Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

Pryce, J. E., Arias, J., Bowman, P. J., Davis, S. R., Macdonald, K. A., Waghorn, G. C., Wales, W. J., Williams, Y. J., Spelman, R. J. and Hayes, B. J. (2012) Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers. Journal of Dairy Science, 95 4: 2108-2119. doi:10.3168/jds.2011-4628


Author Pryce, J. E.
Arias, J.
Bowman, P. J.
Davis, S. R.
Macdonald, K. A.
Waghorn, G. C.
Wales, W. J.
Williams, Y. J.
Spelman, R. J.
Hayes, B. J.
Title Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers
Journal name Journal of Dairy Science   Check publisher's open access policy
ISSN 0022-0302
1525-3198
Publication date 2012-04
Sub-type Article (original research)
DOI 10.3168/jds.2011-4628
Open Access Status Not yet assessed
Volume 95
Issue 4
Start page 2108
End page 2119
Total pages 12
Place of publication New York, United States
Publisher Elsevier
Language eng
Formatted abstract
Feed makes up a large proportion of variable costs in dairying. For this reason, selection for traits associated with feed conversion efficiency should lead to greater profitability of dairying. Residual feed intake (RFI) is the difference between actual and predicted feed intakes and is a useful selection criterion for greater feed efficiency. However, measuring individual feed intakes on a large scale is prohibitively expensive. A panel of DNA markers explaining genetic variation in this trait would enable cost-effective genomic selection for this trait. With the aim of enabling genomic selection for RFI, we used data from almost 2,000 heifers measured for growth rate and feed intake in Australia (AU) and New Zealand (NZ) genotyped for 625,000 single nucleotide polymorphism (SNP) markers. Substantial variation in RFI and 250-d body weight (BW250) was demonstrated. Heritabilities of RFI and BW250 estimated using genomic relationships among the heifers were 0.22 and 0.28 in AU heifers and 0.38 and 0.44 in NZ heifers, respectively. Genomic breeding values for RFI and BW250 were derived using genomic BLUP and 2 Bayesian methods (BayesA, BayesMulti). The accuracies of genomic breeding values for RFI were evaluated using cross-validation. When 624,930 SNP were used to derive the prediction equation, the accuracies averaged 0.37 and 0.31 for RFI in AU and NZ validation data sets, respectively, and 0.40 and 0.25 for BW250 in AU and NZ, respectively. The greatest advantage of using the full 624,930 SNP over a reduced panel of 36,673 SNP (the widely used BovineSNP50 array) was when the reference population included only animals from either the AU or the NZ experiment. Finally, the Bayesian methods were also used for quantitative trait loci detection. On chromosome 14 at around 25 Mb, several SNP closest to PLAG1 (a gene believed to affect stature in humans and cattle) had an effect on BW250 in both AU and NZ populations. In addition, 8 SNP with large effects on RFI were located on chromosome 14 at around 35.7 Mb. These SNP may be associated with the gene NCOA2, which has a role in controlling energy metabolism.
Keyword Feed conversion efficiency
Genomic selection
Residual feed intake
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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