Genome-wide association studies for feedlot and growth traits in cattle

Bolormaa, S., Hayes, B. J., Savin, K., Hawken, R., Barendse, W., Arthur, P. F., Herd, R. M. and Goddard, M. E. (2014) Genome-wide association studies for feedlot and growth traits in cattle. Journal of Animal Science, 89 6: 1684-1697. doi:10.2527/jas.2010-3079

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Author Bolormaa, S.
Hayes, B. J.
Savin, K.
Hawken, R.
Barendse, W.
Arthur, P. F.
Herd, R. M.
Goddard, M. E.
Title Genome-wide association studies for feedlot and growth traits in cattle
Journal name Journal of Animal Science   Check publisher's open access policy
ISSN 0021-8812
1525-3163
Publication date 2014-12-04
Sub-type Article (original research)
DOI 10.2527/jas.2010-3079
Open Access Status File (Publisher version)
Volume 89
Issue 6
Start page 1684
End page 1697
Total pages 14
Place of publication Champaign, IL, United States
Publisher American Society of Animal Science
Language eng
Formatted abstract
A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10 -5. In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.
Keyword Beef and dairy cattle
Body weight
Feed intake
Height
Residual feed intake
Single nucleotide polymorphism
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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