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Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle
Dalarna University, School of Technology and Business Studies, Statistics. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.ORCID iD: 0000-0002-1057-5401
Dalarna University, School of Technology and Business Studies, Statistics. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.
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2013 (English)In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 96, no 4, 2627-2636 p.Article in journal (Refereed) Published
Abstract [en]

Trait uniformity, or micro-environmental sensitivity, may be studied through individual differences in residual variance. These differences appear to be heritable, and the need exists, therefore, to fit models to predict breeding values explaining differences in residual variance. The aim of this paper is to estimate breeding values for micro-environmental sensitivity (vEBV) in milk yield and somatic cell score, and their associated variance components, on a large dairy cattle data set having more than 1.6 million records. Estimation of variance components, ordinary breeding values, and vEBV was performed using standard variance component estimation software (ASReml), applying the methodology for double hierarchical generalized linear models. Estimation using ASReml took less than 7 d on a Linux server. The genetic standard deviations for residual variance were 0.21 and 0.22 for somatic cell score and milk yield, respectively, which indicate moderate genetic variance for residual variance and imply that a standard deviation change in vEBV for one of these traits would alter the residual variance by 20%. This study shows that estimation of variance components, estimated breeding values and vEBV, is feasible for large dairy cattle data sets using standard variance component estimation software. The possibility to select for uniformity in Holstein dairy cattle based on these estimates is discussed.

Place, publisher, year, edition, pages
Elsevier, 2013. Vol. 96, no 4, 2627-2636 p.
Keyword [en]
dairy cattle, genetic heterogeneity, milk yield, somatic cell score
National Category
Probability Theory and Statistics
Research subject
Komplexa system - mikrodataanalys
Identifiers
URN: urn:nbn:se:du-12687DOI: 10.3168/jds.2012-6198ISI: 000316772000062OAI: oai:DiVA.org:du-12687DiVA: diva2:634636
Available from: 2013-07-01 Created: 2013-07-01 Last updated: 2015-06-29Bibliographically approved
In thesis
1. Genetic Heteroscedasticity for Domestic Animal Traits
Open this publication in new window or tab >>Genetic Heteroscedasticity for Domestic Animal Traits
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Animal traits differ not only in mean, but also in variation around the mean. For instance, one sire’s daughter group may be very homogeneous, while another sire’s daughters are much more heterogeneous in performance. The difference in residual variance can partially be explained by genetic differences. Models for such genetic heterogeneity of environmental variance include genetic effects for the mean and residual variance, and a correlation between the genetic effects for the mean and residual variance to measure how the residual variance might vary with the mean.

The aim of this thesis was to develop a method based on double hierarchical generalized linear models for estimating genetic heteroscedasticity, and to apply it on four traits in two domestic animal species; teat count and litter size in pigs, and milk production and somatic cell count in dairy cows.

The method developed is fast and has been implemented in software that is widely used in animal breeding, which makes it convenient to use. It is based on an approximation of double hierarchical generalized linear models by normal distributions. When having repeated observations on individuals or genetic groups, the estimates were found to be unbiased.

For the traits studied, the estimated heritability values for the mean and the residual variance, and the genetic coefficients of variation, were found in the usual ranges reported. The genetic correlation between mean and residual variance was estimated for the pig traits only, and was found to be favorable for litter size, but unfavorable for teat count.

Place, publisher, year, edition, pages
Uppsala: Sveriges Lantbruksuniversitet, 2014. 54 p.
Series
Acta Universitatis agriculturae Sueciae, ISSN 1652-6880 ; 2014:43
Keyword
Quantitative genetics, genetic heteroscedasticity of residuals, genetic heterogeneity of environmental variation, genetic heterogeneity of residual variance, double hierarchical generalized linear models, teat count in pigs, litter size in pigs, milk yield in cows, somatic cell count in cows
National Category
Animal and Dairy Science Probability Theory and Statistics
Research subject
Komplexa system - mikrodataanalys
Identifiers
urn:nbn:se:du-14310 (URN)978-91-576-8035-8 (ISBN)978-91-576-8034-1 (ISBN)
Public defence
2014-06-11, Room L, Undervisningsplan 8, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2014-06-16 Created: 2014-06-16 Last updated: 2015-06-08Bibliographically approved

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