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Performance of different SNP panels for parentage testing in two East Asian cattle breeds
Author(s) -
Strucken E. M.,
Gudex B.,
Ferdosi M. H.,
Lee H. K.,
Song K. D.,
Gibson J. P.,
Kelly M.,
Piper E. K.,
PortoNeto L. R.,
Lee S. H.,
Gondro C.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12154
Subject(s) - hanwoo , single nucleotide polymorphism , korean native , biology , genetics , population , sire , snp , herd , genotype , gene , demography , zoology , ecology , sociology
Summary The International Society for Animal Genetics ( ISAG ) proposed a panel of single nucleotide polymorphisms ( SNP s) for parentage testing in cattle (a core panel of 100 SNP s and an additional list of 100 SNP s). 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 SNP s, and a second panel for the Hanwoo, which still had some false‐positive assignments with 100 SNP s but no false positives using 200 SNP s. 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.