Testing a new SNP-chip on the Alpine and Apennine brown bear (Ursus arctos) populations using non-invasive samples

Brown bears in Italy persist in two isolated populations, one in the Alpine and the other in the Apennine mountain range. Both are threatened and elusive. Non-invasive genetics provides a good way to monitor the populations. Microsatellites (STRs) have been the marker of choice for non-invasive genetic monitoring, but due to non-invasive bad quality samples, these analyses were plagued by low amplification rates and genotyping errors. Moreover, to compare microsatellite genotypes, allele calibration is needed between laboratories, leading to difficulties in individual identification. In contrast, SNP genotyping is directly comparable between laboratories, and more sensitive and accurate. Here we test a 96-marker SNP chip developed for the Scandinavian brown bear population on the Italian populations. A subset of these SNPs was found informative and could reliable confirm species, sex and, only in the Alpine population, distinguish individuals. A total of 51 informative SNPs provided better resolution power than 15 STRs, used in the routine monitoring of the Alpine population in Italy. In contrast, only 15 SNPs were found to be informative for the Apennine population, which did not have enough resolution to discriminate individuals and were less informative than 11 STRs. While highly useful in the Alpine population, additional SNP markers must be included to reach the same level of resolution in the Apennine population.