Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information

E.M.M. van der Heide*, R.F. Veerkamp, M.L. van Pelt, C. Kamphuis, B.J. Ducro

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

Original languageEnglish
Pages (from-to)556-571
JournalJournal of Dairy Science
Volume103
Issue number1
Early online date6 Nov 2019
DOIs
Publication statusPublished - Jan 2020

Fingerprint

breeding value
dairy cattle
Breeding
heifers
genomics
Animal Mammary Glands
udders
prediction
Lactation
Fertility
Foot
Leg
Milk
Parturition
Technology
dairy farming
calving
legs
Health
lactation

Keywords

  • dairy cow
  • individual prediction
  • longevity
  • survival

Cite this

@article{32115ccf03c948318c27d46c00a7296d,
title = "Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information",
abstract = "Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70{\%} of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30{\%} of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0{\%} more surviving heifers when the highest scoring 50{\%} of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.",
keywords = "dairy cow, individual prediction, longevity, survival",
author = "{van der Heide}, E.M.M. and R.F. Veerkamp and {van Pelt}, M.L. and C. Kamphuis and B.J. Ducro",
year = "2020",
month = "1",
doi = "10.3168/jds.2019-16626",
language = "English",
volume = "103",
pages = "556--571",
journal = "Journal of Dairy Science",
issn = "0022-0302",
publisher = "American Dairy Science Association",
number = "1",

}

Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information. / van der Heide, E.M.M.; Veerkamp, R.F.; van Pelt, M.L.; Kamphuis, C.; Ducro, B.J.

In: Journal of Dairy Science, Vol. 103, No. 1, 01.2020, p. 556-571.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Predicting survival in dairy cattle by combining genomic breeding values and phenotypic information

AU - van der Heide, E.M.M.

AU - Veerkamp, R.F.

AU - van Pelt, M.L.

AU - Kamphuis, C.

AU - Ducro, B.J.

PY - 2020/1

Y1 - 2020/1

N2 - Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

AB - Advances in technology and improved data collection have increased the availability of genomic estimated breeding values (gEBV) and phenotypic information on dairy farms. This information could be used for the prediction of complex traits such as survival, which can in turn be used in replacement heifer management. In this study, we investigated which gEBV and phenotypic variables are of use in the prediction of survival. Survival was defined as survival to second lactation, plus 2 wk, a binary trait. A data set was obtained of 6,847 heifers that were all genotyped at birth. Each heifer had 50 gEBV and up to 62 phenotypic variables that became gradually available over time. Stepwise variable selection on 70% of the data was used to create multiple regression models to predict survival with data available at 5 decision moments: distinct points in the life of a heifer at which new phenotypic information becomes available. The remaining 30% of the data were kept apart to investigate predictive performance of the models on independent data. A combination of gEBV and phenotypic variables always resulted in the model with the highest Akaike information criterion value. The gEBV selected were longevity, feet and leg score, exterior score, udder score, and udder health score. Phenotypic variables on fertility, age at first calving, and milk quantity were important once available. It was impossible to predict individual survival accurately, but the mean predicted probability of survival of the surviving heifers was always higher than the mean predicted probability of the nonsurviving group (difference ranged from 0.014 to 0.028). The model obtained 2.0 to 3.0% more surviving heifers when the highest scoring 50% of heifers were selected compared with randomly selected heifers. Combining phenotypic information and gEBV always resulted in the highest scoring models for the prediction of survival, and especially improved early predictive performance. By selecting the heifers with the highest predicted probability of survival, increased survival could be realized at the population level in practice.

KW - dairy cow

KW - individual prediction

KW - longevity

KW - survival

U2 - 10.3168/jds.2019-16626

DO - 10.3168/jds.2019-16626

M3 - Article

VL - 103

SP - 556

EP - 571

JO - Journal of Dairy Science

JF - Journal of Dairy Science

SN - 0022-0302

IS - 1

ER -