2024-03-29T01:27:20Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1533962022-10-27T08:54:35Zcom_10261_13com_10261_8col_10261_266
Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
Kleinman-Ruiz, Daniel
Martínez-Cruz, Begoña
Soriano, Laura
Lucena-Pérez, María
Cruz, Fernando
Villanueva, Beatriz
Fernández, Jesús
Godoy, José A.
Ministerio de Economía y Competitividad (España)
Banco Santander
Consejo Superior de Investigaciones Científicas (España)
La Caixa
European Commission
SNPs
STRs
Genetic management
Monitoring
Non-invasive
Genome-wide
Lynx pardinus
[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 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.
[Methods]
We 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.
[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.
2017-07-23T03:15:36Z
2017-07-23T03:15:36Z
2017-07-21
2017-07-23T03:15:37Z
artículo
BMC Genomics 18(1): 556 (2017)
1471-2164
http://hdl.handle.net/10261/153396
10.1186/s12864-017-3946-5
http://dx.doi.org/10.13039/501100003329
http://dx.doi.org/10.13039/501100003339
http://dx.doi.org/10.13039/501100000780
http://dx.doi.org/10.13039/100010784
28732460
en
Publisher's version
application/pdf
Kleinman-Ruiz, Daniel; Martínez-Cruz, Begoña; Soriano, Laura ; Lucena-Pérez, María; Cruz, Fernando ; Villanueva, Beatriz; Fernández, Jesús; Godoy, José A.; 2017; "Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx [Dataset]". http://dx.doi.org/10.20350/digitalCSIC/8506
http://dx.doi.org/10.1186/s12864-017-3946-5
Sí
info:eu-repo/grantAgreement/EC/FP7/264125
The Author(s).
http://creativecommons.org/licenses/by/4.0/
openAccess
BioMed Central