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

Title
Performance of different SNP panels for parentage testing in two East Asian cattle breeds
Publication Date
2014
Author(s)
Strucken, Eva
( author )
OrcID: https://orcid.org/0000-0002-2715-0733
Email: estrucke@une.edu.au
UNE Id une-id:estrucke
Gudex, Boyd
Gondro, Cedric
( author )
OrcID: https://orcid.org/0000-0003-0666-656X
Email: cgondro2@une.edu.au
UNE Id une-id:cgondro2
Ferdosi, Mohammad
( author )
OrcID: https://orcid.org/0000-0001-5385-4913
Email: mferdos3@une.edu.au
UNE Id une-id:mferdos3
Lee, H K
Song, K D
Gibson, John
Kelly, M
Piper, E K
Porto-Neto, L R
Lee, S H
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Wiley-Blackwell Publishing Ltd
Place of publication
United Kingdom
DOI
10.1111/age.12154
UNE publication id
une:15771
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.
Link
Citation
Animal Genetics, 45(4), p. 572-575
ISSN
1365-2052
0268-9146
Start page
572
End page
575

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