An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population.

摘要: Because of their high variability, microsatellites are still considered the marker choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) becoming increasing popular many areas molecular ecology, owing to high-throughput, easy transferability between laboratories low genotyping error. An ongoing discussion concerns relative power SNPs compared microsatellites-that is, how SNP loci needed replace a panel microsatellites? Here, we evaluate assignment 80 (H(E) = 0.30, independent alleles) 11 0.85, 192 population about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, only, newly developed (SNPPIT). Assignment success was higher than microsatellites, especially parent pairs, irrespective method used. Colony2 assigned larger proportion offspring at least one other methods, although Cervus SNPPIT detected more pairs. Identification full-sib groups without parental information from relatedness measures possible using both systems, explicit reconstruction such impossible because computation time. Our results confirm applicability analyses refute predictability number alleles.