Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca)

The jaguar (Panthera onca) is an iconic top predator that is threatened by
habitat loss and fragmentation, along with an emerging expansion of
poaching for the illegal trade of live individuals and their parts. To
address the need for tools that improve surveillance and monitoring of its
remaining populations, we have developed a genome-enabled single
nucleotide polymorphism (SNP) panel targeting this species. From a dataset
of 58 complete jaguar genomes, we identified and selected highly
informative SNPs for geographic traceability, individual identification,
kinship, and sexing. Our panel, named ‘Jag-SNP’, comprises 459 SNPs
selected from an initial pool of 13,373,949 markers based on the
inter-biome FST, followed by rigorous filtering and addition of eight
sex-linked SNPs. We then randomly selected subsets of this panel and
identified an 84-SNP set that exhibited a similar resolving power. With
both the 459-SNP panel and its 84-SNP subset, samples were assigned with
98% success to their biomes of origin and 65-69% of them were assigned to
within 500 km of their origin. Furthermore, ca. 10-18 SNPs within these
panels were sufficient to distinguish individuals, while 6 sex-linked SNPs
perfectly separated males and females. We used whole-genome data from an
additional 18 jaguars to further test these panels, which correctly
recovered kinship relationships and allowed inference of geographic origin
of samples collected outside the spatial scope of the original sample set.
These results support the strong potential of these panels as an efficient
tool for application in forensic, genetic, ecological, behavioral and
conservation projects targeting jaguars.