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A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus).

Ferchaud AL, Pedersen SH, Bekkevold D, Jian J, Niu Y, Hansen MM - BMC Genomics (2014)

Bottom Line: Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new.We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback.The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark. michael.m.hansen@biology.au.dk.

ABSTRACT

Background: The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background.

Results: RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new.

Conclusions: We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

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Map showing the location of sampled three-spine stickleback populations in Jutland, Denmark.
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Fig1: Map showing the location of sampled three-spine stickleback populations in Jutland, Denmark.

Mentions: Sixty threespine sticklebacks, 20 from each site, were sampled by cast nets or minnow traps from three localities in Jutland, Denmark: 1) Lake Hald, a 3.3 km2 freshwater lake, 2) a small unnamed freshwater pond (ca. 0.01 km2) near the town of Hadsten and 3) the Mariager Fjord, a marine environment (see Figure 1). These individuals were analyzed using RAD sequencing [11, 21] in order to identify SNPs. 4) An additional 96 individuals were sampled close to the outlet of the Odder River, Jutland, Denmark (see Figure 1). Individuals from this estuarine population were genotyped in order to validate the generated SNP array. The first two samples (Lake Hald and Hadsten) consisted of morphs with low numbers of lateral plates (“low-plated”), as typically observed in freshwater [10]. The third, marine sample consisted of the typical marine morph with high numbers of lateral plates (“high-plated”), whereas the fourth estuarine population consisted of a mixture of low and high-plated morphs.Figure 1


A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus).

Ferchaud AL, Pedersen SH, Bekkevold D, Jian J, Niu Y, Hansen MM - BMC Genomics (2014)

Map showing the location of sampled three-spine stickleback populations in Jutland, Denmark.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4196021&req=5

Fig1: Map showing the location of sampled three-spine stickleback populations in Jutland, Denmark.
Mentions: Sixty threespine sticklebacks, 20 from each site, were sampled by cast nets or minnow traps from three localities in Jutland, Denmark: 1) Lake Hald, a 3.3 km2 freshwater lake, 2) a small unnamed freshwater pond (ca. 0.01 km2) near the town of Hadsten and 3) the Mariager Fjord, a marine environment (see Figure 1). These individuals were analyzed using RAD sequencing [11, 21] in order to identify SNPs. 4) An additional 96 individuals were sampled close to the outlet of the Odder River, Jutland, Denmark (see Figure 1). Individuals from this estuarine population were genotyped in order to validate the generated SNP array. The first two samples (Lake Hald and Hadsten) consisted of morphs with low numbers of lateral plates (“low-plated”), as typically observed in freshwater [10]. The third, marine sample consisted of the typical marine morph with high numbers of lateral plates (“high-plated”), whereas the fourth estuarine population consisted of a mixture of low and high-plated morphs.Figure 1

Bottom Line: Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new.We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback.The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark. michael.m.hansen@biology.au.dk.

ABSTRACT

Background: The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background.

Results: RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new.

Conclusions: We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

Show MeSH