| Animal sciences & veterinary medicine |
|
|
|
|
| Comparison of genetic parameter evaluation methods for body mass of the five-week-old layer |
Jun GUO( ),Liang QU,Taocun DOU,Manman SHEN,Yuping HU,Kehua WANG() |
| Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Sciences, Yangzhou 225125, Jiangsu, China |
|
|
|
Abstract This study aimed to investigate the selection potential for early body mass in a layer resource population, and to compare three inference methods based on their efficiency and accuracy, including restricted maximum likelihood method (REML), Markov chain Monte Carlo method (MCMC), and integrated nested Laplace approximations (INLA). The genetic parameters were estimated by animal models. The layers were collected from a resource population, which were set up by Dongxiang blue-shelled layers crossbred with White Leghorn layers. The total amount of layers, made up of three generations, were 5 405. The phenotypic variance was dissected with the REML and Bayesian approaches. The results showed: 1) The heritability on body mass of the five-week-old layers ranged from 0.49 to 0.59, depending on the estimation method. 2) The MCMC method seemed a slow and low accuracy for genetic evaluation. 3) The use of INLA method could calculate the standard error for variance components, without approximations or use of normality assumptions. 4) Due to the advantage of computation time and accuracy, REML remained the best practical choice for the genetic evaluation in the poultry production. Considering the abundance of genetic potential in the resource population of five-week-old layer, it is better to select on early body mass with animal model.
|
|
Received: 13 March 2019
Published: 20 January 2020
|
|
|
|
Corresponding Authors:
Kehua WANG
E-mail: guojun.yz@gmail.com;sqbreeding@126.com
|
蛋鸡5周龄体质量遗传参数及估计方法比较
为调查蛋鸡资源群体早期体质量选育潜力，比较了限制最大似然法、马尔科夫链蒙特卡洛方法和积分嵌套拉普拉斯逼近方法的效率和结果准确性，应用动物模型估计遗传参数。试验鸡来自东乡绿壳蛋鸡与白来航鸡F2资源群体，包括3个世代总计5 405只鸡，采用限制最大似然法和贝叶斯法剖分5周龄蛋鸡体质量表型方差。结果表明：蛋鸡F2资源群体5周龄体质量遗传力为0.49～0.59，具体因算法而定；马尔科夫链蒙特卡洛方法计算用时较长、准确性稍差；积分嵌套拉普拉斯逼近方法能够准确给出方差组分的标准误，而不是近似的或依据正态分布推测的；限制最大似然法计算用时短，结果准确，目前为最佳选择。由于蛋鸡资源群体5周龄蛋鸡体质量选育潜力大，将来可以通过个体选育获取遗传进展。
关键词：
贝叶斯法,
动物模型,
蛋鸡,
限制最大似然法,
遗传力
|
|
| [1] |
HILL W G. Applications of population genetics to animal breeding, from Wright, Fisher and Lush to genomic prediction. Genetics, 2014,196(1):1-16.
|
|
|
| [2] |
GIANOLA D, ROSA G J M. One hundred years of statistical developments in animal breeding. Annual Review of Animal Biosciences, 2015,3(1):19-56.
|
|
|
| [3] |
PATTERSON H D, THOMPSON R. Recovery of inter-block information when block sizes are unequal. Biometrika, 1971,58(3):545-554.
|
|
|
| [4] |
THOMPSON R. Estimation of quantitative genetic parameters. Proceedings of the Royal Society B: Biological Sciences, 2008,275(1635):679-686.
|
|
|
| [5] |
SORENSEN D, GIANOLA D. Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. New York, US: Springer Science & Business Media, 2002.
|
|
|
| [6] |
RUE H, MARTINO S, CHOPIN N. Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2009,71(2):319-392.
|
|
|
| [7] |
HOLAND A M, STEINSLAND I, MARTINO S, et al. Animal models and integrated nested Laplace approximations. G3: Genes, Genomes, Genetics, 2013,3(8):1241-1251.
|
|
|
| [8] |
RUE H, RIEBLER A, S?RBYE S H, et al. Bayesian computing with INLA: a review. Annual Review of Statistics and Its Application, 2017,4(1):395-421.
|
|
|
| [9] |
ANDERSON K E, HAVENSTEIN G B, JENKINS P K, et al. Changes in commercial laying stock performance, 1958—2011: thirty-seven flocks of the North Carolina random sample and subsequent layer performance and management tests. World’s Poultry Science Journal, 2013,69(3):489-514.
|
|
|
| [10] |
NORRIS D, NGAMBI J W. Genetic parameter estimates for body weight in local Venda chickens. Tropical Animal Health and Production, 2006,38(7/8):605-609.
|
|
|
| [11] |
NAVARRO P, VISSCHER P, CHATZIPLIS D, et al. Genetic parameters for blood oxygen saturation, body weight and breast conformation in 4 meat-type chicken lines. British Poultry Science, 2006,47(6):659-670.
|
|
|
| [12] |
MANIATIS G, DEMIRIS N, KRANIS A, et al. Model comparison and estimation of genetic parameters for body weight in commercial broilers. Canadian Journal of Animal Science, 2013,93(1):67-77.
|
|
|
| [13] |
WICKHAM H. ggplot2: Elegant Graphics for Data Analysis. New York， US: Springer, 2016.
|
|
|
| [14] |
WOLAK M E. Nadiv: an R package to create relatedness matrices for estimating non-additive genetic variances in animal models. Methods in Ecology and Evolution, 2012,3(5):792-796.
|
|
|
| [15] |
MEYER K. Estimation of genetic parameters: it takes three to tango. Journal of Animal Breeding and Genetics, 2008,125(6):361-362.
|
|
|
| [16] |
HADFIELD J D. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. Journal of Statistical Software, 2010,33(2):22.
|
|
|
| [17] |
BROWNE W J, DRAPER D. A comparison of Bayesian and likelihood-based methods for fitting multilevel models. Bayesian Analysis, 2006,1(3):473-514.
|
|
|
| [18] |
MANIATIS G, DEMIRIS N, KRANIS A, et al. Comparison of inference methods of genetic parameters with an application to body weight in broilers. Archives Animal Breeding, 2015,58(2):277-286.
|
|
|
| [19] |
MATHEW B, HOLAND A M, KOISTINEN P, et al. Reparametrization-based estimation of genetic parameters in multi-trait animal model using integrated nested Laplace approximation. Theoretical and Applied Genetics, 2016,129(2):215-225.
|
|
|
| [20] |
KAPELL D N R G, HILL W G, NEETESON A M, et al. Genetic parameters of foot-pad dermatitis and body weight in purebred broiler lines in 2 contrasting environments. Poultry Science, 2012,91(3):565-574.
|
|
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
