Performance of different SNP panels for parentage testing in two East Asian cattle breeds

Strucken, E. M., Gudex, B., Ferdosi, M. H., Lee, H. K., Song, K. D., Gibson, J. P., Kelly, M., Piper, E. K., Porto-Neto, L. R., Lee, S. H. and Gondro, C. (2014) Performance of different SNP panels for parentage testing in two East Asian cattle breeds. Animal Genetics, 45 4: 572-575. doi:10.1111/age.12154

Author Strucken, E. M.
Gudex, B.
Ferdosi, M. H.
Lee, H. K.
Song, K. D.
Gibson, J. P.
Kelly, M.
Piper, E. K.
Porto-Neto, L. R.
Lee, S. H.
Gondro, C.
Title Performance of different SNP panels for parentage testing in two East Asian cattle breeds
Journal name Animal Genetics   Check publisher's open access policy
ISSN 0268-9146
Publication date 2014-01-01
Year available 2014
Sub-type Article (original research)
DOI 10.1111/age.12154
Open Access Status
Volume 45
Issue 4
Start page 572
End page 575
Total pages 4
Place of publication Chichester, West Sussex, United Kingdom
Publisher Blackwell Publishing
Language eng
Abstract The International Society for Animal Genetics (ISAG) proposed a panel of single nucleotide polymorphisms (SNPs) for parentage testing in cattle (a core panel of 100 SNPs and an additional list of 100 SNPs). However, markers specific to East Asian taurine cattle breeds were not included, and no information is available as to whether the ISAG panel performs adequately for these breeds. We tested ISAG's core (100 SNP) and full (200 SNP) panels on two East Asian taurine breeds: the Korean Hanwoo and the Japanese Wagyu, the latter from the Australian herd. Even though the power of exclusion was high at 0.99 for both ISAG panels, the core panel performed poorly with 3.01% false-positive assignments in the Hanwoo population and 3.57% in the Wagyu. The full ISAG panel identified all sire-offspring relations correctly in both populations with 0.02% of relations wrongly excluded in the Hanwoo population. Based on these results, we created and tested two population-specific marker panels: one for the Wagyu population, which showed no false-positive assignments with either 100 or 200 SNPs, and a second panel for the Hanwoo, which still had some false-positive assignments with 100 SNPs but no false positives using 200 SNPs. In conclusion, for parentage assignment in East Asian cattle breeds, only the full ISAG panel is adequate for parentage testing. If fewer markers should be used, it is advisable to use population-specific markers rather than the ISAG panel.
Keyword false-positive
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Veterinary Science Publications
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