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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 (WSU)

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:

The goal of this sub-project was to produce a high density genetic map to aid in the assembly of the rainbow trout reference genome sequence. Due to technical difficulties the sub-objective of producing additional doubled-haploid rainbow trout for genetic mapping could not be achieved. Instead we have analyzed genetic markers on eight families from the NCCCWA experimental breeding population which will aid in the reference genome sequence assembly. We still intend to produce the offspring from the doubled haploid clonal line hybrids when we overcome the current technical difficulties, and they will be used as resource material for a rainbow trout genetic map.


Last Modified: 12/22/2014
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