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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

2012 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:

This project has the overall goals of developing state of the art resources for genetic analyses in rainbow trout, primarily a genetic marker array that is constructed using information from research and commercial populations that are overlaid on the genome sequence, which must first be obtained. Significant progress was made in obtaining the genome sequence (Objective.
1)and developing the genetic marker of choice, single nucleotide polymorphisms (SNP, Objective 2).

Objective 1: Our strategy for sequencing the trout genome includes construction of a physical map built from small overlapping fragments of the genome which can easily be sequenced. This year we improved the physical map by adding over 20,000 new fragments to our analysis, providing a 13% increase in map information. The new map covers approximately 80% of the rainbow trout genome, of which we have sequence information for 95%; therefore the current draft of our sequence represents ~70% of the genome. A genetic map revealing the order of 5000 SNPs on trout chromosomes was constructed to aid in ordering the overlapping fragments of the physical map.

Objective 2: Progress was made in identifying a set of over 109,000 SNPs from 8 research populations. The usefulness of this data set was validated on 18 populations from commercial and research sources to demonstrate the need for stringent marker selection criteria prior to construction of high-density genotyping platforms that aim to benefit all populations. To date this data set is the resource on which an international trout genotyping collaboration is being developed.


Last Modified: 9/20/2014
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