A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (P_E) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10⁻⁴⁸ (BON) to 1.11 × 10⁻⁵⁴ (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.

国际动物遗传学会（ISAG）已推荐一组200个单核苷酸多态性（SNP）用于牛的亲子鉴定。当ISAG小组中包含的SNP在欧洲的Bos taurus和Bos indicus中隔离时品种，其在南非（SA）桑加牛中的适用性从未得到评估。因此，这项研究评估了ISAG专家组在SA Bonsmara（BON）和Drakensberger（DRB）牛中的有用性。可获得来自64个BON和97个DRB父亲后代对的185个ISAG SNP的基因型，所有这些基因型均用119,375个SNP进行了验证。在185个ISAG SNP中，BON和DRB中分别有14个和18个（两个品种共有9个），要么是单态的，要么在经过验证的后代对之间表现出至少一种不一致，或者呼叫率或聚类问题差。185个ISAG SNP的平均次要等位基因频率在BON中为0.331，在DRB中为0.359。排除亲子关系的组合概率（P _E）在两个品种中都相同（99.46％），而同一性的概率从1.61×10 ^-48（BON）到1.11×10 ^-54（DRB）。ISAG小组根据具有至少两个不一致的SNP的阈值，分别将15个（23.4％）和32（33％）个已验证的BON和DRB父系后代确定为假阴性。与使用119,375个SNP进行父亲发现相比，仅使用ISAG小组进行的父亲发现正确识别了44个（使用119,375个SNP识别的64个）唯一的后代BON对和62个（使用119,375个SNP识别的97个）唯一的父亲。 -在所有父项都被遮盖时生成DRB。5个BON和3个DRB后代获得了1个以上的父亲提名。这项研究表明，使用ISAG面板可能会导致给定动物的错误排除和多个候选父本。因此，选择更多信息丰富的SNP是