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

BMC Genomics

Research Article

José A. Godoy¹  Maria Lucena-Perez¹  Daniel Kleinman-Ruiz¹  Laura Soriano¹  Begoña Martínez-Cruz¹  Fernando Cruz²  Jesús Fernández³  Beatriz Villanueva³ 

[1] Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD-CSIC), Calle Americo Vespucio 26, 41092, Sevilla, Spain;Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD-CSIC), Calle Americo Vespucio 26, 41092, Sevilla, Spain;CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain;Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña Km. 7, 28040, Madrid, Spain;

关键词: SNPs;    STRs;    Genetic management;    Monitoring;    Non-invasive;    Genome-wide;   

DOI  :  10.1186/s12864-017-3946-5

 received in 2017-04-26, accepted in 2017-07-13,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth 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 1536 were selected and genotyped in an extended Iberian lynx sample.MethodsWe validated 1492 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.ResultsWe 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.ConclusionsThese 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.

【 授权许可】

CC BY   
© The Author(s). 2017