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

BMC Genetics

Research Article

Carlos D Bustamante¹  Xin Ma¹  Adam R Boyko¹  Larissa M Williams²  Marjorie F Oleksiak³ 

[1] Department of Biological Statistics and Computational Biology, Cornell University, 14853, Ithaca, NY, USA;Department of Environmental and Molecular Toxicology, North Carolina State University, Box 7633, 27695-7633, Raleigh, NC, USA;Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, 33149, Miami, FL, USA;

关键词: Principle Component Analysis;    Allelic Richness;    Southern Population;    Northern Population;    Putative SNPs;   

DOI  :  10.1186/1471-2156-11-32

 received in 2010-02-05, accepted in 2010-04-30,  发布年份 2010

来源: Springer

【 摘 要 】

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

【 授权许可】

Unknown   
© Williams et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.