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Open Access Highly Accessed Research article

SNP identification, verification, and utility for population genetics in a non-model genus

Larissa M Williams1, Xin Ma2, Adam R Boyko2, Carlos D Bustamante2 and Marjorie F Oleksiak3*

Author Affiliations

1 Department of Environmental and Molecular Toxicology, Box 7633, North Carolina State University, Raleigh, NC 27695-7633, USA

2 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA

3 Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA

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BMC Genetics 2010, 11:32  doi:10.1186/1471-2156-11-32

Published: 30 April 2010

Abstract

Background

By targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost, Fundulus heteroclitus as well as closely related Fundulus species (F. grandis, F. majalis and F. similis).

Results

We used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of Fundulus. Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the F. heteroclitus genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in F. heteroclitus EST sequences were verified in most (86.5%) F. heteroclitus individuals; fewer were genotyped in F. grandis (74.4%), F. majalis (72.9%), and F. similis (60.7%) individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in F. heteroclitus populations. In F. grandis, SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations.

Conclusions

In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.