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

BMC Genomics

Michael M Hansen³  Yongchao Niu¹  Jianbo Jian¹  Dorte Bekkevold²  Susanne H Pedersen³  Anne-Laure Ferchaud³ 

[1] BGI-shenzhen, Main Building, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China;National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark;Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark

关键词: Low-density array;    RAD sequencing;    Single nucleotide polymorphism;    Threespine stickleback;   

Others  :  1136268
DOI  :  10.1186/1471-2164-15-867

 received in 2014-03-24, accepted in 2014-09-29,  发布年份 2014

【 摘 要 】

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).

【 授权许可】

   
2014 Ferchaud et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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