Design of a SNP panel for highly accurate paternity identification in Eşme sheep

SNP paternity testing panels offer high-resolution capabilities for determining livestock paternity, thereby enhancing the reliability of genetic verification and ensuring pedigree record accuracy. In this study, we aimed to develop a SNP-based paternity test panel utilizing a 50K SNP chip for paternity testing and pedigree verification in the Eşme sheep breed. Additionally, the study sought to validate the paternity test panel. Based on data from 26 rams and 524 lambs of the Eşme sheep breed, the results indicated that the 50K SNP chip used demonstrated a very high genotyping rate, with the majority of its 53,738 SNPs exhibiting significant polymorphism. After filtering, the most suitable 144 SNP markers were identified for the paternity test panel. The minor allele frequency (MAF) values of the 144 selected SNPs ranged from 0.48 to 0.50. The combined probability of exclusion (CPE) and the combined probability of identification (CPI) values for the panel containing these 144 SNP markers were 0.999999995 and 4.9 × 10–62, respectively. Using this SNP paternity test panel, the pedigree error rate was remarkably low—only 3.44%—in paternity tests conducted across 11 breeders’ flocks that utilized hand mating. In this study, a 50K SNP chip developed from DNA samples of various sheep breeds worldwide, including indigenous breeds from Türkiye, was utilized. This suggests that the SNP-based paternity test panel presented in this research may also be applicable to other indigenous sheep breeds in Türkiye. The widespread implementation of this test panel will not only reduce pedigree errors but also yield more accurate estimates of genetic parameters within the population.