Progress 02/01/07 to 07/31/08
Outputs
OUTPUTS: A BAC library (HindIII partial digest; pcc1BAC vector) was constructed in 2007 by Amplicon Express (Pullman, WA, USA) from a single inbred Pacific oyster male from a resource line used for previous USDA NRI projects (courtesy of Dennis Hedgecock, USC). It consists of 73 728 clones, providing an estimated 10X genome coverage. The library was fingerprinted at the Genome Sciences Center (Vancouver, Canada)to provide a BAC-based physical map of the oyster genome. Of the 64,403 clones assembled, 96% were placed into 3,374 contigs (average number of clones per contig = 18), with 2,578 singletons. The resulting map is currently housed at the GSC and accessible to the research community using iCE (internet Contig Browser), and will be maintained subsequently at the University of Delaware and/or Clemson University Genomics Institute, where genetic data will be added to the physical map to serve as a community resource for molecular breeding and genetic analysis. The first-generation
BAC map was presented to the NRI Animal Genome Annual Investigator Meeting (11 January 2008) in San Diego, and at the National Shellfisheries Association annual meeting (8 April 2008) in Providence.
PARTICIPANTS: The BAC fingerprinting was conducted at the Genome Sciences Centre (Vancouver, BC) under the leadership of Dr. Jacquie Schein (http://www.bcgsc.ca/faculty/jschein). Dr. Patrick Gaffney (University of Delaware College of Marine and Earth Studies) served as project coordinator. Dr. Dennis Hedgecock (University of Southern California) and Dr. Joth Davis (Taylor Shellfish) provided the inbred oyster for library construction. Amplicon Express (Pullman, WA) constructed the BAC library.
TARGET AUDIENCES: The Pacific oyster Crassostrea gigas is distributed worldwide, and for the past several years has had the highest annual production of any freshwater or marine organism (4.2 million metric tons, worth US$3.5 billion). The production of hatchery-based production of seed is increasing worldwide, allowing the development of selective breeding of domesticated stocks to improve growth, disease resistance and quality traits such as shell shape or meat/shell ratio. In this context, the development of genetic and genomic resources, such as genetic and physical maps, is viewed as an essential step towards effective domestication and genetic improvement. The results of this project will advance the development of genomic resources in the Pacific oyster, ultimately translating into more efficient aquacultural production.
PROJECT MODIFICATIONS: The project proceeded as initially proposed. Analysis of a previous BAC library showed a high level of polymorphism, making a new library from a single highly inbred individual desirable for effective physical map assembly. This library was constructed thanks to supplemental funding, and the fingerprinting project was completed as planned.
Impacts
The development of the BAC-based physical map of the Pacific oyster genome has sparked worldwide interest in genome studies of this major aquaculture species. Since its release in early 2008, a follow-up proposal for complete BAC-end sequencing (all 73,728 clones) has been submitted to the French sequencing agency, Genoscope (P. Gaffney, co-PI). At the same time, discussions with Chinese government officials and scientists have led to an agreement for draft genome sequencing, using the same BAC library. The current plan is to use a minimal tiling path developed from the BAC map to select BAC clones for complete sequencing, for the first phase of genome sequencing. In addition, a planned submission to the USDA NRI Animal Genome Program will develop > 1000 SNP markers in the resource line and probe the BAC library to identify BAC clones containing the SNP loci, to allow integration of physical and genetic maps.
Publications
- No publications reported this period
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