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.
Sub-Objective 1.a. Reference Genome Assembly: A draft genome assembly has been prepared and made publicly available through Iowa State University (http://www.animalgenome.org/bioinfo/). In this assembly, approximately 70% of the rainbow trout genome sequence was assigned to long stretches of continuous sequence called scaffolds or contigs.