Parentage Assignment using genetic markers in the common carp (Cyprinus carpio)

Abstract: This study investigated the effect of varying single nucleotide polymorphisms (SNPs) marker density, error threshold selection, and different SNP selection strategies on parentage assignment accuracy in carp populations. Using a marker set of 15,615 SNPs, we found a positive correlation between the quantity of SNP markers and the accuracy of parentage assignments, consistent with existing literature. We discovered that error threshold selection significantly influenced assignment accuracy and recommended its careful consideration based on population genetic characteristics. Furthermore, our interval-based SNP selection analysis showed that SNP density crucially impacts parentage assignment accuracy. Notably, random SNP selection across the genome yielded more accurate assignments than chromosome-specific selection, emphasizing the importance of diverse and representative SNP sets. These findings provide valuable guidance for future genetic research in parentage assignment.