Location: Cool and Cold Water Aquaculture Research
2013 Annual Report
Single Nucleotide Polymorphism (SNP) Discovery: A large dataset of high quality restriction associated DNA (RAD) SNPs that passed our rigorous analysis pipeline was generated from a panel of 11 homozygous doubled haploid rainbow trout lines as a resource for designing a high density SNP chip genotyping assay. The current bioinformatics pipeline for analyzing RAD sequence data was found to be very useful for assessing genetic diversity within a single rainbow trout population or between a pair of populations, but not for comparing more than two populations in a single analysis. The generally low percentage of RAD SNPs shared between populations in a pairwise comparison suggests that for a SNP chip to be useful for a wide range of genetic analyses in rainbow trout it will be important to select genetic markers having polymorphisms shared by as many populations as possible.
SNP Chip Design: An Affymetrix Axiom chip design composed of 57,500 SNPs was completed using primarily the RAD SNPs dataset we generated from the homozygous rainbow trout lines but also by using other SNP datasets that were generated by US and international collaborators. Production, validation and evaluation of the 57K SNP chip is currently ongoing.