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United States Department of Agriculture

Agricultural Research Service

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Research Project: Generation of a SNP Chip for genomic analysis in rainbow trout (MTSU)- CFDA 10.310

Location: Cool and Cold Water Aquaculture Research

Project Number: 1930-31000-009-15
Project Type: General Cooperative Agreement

Start Date: Nov 01, 2012
End Date: Oct 31, 2013

Objective:
1. Produce a draft reference genome sequence for rainbow trout. 2. Produce a high density SNP chip for rainbow trout.

Approach:
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. 2.d. Use RNA-seq to identify putative SNPs from coding sequences that are potentially associated with aquaculture production traits and validate the putative SNPs through genotyping of phenotyped rainbow trout from the NCCCWA breeding program populations.

Last Modified: 8/29/2014
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