Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

High Frequency Of SNPs In The Pacific Oyster Genome

Jason P. Curole , Dennis Hedgecock

  Department of Marine Biology, University of Southern California, 3616 Trousdale Pkwy., AHF, Los Angeles, CA, 90089, USA

The Pacific oyster has emerged as a model system to understand the genetic and physiological mechanisms of growth heterosis, which is manifest as superior hybrid yield in controlled crosses among inbred lines.  A set of "candidate" loci for heterosis has been identified through comparative MPSS analysis of gene expression in hybrid and inbred oysters (Hedgecock et al. PAG X).  Further evaluation of candidate loci by QTL methods, for example, requires discovery of polymorphisms at candidate loci that would permit linkage mapping.  Single nucleotide polymorphisms (SNPs) are the most common form of polymorphism in the genome and are useful for an array of genetic analyses.  We have undertaken a study to identify SNPs at expressed sequences (ESTs) in the Pacific oyster genome, with a particular emphasis on identified candidate loci.  Our sample panel for SNP discovery consists of the F₁ parents of existing F₂ mapping families.  Primers were designed to ESTs, ten of which are MPSS candidates, ESTs were PCR amplified, amplicons cloned, and six clones sequenced; SNPs were identified from aligned sequences using the PolyBayes algorithm. Preliminary results suggest that SNPs are highly abundant in the oyster genome, with initial estimates of 1 SNP per 40bp.  More remarkably, there is 1 insertion/deletion every 33bp.  These data show that there is abundant polymorphism in the oyster genome, which will facilitate several genetic analyses, including genetic mapping of loci responsible for heterosis, pedigree analysis of lines, allele-specific expression at candidate loci and genetic structure of natural populations