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

Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF - BMC Genet. (2010)

Bottom Line: In F. grandis, SNPs were less polymorphic but still established isolation by distance.Markers differentiated species and populations.In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.

View Article: PubMed Central - HTML - PubMed

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

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.

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Sampling sites for Fundulus species. F. heteroclitus was collected along the east coast of the United States and F. grandis was collected along the Gulf of Mexico coast.
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Figure 1: Sampling sites for Fundulus species. F. heteroclitus was collected along the east coast of the United States and F. grandis was collected along the Gulf of Mexico coast.

Mentions: F. heteroclitus were collected using minnow traps during the spring of 2005. Spleen and testes were sampled from 20 individuals from each of ten collection sites along the East coast of the United States (Figure 1). F. grandis were collected using minnow traps during the winter of 2009 (Figure 1). Fin clips were sampled from 15 individuals from each of the six collection sites along the Gulf Coast of the United States. Spleen from F. majalis was extracted from 13 individuals from Woods Hole, Massachusetts and 10 individuals from Sapelo Island, GA. Spleen also was extracted from F. similis collected from Pensacola, Florida (3 individuals) and Corpus Christi, Texas (8 individuals).


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

Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF - BMC Genet. (2010)

Sampling sites for Fundulus species. F. heteroclitus was collected along the east coast of the United States and F. grandis was collected along the Gulf of Mexico coast.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874759&req=5

Figure 1: Sampling sites for Fundulus species. F. heteroclitus was collected along the east coast of the United States and F. grandis was collected along the Gulf of Mexico coast.
Mentions: F. heteroclitus were collected using minnow traps during the spring of 2005. Spleen and testes were sampled from 20 individuals from each of ten collection sites along the East coast of the United States (Figure 1). F. grandis were collected using minnow traps during the winter of 2009 (Figure 1). Fin clips were sampled from 15 individuals from each of the six collection sites along the Gulf Coast of the United States. Spleen from F. majalis was extracted from 13 individuals from Woods Hole, Massachusetts and 10 individuals from Sapelo Island, GA. Spleen also was extracted from F. similis collected from Pensacola, Florida (3 individuals) and Corpus Christi, Texas (8 individuals).

Bottom Line: In F. grandis, SNPs were less polymorphic but still established isolation by distance.Markers differentiated species and populations.In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH