations were carried out using the Generalized Quasi-Likelihood Score method (GQLS), which considers the logistic regression to associate phenotypic information... (Complete abstract click electronic access below

Estudo da habilidade de permanência de fêmeas da raça Canchim aos 76 meses de idade

As características reprodutivas das fêmeas são de grande importância na exploração de bovinos de corte no Brasil, pois estas influenciam diretamente no número de bezerros produzidos. A habilidade de permanência de fêmeas no rebanho apresenta grande impacto nos custos das propriedades rurais, pois está diretamente ligada à capacidade das vacas em produzir determinado número de bezerros em um espaço de tempo. O objetivo deste trabalho foi estudar a habilidade de permanência de fêmeas no rebanho aos 76 meses de idade (HP) e suas associações genéticas com a idade ao primeiro parto (IPP), peso corporal de machos e de fêmeas aos 420 dias de idade (P420) e perímetro escrotal aos 420 dias de idade (PE420), para fornecer subsídios ao programa de avaliação genética da raça Canchim. Por se tratar de uma característica binária, definiu-se HP como sucesso (2) quando as fêmeas obtiveram no mínimo três bezerros até os 76 meses de idade e fracasso (1) para as demais. No modelo animal, foi incluído o efeito fixo de grupo de contemporâneos (GC) e os efeitos aleatórios aditivos direto e residual. Os dados foram analisados por meio de inferência Bayesiana, em análise bi-característica de HP com as demais características. Aos 76 meses de idade 40,77% das vacas obtiveram sucesso. As médias de IPP, P420 e PE420 foram iguais a 40,28 ± 7,85 meses, 254,92 ± 45,05 kg e 24,63 ± 3,84 cm, respectivamente. As estimativas de herdabilidade obtidas para HP, IPP, P420 e PE420 foram iguais a 0,03 ± 0,01; 0,04 ± 0,01; 0,24 ± 0,04 e 0,24 ± 0,06, respectivamente. As associações genéticas da característica HP com IPP, P420 e PE420 foram iguais a -0,63 ± 0,20; -0,09 ± 0,11 e 0,45 ± 0,21, respectivamente. As correlações ambientais, de HP com IPP e P420 foram iguais...Improvement of female fertility has become of fundamental importance for profit maximization in the beef cattle herds in Brazil. The stayability trait was defined as whether or not a cow calved in a herd at a specific age. Therefore, the objectives of the present study are to analyze stayability (Stay) and its genetic association with age at first calving (AFC), body weight in males and females at 420 days of age (BW420) and scrotal circumference at 420 days of age (SC420), in Canchim cattle. In this research, Stay was defined as success (2) for females that had a minimum of three calves at 76 months of age and failure (1) for the others. Genetic parameters were estimated for all traits. The animal model included the fixed effect of contemporary group (CG) and the additive direct and residual random effects. The data was studied using Bayesian inference in two-trait analyses. At 76 months of age the percent of success was equal to 40.77%. The means for AFC, BW420 and SC420 were equal to 40.28 ± 7.85 months, 254.92 ± 45.05 kg e 24.63 ± 3.84 cm, respectively. The analyses provided heritability estimates of 0.03 ± 0.01, 0.04 ± 0.01, 0.24 ± 0.04 and 0.24 ± 0.06 for Stay, AFC, BW420 and SC420, respectively. The estimates of posterior genetic association were equal to -0.63 ± 0.20, -0.09 ± 0.11 and 0.45 ± 0.21 between Stay with AFC, BW420 and SC420, respectively. The environmental association between Stay with AFC and BW420 were 0.02 ± 0.01 and -0.06 ± 0.04, respectively, and for SC420 the environmental correlation was computed as zero. Selection for higher BW420 should not improve the Stayability trait. However, selection for SC420 should improve this trait and also contribute positively in Stayability. The improvement of age at first calving and Stayability should not be obtained by selection for these traits, but mainly, by changes in management and environmental conditions.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

REPRODUCTIVE TRAITS SELECTION IN NELORE BEEF CATTLE

Genetic breeding programs of beef cattle in Brazil are including new features, mainly related to reproductive efficiency.Thus, it is necessary to study the effectiveness of selection and quantify genetic gain for these traits in herds. This study estimated genetic and phenotypic parameters and genetic trends for reproductive traits used in breeding programs for Nelore beef cattle. The traits studied were the scrotal circumference (SC) at 365 and 450 days of age (SC365 and SC450), age at first calving (AFC) and gestation length, as a cow trait (GLcow) and a calf trait (GLcalf). The (co)variance components were obtained with the Restricted Maximum Likelihood Methodology in a single and double-trait analysis of the animal model. For scrotal circumference (SC365 and SC450), positive and favorable genetic gains were observed. For AFC, GLcow and GLcalf, the trends were favorable for selection, but without significant genetic gain. Selection for large SC may reduce AFC and improve female reproductive efficiency. The selection for reproductive traits (SC365, SC450, AFC and GL) may improve reproductive and productive efficiency of Nelore cattle, if used as a selection criterion

El clima y sus implicaciones para la producción de leche en el cerrado brasileño

Objective. To analyze the climate in the last thirty years in the Northwest of Minas and its impacts on dairy production. Materials and Methods. The database of the National Institute of Meteorology was used during the period from 1985 to 2017 in the cities of Unaí, Paracatu, Arinos and Formoso/MG. For each month and year, the average minimum temperature (Tmin), maximum temperature (Tmax), relative humidity (RH), Temperature and Humidity Index (THI), Wet-bulbe Globe Temperature Index (WBGT), estimate of the decrease in milk production (DMP) and DMP on critical days (DMPc) were calculated. Results. The results were evaluated using the lm function of R, and the t test to test the null hypothesis that the regression coefficient was equal to zero with a significance level of 5%. An increase in Tmax and Tmim values by 0.6-0.9°C respectively was observed. The THI and WBGT values in the municipalities show states of danger and emergency. The DMP obtained were 2.8 kg cow-1 day-1 (Paracatu and Formoso), 3.2 kg cow-1 day-1 in Unaí and between 3.7 and 4.6 kg cow-1 day-1 in Arinos. Conclusions. It is verified that the thermal condition in the studied cities is outside the considered thermoneutral zone, being necessary primary and secondary environmental modifications to guarantee the welfare of the animals and satisfactory livestock indexes.Objetivo. Analizar el clima en los últimos treinta años en el Noroeste de Minas y sus impactos en la producción lechera. Materiales y Métodos. Se utilizó la base de datos del Instituto Nacional de Meteorología durante el período de 1985 a 2017 en las ciudades de Unaí, Paracatu, Arinos y Formoso/MG. Para cada mes y año, la temperatura mínima promedio, la temperatura máxima, la humedad relativa, el índice de temperatura y humedad, el índice de temperatura de bulbo húmedo y globo, la estimación de la disminución de producción la leche. Resultados. Los resultados fueron evaluados utilizando la función lm de R, y la prueba t para probar la hipótesis nula de que el coeficiente de regresión fue igual a cero con un nivel de significación del 5%. Se observó un aumento en los valores de temperatura máxima y temperatura mínima de 0.6-0.9°C respectivamente. Los valores del índice de temperatura y humedad e índice de temperatura de bulbo húmedo y globo en los municipios muestran estados de peligro y emergencia. La estimación de la disminución de producción de leche obtenidos fueron 2.8 kg vaca-1 día-1 (Paracatu y Formoso), 3.2 kg vaca-1 día-1 en Unaí y entre 3.7 y 4.6 kg vaca-1 día-1 en Arinos. Conclusiones. Se verifica que la condición térmica en las ciudades estudiadas se encuentra fuera de la zona termoneutra considerada, siendo necesarias modificaciones ambientales primarias y secundarias para garantizar el bienestar de los animales e índices zootécnicos satisfactorios

Genetic analysis on accumulated productivity and calving intervals in Nelore cattle

The aim of this study was to estimate genetic parameters for accumulated productivity (ACP), first calving interval (CI1), second calving interval (CI2), and mean calving interval (MCI) in Nelore beef cattle. The ACP trait is a reproduction index and comprises the total number of calves born per dam, weight of weaned calves, and age of the dam at calving. Genetic parameters were estimated by the average information restricted maximum likelihood method in two-trait analyses. The average heritability estimate for ACP was 0.17 (0.03). For CI1, CI2, and MCI, the heritability estimates were 0.02, 0.02, and 0.06, respectively. Genetic correlations between ACP with CI1, CI2, and MCI were -0.16 ± 0.47, -0.29 ± 0.53, and -0.40 ± 0.27, respectively. Despite of the low heritability estimates obtained in our study, reproduction traits should be further studied and their inclusion in the selection criteria must be evaluated in order to improve the performance of females because these traits are of great economic importance in beef cattle. Accumulated productivity could contribute to decrease the mean calving interval in Nelore cattle.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Effect of IGF1, GH, and PIT1 markers on the genetic parameters of growth and reproduction traits in Canchim cattle

The availability of dense genomic information has increased genome-wide association studies for the bovine species; however research to assess the effect of single genes on production traits is still important to elucidate the genes functions. On this study the association of IGF1, GH, and PIT1 markers with growth and reproductive traits (birth weight, weaning weight, weight at 12 and 18 months of age, preweaning average daily weight gain, age and weight at first calving, and scrotal circumference at 12 and 18 months of age) were assessed by means of the variance component approach. The phenotypes were adjusted and then analyzed under two animal models, one which considered the polygenic and genotype (IGF1, GH or PIT1 markers) effects (Model 1), and the other which considers only the polygenic effect (Model 2). When the likelihood ratio test and the Bonferroni correction was applied at 5 % significance level, the genetic markers for the IGF1, GH, and PIT1 genes did not influence significantly the traits (p > 0.002). However, evidence of association of IGF1 with birth weight (p = 0.06) and GH with weight at first calving (p = 0.03) and with weight at 12 months of age (p = 0.08) was observed. In conclusion we could not confirm the associations between IGF1, GH, and PIT1 and growth traits that were previously reported in Canchim cattle, and no association was observed between these genes and reproductive traits. Future studies involving functional markers of IGF1, GH and PIT1 genes may help to clarify the role of these genes in growth and reproductive processes.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil

Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP