scholarly journals Accuracy of Genomic-Polygenic and Polygenic Breeding Values for Age at First Calving and Milk Yield in Thai Multibreed Dairy Cattle

2019 ◽  
Vol 19 (3) ◽  
pp. 633-645
Author(s):  
Tawirat Konkruea ◽  
Skorn Koonawootrittriron ◽  
Mauricio A. Elzo ◽  
Thanathip Suwanasopee

AbstractSingle-nucleotide polymorphisms (SNPs) have been used in genomic prediction and shown to increase prediction accuracy and selection responses for economic traits in dairy cattle. The successful report in genomic prediction for improving age at first calving (AFC) and 305-d milk yield (MY) in multibreed dairy population is limited. Therefore, the objective of this research was to compare estimates of variance components, genetic parameters, and prediction accuracies for AFC and MY using a genomic-polygenic model (GPM) and a polygenic model (PM). The AFC and MY records of 9,106 first-lactating multibreed dairy cows, calved between 1991 and 2014, were collected from 1,012 Thai dairy farms. The SNP genotyped individuals were selected from cows that had completed pedigree and phenotypes information. The total genomic DNA samples of 2,661 dairy cattle were genotyped using various GeneSeek Genomic Profiler low-density bead chips (9K, 20K, and 80K). The 2-trait GPM and PM contained herd-year-season and heterosis as fixed effects, and animal additive genetic and residual as random effects. Variance components and genetic parameters were estimated using the procedure of average information-restricted maximum likelihood (AI-REML). Estimates of additive genetic variance components and heritabilities from GPM were higher than PM for AFC and MY. Correlations between AFC and MY were near zero for both models. Mean EBV accuracies were higher for GPM (32.95% for AFC and 38.24% for MY) than for PM (32.65% for AFC, and 32.99% for MY). Mean sire EBV accuracies were higher for GPM (31.35% for AFC and 36.25% for MY) than for PM (28.37% for AFC and 28.80% for MY). Thus, the GPM should be considered the model of choice to increase accuracy of genetic predictions for AFC and MY in the Thai multibreed dairy population.

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Evert W. Brascamp ◽  
Piter Bijma

Abstract Background In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) and by the breeding value for the queen effect of the queen of the colony. Because the worker group consists of multiple individuals, interpretation of the variance components and heritabilities of phenotypes observed on the colony and of the accuracy of selection is not straightforward. The additive genetic variance among worker groups depends on the additive genetic relationship between the drone-producing queens (DPQ) that produce the drones that mate with the queen. Results Here, we clarify how the relatedness between DPQ affects phenotypic variance, heritability and accuracy of the estimated breeding values of replacement queens. Second, we use simulation to investigate the effect of assumptions about the relatedness between DPQ in the base population on estimates of genetic parameters. Relatedness between DPQ in the base generation may differ considerably between populations because of their history. Conclusions Our results show that estimates of (co)variance components and derived genetic parameters were seriously biased (25% too high or too low) when assumptions on the relationship between DPQ in the statistical analysis did not agree with reality.


2021 ◽  
pp. 17-22
Author(s):  
Afees Abiola Ajasa ◽  
Imre Füller ◽  
Barnabás Vágó ◽  
István Komlósi ◽  
János Posta

The aim of the current research was to estimate variance components and genetic parameters of weaning weight in Hungarian Simmental cattle. Weaning weight records were obtained from the Association of Hungarian Simmental Breeders. The dataset comprised of 44,278 animals born from 1975 to 2020. The data was analyzed using the restricted maximum likelihood methodology of the Wombat software. We fitted a total of six models to the weaning weight data of Hungarian Simmental cattle. Models ranged from a simple model with animals as the only random effect to a model that had maternal environmental effects as additional random effects as well as direct maternal genetic covariance. Fixed effects in the model comprised of herd, birth year, calving order and sex. Likelihood ratio test was used to determine the best fit model for the data. Results indicated that allowing for direct-maternal genetic covariance increases the direct and maternal effect dramatically. The best fit model had direct and maternal genetic effects as the only random effect with non-zero direct-maternal genetic correlation. Direct heritability, maternal heritability and direct maternal correlation of the best fit model was 0.57, 0.16 and -0.78 respectively. The result indicates that problem of (co-)sampling variation occurs when attempting to partition additive genetic variance into direct and maternal components.


2007 ◽  
Vol 7 (2) ◽  
pp. 12 ◽  
Author(s):  
Rodrigo Alfredo Martínez ◽  
Juan Esteban Pérez ◽  
Teófilo Herazo

<p>Se establecieron componentes de varianza, así como parámetros fenotípicos y genéticos, respecto de las variables ‘peso al nacimiento’, ‘peso al destete’ (ajustado a los 270 días) y ‘peso a los 480 días’ en un hato del ganado criollo colombiano Costeño con Cuernos. Se analizaron 2.281 registros de pesos al nacer, 1.722 de pesos al destete  y 1.086 de pesos ajustados a los 480 días utilizando la metodología de máxima verosimilitud restringida (DFREML). También se ajustó un modelo animal que incluyó efectos genéticos directos, maternos y de ambiente permanente, asumiendo como efectos fijos el año de nacimiento, el sexo del ternero y el número de partos de la madre; finalmente, se estimaron los parámetros genéticos ‘heredabilidad’, ‘repetibilildad’ y se establecieron correlaciones genéticas y fenotípicas. Se reportan bajas estimaciones de heredabilidad de los efectos directos, que varían entre 0,17 ± 0,001 y 0,21 ± 0,074 para los pesos al nacer y al destete, respectivamente; así mismo, fue baja la heredabilidad de los efectos genéticos maternos con relación al peso al nacimiento, aunque estos estimados aumentaron respecto de los pesos al nacer y al destete. Las correlaciones entre efectos directos y maternos fueron negativas, pero el mayor valor se encontró para el peso al nacimiento (-0,89). La contribución del ambiente permanente como proporción de la varianza fenotípica total fue baja y disminuyó a medida que aumentó la edad del animal.</p><p> </p><p><strong>Genetic and phenotypic evaluation to characterize growth traits of the native Colombian breed Costeño con Cuernos</strong></p><p>For a herd of native Colombian breed of cattle -Costeño con Cuernos (CCC)- estimates of variance components for phenotypic and genetic parameters were obtained for birth weight, weight at weaning (adjusted to 270 days) and weight at 480 days. Using the restricted maximum likelihood (REMI) methodology, 2281 birth weight records (PN), 1722 weaning weight records and 1086 weight records adjusted to 480 days were analyze by fitting a model which included direct and maternal genetics effects as well as permanent environmental effects, assuming that fixed effects were year of birth weight, calf gender and the mother number of births. The genetic parameters for heritability, repeatability, genetic and phenotypic correlation were estimated and genotypic and phenotypic correlation was established. Heritability estimates for direct effects are low and range from 0.17 ± 0.001 and 0.21 ± 0.074 for birth and weaning weight respectively; while estimates for maternal genetics effects were also low for PN, they were higher for weaning weight and weight at 480 days. There was a negative correlation between direct and maternal effects, and the higher value was for PN (-0.89). The contribution of the variable permanent environment measured as the contribution of the phenotypic variance was low and diminished as animal age increased.</p>


2016 ◽  
Vol 59 (2) ◽  
pp. 243-248 ◽  
Author(s):  
Hafedh Ben Zaabza ◽  
Abderrahmen Ben Gara ◽  
Hedi Hammami ◽  
Mohamed Amine Ferchichi ◽  
Boulbaba Rekik

Abstract. A multi-trait repeatability animal model under restricted maximum likelihood (REML) and Bayesian methods was used to estimate genetic parameters of milk, fat, and protein yields in Tunisian Holstein cows. The estimates of heritability for milk, fat, and protein yields from the REML procedure were 0.21 ± 0.05, 0.159 ± 0.04, and 0.158 ± 0.04, respectively. The corresponding results from the Bayesian procedure were 0.273 ± 0.02, 0.198 ± 0.01, and 0.187 ± 0.01. Heritability estimates tended to be larger via the Bayesian than those obtained by the REML method. Genetic and permanent environmental variances estimated by REML were smaller than those obtained by the Bayesian analysis. Inversely, REML estimates of the residual variances were larger than Bayesian estimates. Genetic and permanent correlation estimates were on the other hand comparable by both REML and Bayesian methods with permanent environmental being larger than genetic correlations. Results from this study confirm previous reports on genetic parameters for milk traits in Tunisian Holsteins and suggest that a multi-trait approach can be an alternative for implementing a routine genetic evaluation of the Tunisian dairy cattle population.


1986 ◽  
Vol 66 (1) ◽  
pp. 53-65 ◽  
Author(s):  
T. R. BATRA ◽  
A. J. LEE ◽  
A. J. McALLISTER

The relationships between reproduction traits, body weight and milk yield were investigated using data from 1611 heifers and 733 cows from two lines of the National Cooperative Dairy Cattle Breeding Project. The data were analyzed separately for heifers and cows within lines using a mixed linear model containing fixed effects for station, year of birth, season of birth and random effect of sires. Heritability estimates and genetic correlations were estimated by a paternal half-sib analysis. Heritability estimates for heifer and cow reproduction traits ranged between 0 and 26% while those of body weights at calving and 112 d postpartum and milk yield ranged from 24 to 43%. Heifers with difficult calving had a higher incidence of retained placenta than those with normal calving. Phenotypic correlations between heifer reproduction traits and milk yield during first lactation were small. High milk production in cows was associated with longer calving interval. Phenotypic correlations between heifer's and cow's reproduction traits were small. Difficult calving in heifers impairs reproductive performance after calving resulting in greater number of days from calving to first and last breeding and leading to a longer calving interval. Key words: Reproduction traits, heifers, cows, milk yield, dairy cattle


2000 ◽  
Vol 71 (3) ◽  
pp. 411-419 ◽  
Author(s):  
H. N. Kadarmideen ◽  
R. Thompson ◽  
G. Simm

AbstractThis study provides estimates of genetic parameters for various diseases, fertility and 305-day milk production traits in dairy cattle using data from a UK national milk recording scheme. The data set consisted of 63891 multiple lactation records on diseases (mastitis, lameness, milk fever, ketosis and tetany), fertility traits (calving interval, conception to first service, number of services for a conception, and number of days to first service), dystocia and 305-day milk, fat and protein yield. All traits were analysed by multi-trait repeatability linear animal models (LM). Binary diseases and fertility traits were further analysed by threshold sire models (TM). Both LM and TM analyses were based on the generalized linear mixed model framework. The LM included herd-year-season of calving (HYS), age at calving and parity as fixed effects and genetic, permanent environmental and residual effects as random. The TM analyses included the same effects as for LM, but HYS effects were treated as random to avoid convergence problems when HYS sub-classes had 0 or 100% incidence. Because HYS effects were treated as random, herd effects were fitted as fixed effects to account for effect of herds in the data. The LM estimates of heritability ranged from 0•389 to 0•399 for 305-day milk production traits, 0•010 to 0•029 for fertility traits and 0•004 to 0•038 for diseases. The LM estimates of repeatability ranged from 0•556 to 0•586 for 305-day milk production traits, 0•029 to 0•086 for fertility traits and 0•004 to 0•100 for diseases. The TM estimates of heritabilities and repeatabilities were greater than LM estimates for binary traits and were in the range 0•012 to 0•126 and 0•013 to 0•168, respectively. Genetic correlations between milk production traits and fertility and diseases were all unfavorable: they ranged from 0•07 to 0•37 for milk production and diseases, 0•31 to 0•54 for milk production and poor fertility and 0•06 to 0•41 for diseases and poor fertility. These results show that future selection programmes should include disease and fertility for genetic improvement of health and reproduction and for sustained economic growth in the dairy cattle industry.


2019 ◽  
Vol 50 (6) ◽  
Author(s):  
Hermiz & Baper

Body weights at birth (469), weaning (394) and at six month of age (358) for kids utilized in this study were raised at private project in Duhok governorate, Iraq during two kidding season (2016-2017) and (2017-2018). GLM within SAS programme was used to analyze the data which include the fixed effects (age of doe, year and season of kidding, sex of kid and type of birth, regression on doe weight at kidding, and the regression of later weights of kids on earlier weights) influencing the studied traits. Restricted Maximum Likelihood Method was used to estimate repeatability, heritability, genetic and phenotypic correlations after adjusting the records for fixed effects. Variance components of random effects were tested for positive definite. Overall mean of weights at birth (BWT), weaning (WWT) and 6 month of age (WT6M) were 2.92, 15.32 and 24.45 kg, respectively. Differences among groups of age of doe in all studied traits were not significant, while year of kidding and sex of kid affect all traits significantly (p<0.01). Season of kidding affect BWT and WWT significantly (P<0.01). Single born kids were heavier (P<0.01) than twins in BWT only. Regression of BWT on doe weight at kidding (0.033 kg/kg) was significant (P<0.01), while the regressions of WWT and WT6M were not significant. The regression coefficients of WWT on BWT (1.906 kg/kg) and of WT6M on WWT (0.835 kg/kg) were highly significant (P<0.01). Repeatability estimates for BWT, WWT and WT6M were 0.47, 0.45 and 0.35, respectively; on the same order the estimates of heritability were 0.41, 0.61 and 0.79. Genetic correlations between BWT with each of WWT (0.45) and WT6M (0.55), and between WWT and WT6M (0.68) were highly significant. All phenotypic correlations between each pair of body weights were higher than genetic correlations and ranged between 0.48 and 0.73.


2021 ◽  
Vol 34 (2) ◽  
pp. 163-171 ◽  
Author(s):  
Renata Negri ◽  
Ignacio Aguilar ◽  
Giovani Luis Feltes ◽  
Juliana Dementshuk Machado ◽  
José Braccini Neto ◽  
...  

Objective: Considering the importance of dairy farming and the negative effects of heat stress, more tolerant genotypes need to be identified. The objective of this study was to investigate the effect of heat stress via temperature-humidity index (THI) and diurnal temperature variation (DTV) in the genetic evaluations for daily milk yield of Holstein dairy cattle, using random regression models.Methods: The data comprised 94,549 test-day records of 11,294 first parity Holstein cows from Brazil, collected from 1997 to 2013, and bioclimatic data (THI and DTV) from 18 weather stations. Least square linear regression models were used to determine the THI and DTV thresholds for milk yield losses caused by heat stress. In addition to the standard model (SM, without bioclimatic variables), THI and DTV were combined in various ways and tested for different days, totaling 41 models.Results: The THI and DTV thresholds for milk yield losses was THI = 74 (–0.106 kg/d/THI) and DTV = 13 (–0.045 kg/d/DTV). The model that included THI and DTV as fixed effects, considering the two-day average, presented better fit (–2logL, Akaike information criterion, and Bayesian information criterion). The estimated breeding values (EBVs) and the reliabilities of the EBVs improved when using this model.Conclusion: Sires are re-ranking when heat stress indicators are included in the model. Genetic evaluation using the mean of two days of THI and DTV as fixed effect, improved EBVs and EBVs reliability.


2020 ◽  
Vol 33 (1) ◽  
pp. 60-70
Author(s):  
Gabrieli S Romano ◽  
Luis Fernando B Pinto ◽  
Altair A Valloto ◽  
José-Augusto Horst ◽  
Victor B Pedrosa

Background: Somatic cell score is an important parameter to predict milk quality and health of cows. However, in countries like Brazil, this trait is still not selected on a large scale, and no genetic parameters are reported in the literature. Objective: To estimate the variance components and genetic parameters for somatic cell score, milk yield, fat yield, protein yield, fat percentage, and protein percentage in Holstein cows. Methods: Records from 56,718 animals were used to estimate variance components, heritability, and genetic correlations using a multi-trait animal model by the REML method. Results: The heritability estimates were 0.19 for somatic cell score, 0.22 for milk yield, 0.26 for fat yield, 0.18 for protein yield, 0.61 for fat percentage, and 0.65 for protein percentage. The estimates of genetic correlations among analyzed traits ranged from -0.50 to 0.82. Conclusion: The low heritability observed for somatic cell score indicates that selection for this trait should result in benefits related to animal health and milk quality, but only in the long term. The low correlation between productive traits and somatic cell score indicates that inclusion of somatic cell score in animal breeding programs does not interfere negatively with the genetic selection for milk yield or solids.Keywords: Holstein; genetic correlation; genetic parameters; heritability; mastitis; milk quality; milk yield; multi-trait model; somatic cell score; variance components.  Resumen Antecedentes: El conteo de células somáticas es un parámetro importante para predecir la calidad de la leche y la salud de las vacas. Sin embargo, en países como Brasil, esta característica aún no se selecciona a gran escala y no se reportan parámetros genéticos en la literatura. Objetivo: Estimar los componentes de varianza y parámetros genéticos para el conteo de células somáticas, producción de leche, producción de grasa, producción de proteína, porcentaje de grasa y porcentaje de proteína en vacas de la raza Holstein. Métodos: Se usaron registros de 56.718 animales para estimar los componentes de la varianza, heredabilidad y correlaciones genéticas usando un modelo animal multicaracterístico por medio del método REML. Resultados: Las estimaciones de heredabilidad fueron 0,19 para el conteo de células somáticas, 0,22 para la producción de leche, 0,26 para la producción de grasa, 0,18 para producción de proteína, 0,61 para el porcentaje de grasa y 0,65 para el porcentaje de proteína. Las estimaciones de correlación genética entre las características analizadas variaron entre -0,50 a 0,82. Conclusión: La baja heredabilidad encontrada para conteo de células somáticas demostró que la selección para esta característica podría resultar en beneficios para la salud animal y calidad de la leche, pero sólo a largo plazo. La baja correlación genética existente entre las características productivas y el conteo de células somáticas indica que la inclusión del conteo de células somáticas en programas de selección no interfiere negativamente en la selección genética para la producción de leche o sólidos.Palabras clave: calidad de leche; correlación genética; conteo de células somáticas; componentes de varianza; heredabilidad; Holstein; mastitis; modelo multicaracteristico; parametros geneticos; producción de leche; selección genetica. Resumo Antecedentes: O escore de células somáticas é um parâmetro importante para a predição da qualidade do leite, bem como para a saúde das vacas. No entanto, em alguns países como o Brasil, essa característica não é selecionada em larga escala e não há parâmetros genéticos disponíveis na literatura. Objetivo: Estimar os componentes de variância e parâmetros genéticos para o escore de células somáticas, produção de leite, produção de gordura, produção de proteína, porcentagem de gordura e porcentagem de proteína em vacas da raça Holandesa. Métodos: Foi utilizado um total de 56.718 animais para estimar os componentes de variância, herdabilidade e correlações genéticas, considerando-se o modelo animal multicaracterística por meio do método REML. Resultados: As estimativas de herdabilidade foram de 0,19 para o escore de células somáticas, 0,22 para a produção de leite, 0,26 para a produção de gordura, 0,18 para produção de proteína, 0,61 para a porcentagem de gordura e 0,65 para a porcentagem de proteína. As estimativas de correlação genética entre as características analisadas variaram entre -0,50 a 0,82. Conclusão: A baixa herdabilidade encontrada para o escore de células somáticas demonstrou que a seleção para esta característica poderá resultar em benefícios para a saúde animal e qualidade do leite, porém, somente a longo prazo. A baixa correlação genética existente entre as características produtivas e o escore de células somáticas demonstrou que a inclusão do escore de células somáticas em programas de seleção não causa interferência negativa na seleção genética para a produção de leite ou sólidos.Palavras-chave: componentes de variância; correlação genéticas; escore de células somáticas; herdabilidade; mastite; modelo multicaracterística; parâmetros genéticos; produção de leite; qualidade do leite; raça Holandesa; seleção genética.


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