Development and evaluation of a cichlid SNP panel using the Fluidigm EP-1 system
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TECHNICAL NOTE
Development and evaluation of a cichlid SNP panel using the Fluidigm EP-1 system Ryan J. Kuehl1 · Jeffrey A. Markert1
Received: 19 April 2017 / Accepted: 4 May 2017 © Springer Science+Business Media Dordrecht 2017
Abstract Public databases of SNP markers and microfluidics technology may provide the tools to rapidly assess genetic diversity. We developed and tested a cichlid fish SNP panel derived from loci in GenBank’s dbSNP database and used a Fluidigm EP-1 System for genotyping. Markers were tested on both Salton Sea Tilapia and East African species. Successful amplifications were obtained for 66% of the loci, and 54% of loci screened were variable either within or between lineages. Loci reflected an ascertainment bias favoring the taxon they were initially developed in. Keywords Single nucleotide polymorphism (SNP) · Cichlidae · Fluidigm The fish in the family Cichlidae are famously diverse. Adaptive radiations in the African Great Lakes represent one of the highest rates of speciation known in vertebrates (Kocher 2004). Much diversity also exists throughout the rivers and streams of Africa (Levêque et al. 2008), and connectivity between adjacent populations can be surprisingly low (Alter et al. 2017; Markert et al. 2001, 2010), so many localities may host isolated and genetically unique populations. Electronic supplementary material The online version of this article (doi:10.1007/s12686-017-0766-5) contains supplementary material, which is available to authorized users. * Jeffrey A. Markert [email protected] Ryan J. Kuehl [email protected] 1
Department of Biological Sciences, Providence College, Providence, RI 02918, USA
Cichlidae also contains ‘Tilapia’, an aquaculture staple and an invasive species in many areas, including those (likely the widely cultivated hybrid Oreochromis mossambicus × Urolepis hornorum) that colonized California’s increasingly saline Salton Sea in the middle twentieth century (Costa-Pierce and Doyle 1997). These have become an important food source for migratory birds, partially compensating for lost coastal estuaries (Riedel et al. 2007). Because the lake’s ongoing contraction (Barnum et al. 2017), they are also a potential model in extinction biology. Single Nucleotide Polymorphism (SNP) genotypes are a core tool for assessing genetic diversity (Funk et al. 2012). While restriction site associated DNA (RAD), libraries are often used to detect tens of thousands of SNPs, it can be challenging to add more individuals to a project once the initial assembly is completed. Further, moderate numbers of SNPs may be adequate for addressing many evolutionary and conservation questions (e.g. Spinks et al. 2014). A set of 119 putative loci was selected from Genbank’s dbSNP and searching for ‘cichlidae’ (December 2014). A total of 667 loci were listed. Of these, 323 were developed in the Tilapia species Oreochromis niloticus and 344 were developed in the Lake Malawi ‘haplochromine’ species Cynotilapia afra. Of these, 32 O. niloticus and 64 C. afra de
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