Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx

[Background] The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the 20th century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1.6 million SNPs, of which 1,536 were selected and genotyped in an extended Iberian lynx sample.[Methods] We validated 1,492 SNPs and analysed their heterozygosity, Hardy-Weinberg equilibrium, and linkage disequilibrium. We then selected a panel of 343 minimally linked autosomal SNPs from which we extracted subsets optimized for four different typical tasks in conservation applications: individual identification, parentage assignment, relatedness estimation, and admixture classification, and compared their power to currently used STR panels.[Results] We ascribed 21 SNPs to chromosome X based on their segregation patterns, and identified one additional marker that showed significant differentiation between sexes. For all applications considered, panels of autosomal SNPs showed higher power than the currently used STR set with only a very modest increase in the number of markers.[Conclusions] These novel panels of highly informative genome-wide SNPs provide more powerful, efficient, and flexible tools for the genetic management and non-invasive monitoring of Iberian lynx populations. This example highlights an important outcome of whole-genome studies in genetically threatened species.Funding for this project was provided by the Spanish Dirección General de Investigación Científica y Técnica (CGL2013-47755-P), and Banco de Santander, CSIC and Fundación General CSIC through a “Proyectos Cero” grant. DKR and MLP were supported by PhD contracts from Programa Internacional de Becas "La Caixa-Severo Ochoa". FC and BMC were hired under the EcoGenes project funded by the European FP7 programme (264125-FP7-REGPOT-2010-1). EBD-CSIC received support from the Spanish Ministry of Economy and Competitiveness under the ‘Centro de Excelencia Severo Ochoa 2013-2017’ program, grants SEV-2012-0262.1. SNP dataset: 1492 markers; 329 individuals.-- 2. STR dataset: 36 markers; 463 individuals.csvPeer reviewe