Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

Abstract

Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities.