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

AutorKleinman-Ruiz, Daniel; Martínez-Cruz, Begoña; Soriano, Laura ; Lucena-Pérez, María; Cruz, Fernando ; Villanueva, Beatriz; Fernández, Jesús; Godoy, José A.
Palabras claveSNPs
STRs
Genetic management
Monitoring
Non-invasive
Genome-wide
Lynx pardinus
Fecha de publicación18-jul-2017
EditorCSIC - Estación Biológica de Doñana (EBD)
CitaciónNovel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx [Dataset], 2017
Resumen[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.
URIhttp://hdl.handle.net/10261/153267
DOIhttp://dx.doi.org/10.20350/digitalCSIC/8506
Aparece en las colecciones: (EBD) Conjuntos de datos
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Fichero Descripción Tamaño Formato  
SNPs_lynx_1492x329.csvSNP genotypes dataset1,95 MBUnknownVisualizar/Abrir
STRs_lynx_36x463.csvSTR genotypes dataset133,01 kBUnknownVisualizar/Abrir
readme.txt2,77 kBTextVisualizar/Abrir
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