Effectiveness of SNPs for parentage and sibship assessment in polygamous yellowtail kingfish Seriola lalandi

Single nucleotide polymorphisms (SNPs) have been used for quantitative traits and evolutionary studies, but only recently have they been applied to identify family relationships and construct pedigrees. Pedigree assignments can be challenging for mass spawning, polygamous marine species due to the large number of half-sib families arising from mass spawning, and small size of larvae, so genetic markers are required in order to achieve a highly accurate pedigree assignment. In the present study, sibship and parentage in yellowtail kingfish (Seriola lalandi) were obtained from SNPs and the results were compared with those obtained from DNA microsatellite data. The accuracies of pedigrees formed using COLONY and a more recently developed program, Sequoia, the latter designed to optimize speed of processing large data sets, were compared. We also considered the impact of choosing SNPs with varying minor allele frequencies (MAF from 0.05 to 0.50), varying the actual numbers of SNPs used in a given analysis (from 50 to 1000+) and varying assigned SNP genotyping error rates (0% to 10%). Accuracy of assignment, relative to DNA microsatellites, tended to increase with increasing MAF, and increased, up to a point, with increasing SNP number, but did not change with assigned genotyping error rates up to 10%. Both COLONY and Sequoia analyses, with moderate number of SNPs (500 SNPs) and MAF values (0.20-0.30), were able to predict full-sib pairs of which >95% were also predicted by DNA microsatellites, i.e. the concordance between SNP and microsatellite pedigrees was high; processing speeds were faster with Sequoia albeit with some minor reductions in accuracy. When parental data were included in the analyses, 98% of the individuals assigned to parents using SNPs were also assigned to the same parents using DNA microsatellites. Overall, the present study provides guidance as to the parameters (minor allele frequencies, number of SNPs, SNP genotyping error rates) that optimize accuracy, and once optimized, SNPs can be used efficiently for sibship and parentage assignments for polygamous species such as yellowtail kingfish in comparison to pedigrees obtained from traditional microsatellite markers.