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.

From a dataset of 58 complete jaguar genomes from Brazil (Sartor et al. [in prep]), we used a genotype likelihood approach to identify 13,373,949 SNPs, that were later filtered according to their coverage, depth, mapping quality, missing data, minor allele frequence, linkage disequilibrium, repetitive regions and Hardy-Weinberg Equilibrium. With the remaining 83k SNPs, we grouped individuals according to their biomes of origin (Amazon: n=18; Atlantic Forest: n=14; Cerrado: n=14; Caatinga: n=6; Pantanal: n=6) and calculated pairwise F_ST values between biomes.

To select the most informative sites for geographic assignment, we ranked the 83k SNPS based on their pairwise F_ST values (from highest to lowest) between the sampled biomes and kept the 50 loci with the highest F_ST from each pairwise comparison. We identified a panel comprising 459 SNPs. This set included the top 50 SNPs of each pairwise biome comparison; 41 SNPs were retrieved in more than one comparison and were kept only once in this selected subset. Then, we randomly selected subsets of this 459-SNP panel to assess whether smaller sets of SNPs (which can be genotyped more quicky and affordably) provide similar levels of information. As an example, we identified a set with only 84 SNPs that exhibited a similar resolving power, correctly separating individuals by biomes of origin in a PCA.

To select SNPs that were informative for sexing, we identified 698 SNPs located on the X chromosome and searched for sites that were close to the X-linked genes Amelogenin (AMELX) and Zinc-finger protein (ZFX), which have been used for sex identification of jaguars and other felids (Pilgrim et al. 2005). Subsequently, we analyzed the genotypes of these SNPs in each individual and visualized their distribution in males and females using a PCA. We selected 6 SNPs among these that showed a clear-cut pattern in which all females were homozygous and males were either heterozygous or homozygous for the alternative allele. These SNPs were located in the X-linked genes ZFX, FRMPD4, TRAPPC2, TXLNG, and USP9X.