Variation at CPE but not CEBPA appears to be associated with intramuscular fat deposition in the longissimus muscle of cattle
William Barendse A B , Rowan J. Bunch A and Blair E. Harrison AA Cooperative Research Centre for Beef Genetic Technologies, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Qld 4067, Australia.
B Corresponding author. Email: bill.barendse@csiro.au
Animal Production Science 49(7) 558-562 https://doi.org/10.1071/EA08307
Submitted: 19 December 2008 Accepted: 10 March 2009 Published: 11 June 2009
Abstract
An important step in the localisation of quantitative trait loci is the confirmation of trait-marker associations in independent studies. In this report, we test three single nucleotide polymorphisms (SNP) of two genes for associations to intramuscular fat (IMF) measurements in cattle. We genotyped SNP of carboxypeptidase E (CPE) and ccaat/enhancer binding protein, α (CEBPA) in a sample of a total of 813 cattle of taurine, composite and indicine breeds. All three polymorphisms showed significant differences between breeds, with the widest range found in CEBPA:g.271A > C where the A allele frequency ranged from P = 0.07 in Brahman to 0.88 in Shorthorn. The taurine breeds showed high linkage disequilibrium between the pair of CPE SNP, with all four breeds showing r2 = 1.0. The Brahman and Santa Gertrudis showed r2 ≤ 0.17. Both CPE:g.445C > T and CPE:g.601C > T SNP showed significant allele substitution effects to IMF in animals of taurine ancestry, with an allele substitution effect of α = 0.22, P = 0.020 for CPE:g.445C > T, explaining 0.4% of the phenotypic variance.
Acknowledgements
Peter Allingham and John Henshall and two anonymous referees commented on a draft of the manuscript. We thank Meat and Livestock Australia and the Beef CRC for financial support (WB).
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