Population structure in the eastern oyster Crassostrea virginicaassessed by single nucleotide polymorphisms

摘要

Single nucleotide polymorphisms (SNPs) are abundantly distributed throughout plant and animal genomes. Because the number of loci is virtually unlimited and they are amenable to robust high-throughput genotyping, SNPs are rapidly becoming standard tools for the analysis of population structure, genetic mapping, and taxonomic identification. Our goal is to evaluate population structure of the eastern oyster throughout its range from Atlantic Canada to the Yucatan Peninsula, using a large number of SNPs identified in known genes (Type I SNPs). While previous work has shown a clear genetic break between Atlantic and Gulf coast populations in mitochondrial DNA, studies of geographic variation in nuclear loci (allozymes and anonymous DNA markers) have yielded mixed results. Existing genomic and expressed sequence tag (EST) databases of C. virginica have been mined for the development of both anonymous and type I markers, with recent efforts focused on genes thought to be involved in disease response. Direct sequencing of amplified targets has revealed extensive polymorphism in C. virginica. We have developed a set of nuclear SNP markers to examine the genetic diversity of C. virginica throughout the species range and provide multiple markers for genetic linkage mapping. Significant heterogeneity in allelic frequencies among the geographic locations was observed for each locus. Our results are consistent with the Gulf-Atlantic split previously observed with other markers. In addition, clinal patterns in allelic frequencies in Atlantic populations are suggested for some loci.