Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/1/2010
Publication Date: 1/28/2011
Citation: Castano, C., Palti, Y., Rexroad III, C.E. 2011. SNP analysis with duplicated fish genomes: differentiation of SNPs, paralogous sequence variants and multi-site variants. In: Liu, Z.J., editor. Next Generation Sequencing and Whole Genome Selection in Aquaculture. 1st edition. Malden, MA: Wiley-Blackwell. p. 133-150.
Technical Abstract: High-throughout SNP discovery and genotyping have facilitated genome analyses aimed at identifying factors that affect traits of interest. Platforms that multiplex thousands of SNPs are available for some agricultural species but not yet for aquaculture. Ray-finned fish share an additional (3R) round of ancestral genome duplication in their evolutionary history than other livestock animals and they are likely to encounter higher frequencies of PSVs and MSVs, which can hinder the development of high throughput SNP assays. This problem is more prominent in the salmonids and the common carp, which have undergone more recent and independent (4R) whole genome duplications. Contemporary SNP genotyping platforms have not taken into consideration the existence of duplicated genomes and the algorithms used for genotype calling are not adequate. A reference genome sequence will likely enable successful validation of SNPs from high throughput discovery projects in aquaculture species with duplicated genomes.