Progress 02/01/11 to 11/30/12
Outputs
Progress Report Objectives (from AD-416): 1. Produce a draft reference genome sequence for rainbow trout. 2. Produce a high density SNP chip for rainbow trout. 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. Rainbow trout is one of the most important aquaculture species in the United States and around the world, but little is known about its genetic makeup. To this end we report on the third expansion and improvement of the physical map of the rainbow trout genome which combines genetic information on the inheritance of chromosomes throughout generations with the physical DNA sequences that contain genes that control biological processes. This resource will facilitate the identification of genes affecting important aquaculture production traits and enhance strategies targeting the genetic improvement of this species for production efficiency. This year our efforts resulted in a 13% improvement over previous versions of the map, covering 1.9 gigabase pairs and representing ~80% of the rainbow trout genome. The physical map is integrated with the genetic map through microsatellite genetic markers that were previously mapped.
Impacts
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Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): 1. Produce a draft reference genome sequence for rainbow trout. 2. Produce a high density SNP chip for rainbow trout. 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. The aim of this sub-project was to improve the BAC physical map minimal tiling path for rainbow trout. Rainbow trout is one of the most important aquaculture species in the United States and around the world, but little is known about its genetic makeup. To this end we report on the third expansion and improvement of the physical map of the rainbow trout genome which combines genetic information on the inheritance of chromosomes throughout generations with the physical DNA sequences that contain genes that control biological processes. This resource will facilitate the identification of genes affecting important aquaculture production traits and enhance strategies targeting the genetic improvement of this species for production efficiency. DNA fingerprints from an additional 20,736 bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the second generation physical map of the rainbow trout (Oncorhynchus mykiss) genome. Of the 20,736 new clones, 17,075 produced high quality DNA fingerprints and were used in the new fingerprinting contigs assembly. The current version of the physical map is composed of 185,064 clones of which 179,752 are assembled into contigs and 5,312 are singletons. The number of contigs was reduced from 4,173 and 3,220 in the first and second generation maps, respectively, to 2,804, representing a 13% improvement in the current map. The new map contigs cover 1.9 Gb which is approximately 80% of the rainbow trout genome. The physical map is integrated with the genetic map through microsatellites that were previously isolated from BACs and mapped to the genetic map by linkage analysis. The number of clones in the new minimal tiling path (MTP) is 13, 966 compared to 14,900 in the MTP of the second generation map. The clones from the MTP of the physical map are currently being sequenced and this improved version of the map is used to guide the assembly of a reference genome for rainbow trout.
Impacts
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Publications
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