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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

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. 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.


3.Progress Report:

Variation in muscle yield was measured in 100 families from the USDA rainbow trout breeding program. Variation in muscle yield correlated to genes containing genetic markers in families showing extreme phenotypes (4 high-muscle yield families [50.9% of body weight ± 1.8] versus 4 low-muscle yield families [43.2% of body weight ± 2.1]). A total of 127,401 genetic markers were identified; from these 143 were specific to the “high-muscle yield” group and 96 were specific to the “low-muscle yield”. A subset of the genetic markers which were specific to each group are currently being genotyped and evaluated for association with muscle yield in a ~500-fish panel from 97 families. In addition, differential gene expression between “high-muscle yield” and “low-muscle yield” groups detected 60 genes. Gene pathway analysis of the 239 genetic markers and the 60 differentially expressed genes revealed various biochemical pathways including those involved in amino acid and sugar metabolism.


Last Modified: 10/22/2014
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