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United States Department of Agriculture

Agricultural Research Service


Location: Cool and Cold Water Aquaculture Research

2010 Annual Report

1a.Objectives (from AD-416)
1) Continued development of a rainbow trout genetic map to reveal qualitative and quantitative trait loci affecting traits associated with aquaculture production. 2) Identification and characterization of genes affecting disease resistance, growth, and embryonic development through functional genomic technologies. 3) Development of strategies to implement functional genomic and genetic mapping information into the NCCCWA rainbow trout selective breeding program using bioinformatics. 4) Develop databases and programs to assimilate and coordinate genomic data on the rainbow trout broodstock developed at the NCCCWA. 5) Develop methodology to utilize rainbow trout genomic information in comparative analyses to identify potential critical functional genes and genetic pathways.

1b.Approach (from AD-416)
Aquaculture is the most rapidly growing segment of U.S. agriculture and the only sustainable option for satisfying the globally increasing demand for seafood products. Although demands in domestic and international markets remain high, the growth of the U.S. rainbow trout aquaculture industry has leveled off. In order to compete, U.S. trout farmers must overcome losses due to diseases and improve the growth characteristics of this species. A major constraint to increasing the production efficiency is the lack of genetically improved aquaculture stocks. One approach to address these problems is genetic improvement through selective breeding. NCCCWA has initiated a multidisciplinary approach to selective breeding of rainbow trout. Coordination of the activities proposed in this Project Plan with ongoing pathogenic disease research being conducted by project "Host, Pathogen, and Environmental Interactions in Cool and Cold Water Aquaculture" and growth, stress, and reproduction research being conducted by project "Utilizing Gentic for Enhancing Cool and Cold Water Aquaculture Production", will allow for the identification of genes affecting important aquaculture production traits. The result will be genome information which will allow for increased understanding of the biological mechanisms controlling these disease resistance, growth, stress, tolerance, and embryonic development and exploitation of positive genetic variation on the NCCCWA selective breeding program.

3.Progress Report
This is the final report for 1930-31000-008-00D which terminated December 13, 2009. Project was replaced by 1930-31000-009-00D. Refer to replacement project for accomplishments.

A genetic map was constructed based on a panel of families that represent the starting genetic material of the NCCCWA selective breeding program. It has 1,124 microsatellite loci over 29 linkage groups and a total length of 2,927cM. In project 1930-31000-009-00D it will continue to be used to identify genes affecting disease resistance and stress tolerance. A subset of the markers included in the genetic map was developed into a multiplex assay with the aim of increasing the efficiency of genotyping broodstock. This single-step method of co-amplifying microsatellite markers for genetic studies was developed and optimized to reduce the high costs associated with these analyses.

To complement genetic maps, a first generation physical map of the rainbow trout genome was produced using high throughput DNA fingerprinting of the 10X genome coverage bacterial artificial chromosome (BAC) library. The physical map includes two billion base pairs of DNA and represents 75% - 80% of the trout genome. In the next project this resource will aid in isolating genes affecting production traits.

Immune Response Genes: - MHC - Genes encoded by the major histocompatibility complex (MHC) play an important role in immune response to a variety of pathogens. Genetic variation of markers linked to MHC genes in the NCCCWA 2005 brood-year was characterized and suggestive association was detected between Flavobacterium psychrophilum (Fp) resistance and the trout MHC-IB.

TLRs: Toll-Like Receptors (TLRs) are a family of transmembrane proteins that recognize pathogens and initiate innate and adaptive immune response. In the prior project period we sequenced, mapped and determined the genomic structure and expression of the rainbow trout TLR1, 3, 5, 7, 8a1, 8a2, 9, 20 and 22 genes.

Growth and Development Genes: - UCPs – Uncoupling proteins (UCPs) affect various physiological processes such as control of body weight, fatty acid metabolism, control of reactive oxygen species, and negative regulation of insulin secretion. Two rainbow trout uncoupling protein 2 genes were identified and their expression characterized.

IDs: The Inhibitor of DNA Binding/Differentiation (ID) proteins play a role in determining the number of muscle cells that develop in an organism. All six known ID genes characterized with respect to their expression throughout embryonic development and in adult rainbow trout tissues.

microRNAs: To identify miRNAs that might be important for early embryogenesis in rainbow trout, a miRNA library from a pool of unfertilized eggs and early stage embryos was constructed. Sequence analysis identified 14 miRNAs, 4 of which are novel to rainbow trout.

Oocyte Development: In an effort to identify key oocyte-specific genes involved in the regulation of early embryonic development, a rainbow trout oocyte cDNA library was constructed. Analysis of EST sequences from the library has led to the discovery of two novel oocyte-specific genes (OORP-T and RtGST-1).

Last Modified: 4/23/2014
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