Nadia Mucci, Italian Institute for Environmental Protection and Research (ISPRA)

Preserving genetic diversity in critically endangered taxa is crucial for effective conservation management. The Apennine brown bear (Ursus arctos marsicanus), endemic to Central Italy, comprises only ~50 individuals and represents a morphological, behavioural, and genetic uniqueness worldwide. However, this population shows low genomic variability and high inbreeding levels due to long-term isolation and human-induced bottlenecks. Consequently, continuous monitoring of genetic diversity, population dynamics, and reproductive success is essential for planning effective management strategies and ensuring the long-term persistence of this subspecies.
We selected a panel of 89 highly informative Single Nucleotide Polymorphisms (SNPs) from five Apennine bear genomes and tested their genotyping efficiency on 46 biological samples belonging to 26 individuals. Genotyping was performed using a cost-effective, high-throughput targeted genotyping-by-sequencing approach that combines Molecular Inversion Probes (MIPs) with Illumina next-generation sequencing, a method particularly well suited for low-quality and non-invasively collected samples.
This approach successfully enabled the genotyping of all blood samples (average read number = 8249, Allelic Dropout = 0.03%, False Alleles = 0.01%) and non-invasively collected hair samples (average read number = 3210, Allelic Dropout = 0.05%, False Alleles = 0.01%). The selected SNP panel provided highly accurate individual identifications (PID = 2.4×10–30, PIDsibs = 6.1×10–16), estimates of genome-wide variability (HO = 0.412 ± 0.139, HE = 0.379 ± 0.118), and may be promising for parentage reconstructions.
Overall, our results demonstrate the suitability of this genome-wide SNP panel for monitoring genetic variability and population dynamics trends in the Apennine brown bear, providing essential information to support sound conservation management practices of this small, isolated population living in a human-dominated landscape.