Whole genome survey of big cats (Genus:Panthera) identifies novel microsatellites of utility in conservation genetic study

Abstract

<jats:title>Abstract</jats:title><jats:p>Big cats (Genus: <jats:italic>Panthera</jats:italic>) are among the most threatened mammal groups of the world, owing to illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for <jats:italic>Panthera</jats:italic> species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven <jats:italic>Panthera</jats:italic> genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 99 big cat individuals and 7 Eurasian lynx. The developed markers were polymorphic in most of the tested species. We propose a set of 15 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.</jats:p>

Efficient and cost-effective non-invasive population monitoring as a method to assess the genetic diversity of the last remaining population of Amur leopard (Panthera pardus orientalis) in the Russia Far East

“…The errors due to mis-priming are even more with non-invasive genetics as DNA yield and quality remain low. Here we applied genus specific genomic microsatellites developed for big cat species [ 24 ]. These primers were designed by analysing the whole genome sequences of four big cat species, including Amur leopard.…”

“…The whole process included following three steps: (i) microsatellite prescreening (selection of loci for individual identification), (ii) identification of unique individuals by genotyping of fecal samples with select markers, and (iii) estimation of the genetic diversity of the Amur leopard population. Microsatellite markers developed for big cat species were used to identify individuals and assess genetic diversity [ 24 ]. In total, 35 randomly selected leopard fecal samples were genotyped using 32 microsatellite markers specific to big cats with eight multiplex PCR reactions (MPP1–8) [ 24 ].…”

“…Microsatellite markers developed for big cat species were used to identify individuals and assess genetic diversity [ 24 ]. In total, 35 randomly selected leopard fecal samples were genotyped using 32 microsatellite markers specific to big cats with eight multiplex PCR reactions (MPP1–8) [ 24 ]. Four loci were amplified in each multiplex PCR reaction.…”