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United States Department of Agriculture

Agricultural Research Service

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Research Project: GENERATION OF HIGH DENSITY SNP CHIP FOR GENOMIC ANALYSIS IN RAINBOW TROUT

Location: Cool and Cold Water Aquaculture Research

2013 Annual Report


1a.Objectives (from AD-416):
1) Produce a draft reference genome sequence for rainbow trout. 2) Produce a high density SNP chip for rainbow trout.


1b.Approach (from AD-416):
1.a. Sequence the BACs from the physical map minimal tiling path (MTP) using the new Illumina sequencing platform. 1.b. Produce a dense genetic map using 5,000-10,000 SNPs from the Swanson x Whale Rock doubled haploid (DH) recombinant line of Gary Thorgaard to aid in the integration of the genetic and physical maps and the genome sequence assembly. 2.a. Add more SNPs to the current NCCCWA database of 25,000-50,000 putative SNPs using reduced representation sequencing approaches on the Thorgaard’s androgenetic DH lines and additional outbred populations of economic and scientific interest, and based on the genome sequence assembly from objective 1, select and design SNP markers for a chip of up to 50K SNPs. 2.b. Validate a subset of the SNPs using a smaller genotyping assay (e.g. Illumina’s 3K GoldenGate). 2.c. Produce a commercial high-density SNP assay for whole genome simultaneous genotyping in rainbow trout.


3.Progress 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.


Last Modified: 12/22/2014
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