Abstract
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.
Highlights
By targeting Single nucleotide polymorphisms (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
Species differentiation was demonstrated using principle component analysis (PCA) as well as STRUCTURE analysis. Both analyses showed separation between F. heteroclitus, F. grandis and F. majalis and similis as well as population structure within F. heteroclitus (Figure 4). These analyses provided the most resolution in F. heteroclitus because the SNPs were originally identified in this species
Similar studies using high throughput methods to sequence SNP markers have been developed in Atlantic cod [51], white spruce [52], Eucalyptus [8], and swine [70]
Summary
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. High throughput sequencing and genotyping has become increasingly faster, less expensive and more accurate In recent years this has lead to the establishment of myriad data sets ranging from increased coverage of variation in the human genome at the individual level [1,2,3,4,5] to the sequencing of non-model prokaryotic and eukaryotic genomes and transcriptomes [6,7,8,9,10,11]. For many organisms sequencing of entire genomes is still unattained, but smaller, more targeted portions of the genome can be sequenced and genotyped Such data can provide genome-wide sequence information which can be used to characterize population and selection pressure parameters as well as provide evolutionary insights that are broadly applicable [12].
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