Application of single nucleotide polymorphism markers to chum salmon Oncorhynchus keta: Discovery, genotyping and linkage phase resolution

This study describes (1) the application of new methods to the discovery of informative single nucleotide polymorphism (SNP) markers in chum salmon Oncorhynchus keta, (2) a method to resolve the linkage phase of closely linked SNPs and (3) a method to inexpensively genotype them. Finally, it demonstrates that these SNPs provide information that discriminates among O. keta populations from different geographical regions of the northern Pacific Ocean. These informative markers can be used in conjunction with mixed-stock analysis to learn about the spatial and temporal marine distributions of O. keta and the factors that influence the distributions.