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In this study, we identified several DArT markers that have specific linkage relationships with each other by linkage analysis. Although linkage had been observed between DArT markers in the previous study [58], the identified linkage relationships between specific DArT markers in this study are different from those determined in that study. Therefore, linkage analysis of DArT markers has an advantage over population allelic specific chip technology in exploring polymorphism and linkage relationship at the level of a single DArT marker. Through this linkage analysis, we identified a c.G4140A mutation in the PRKG1 gene in the Panamanian jaguar individuals, which was linked to a c.A2127T mutation in the DAOA gene. The PRKG1 gene is an ortholog of the yeast ADR1 gene, a Rho kinase, and the DAOA gene is a G protein-coupled receptor expressed in the brain. The c.G4140A mutation in the PRKG1 gene has not been reported previously. This mutation was not present in the 41 Carribean jaguar individuals. We also identified the c.G2494C mutation in the SCN11A gene, which was linked to the c.G108C mutation in the ADRB2 gene. These mutations are not included in the gnomAD database and have not been reported previously. Allele-specific polymerase chain reaction analysis showed that these mutations are heterozygous and are thus potentially valuable as a genetic marker for genetic management.
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