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Genome-wide associations for feed utilisation complex in primiparous Holstein–Friesian dairy cows from experimental research herds in four European countries

Published online by Cambridge University Press:  13 June 2012

R. F. Veerkamp ,
M. P. Coffey ,
D. P. Berry ,
Y. de Haas ,
E. Strandberg ,
H. Bovenhuis ,
M. P. L. Calus  and
E. Wall
R. F. Veerkamp
Affiliation:
Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
M. P. Coffey
Affiliation:
Sustainable Livestock Systems Group, Scottish Agricultural College, Roslin Institute Building, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK
D. P. Berry
Affiliation:
Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, County Cork, Ireland
Y. de Haas
Affiliation:
Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
E. Strandberg
Affiliation:
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden
H. Bovenhuis
Affiliation:
Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
M. P. L. Calus
Affiliation:
Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
E. Wall
Affiliation:
Sustainable Livestock Systems Group, Scottish Agricultural College, Roslin Institute Building, Easter Bush Campus, Midlothian EH25 9RG, Scotland, UK
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Abstract

Genome-wide association studies for difficult-to-measure traits are generally limited by the sample size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein–Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with the feed utilisation complex: fat and protein corrected milk yield (FPCM), dry matter intake (DMI), body condition score (BCS) and live-weight (LW). Phenotypic data and 37 590 single nucleotide polymorphisms (SNPs) were available on up to 1629 animals. Genetic parameters of the traits were estimated using a linear animal model with pedigree information, and univariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. The variation in the phenotypes explained by the SNPs on each chromosome was related to the size of the chromosome and was relatively consistent for each trait with the possible exceptions of BTA4 for BCS, BTA7, BTA13, BTA14, BTA18 for LW and BTA27 for DMI. For LW, BCS, DMI and FPCM, 266, 178, 206 and 254 SNPs had a Bayes factor >3, respectively. Olfactory genes and genes involved in the sensory smell process were overrepresented in a 500 kbp window around the significant SNPs. Potential candidate genes were involved with functions linked to insulin, epidermal growth factor and tryptophan.

Keywords

genome-wide associationfeed intakecowlive-weight
Type
Breeding and genetics
Information
animal , Volume 6 , Issue 11 , November 2012 , pp. 1738 - 1749
Copyright
Copyright © The Animal Consortium 2012

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