Development of an informative SNP panel for molecular parentage analysis in large yellow croaker (Larimichthys crocea)

Large yellow croaker is a marine fish with high industrial value. Its traditional breeding in China is established through mass selection and family-based selective breeding. Pedigree records are essential in aquaculture for estimating genetic merits when family-based breeding is applied. Pedigree records can be traced through individual tagging, which is costly and not practical for small fish. Alternatively, the parentage of an individual can be tracked by using DNA markers. Single nucleotide polymorphisms (SNPs) have been widely used in aquaculture for parentage assignments due to their even distribution across the genome and are highly adaptive for robust genotyping of a large number of animals. This study aimed to develop an informative SNP panel for paternity assignment in large yellow croaker and evaluate its accuracy using individuals (n = 635) with known pedigrees. A total of 635 samples randomly selected from 11 families and a mixed group were genotyped using the “NingXin-III 55 K” SNP array. High-quality SNPs with high polymorphism were targeted. The informativeness of the final SNP panel was assessed based on genetic diversity (observed (Hobs) and expected heterozygosity (Hexp) and marker parameters such as discrimination power (DP), probability of exclusion (PE), and polymorphism information content (PIC)). The final panel consisted of 141 highly informative SNPs (DP: 0.610–0.625, PE: 0.111–0.125, PIC: 0.361–0.375). The cumulative probability of exclusion (CPE) for the selected panel (CPE > 0.999999989) met the standard criteria for animal DNA testing (CPE > 0.999). A successful parentage assignment for 635 individuals was performed using the selected SNPs with a probability >99.99%. In addition, the results were validated with principal component analysis and phylogenetic tree. The findings prove that the developed SNP panel enables accurate parentage assignment in the breeding population of large yellow croaker.