Dr. Mark Camara USDA-ARS Shellfish Genetics Program  The USDA-ARS Shellfish Genetics Program, initiated in May 2003, works closely with the Oregon State University Molluscan Broodstock Program (MBP) to improve Pacific oysters germplasm available to the west coast commercial aquaculture industry. The USDA-ARS genetics program and MBP are co-located at Oregon State University’s Hatfield Marine Science Center near the mouth of the Yaquina Bay on the central coast of Oregon (http://hmsc.oregonstate.edu/ ).   The goal of the Shellfish Genetics Program is to develop genetic knowledge that will be useful in developing superior breeding stocks of Pacific oysters and other shellfish species cultured commercially in the Pacific Northwest region. To achieve this goal, the program employs a wide variety of genetic approaches ranging from traditional quantitative genetics through population genetics based on neutral DNA markers and state of the art transcriptomic approaches aimed at discovering the functional genes that control economically important traits such as survival, growth, shell shape, and heavy metals bioaccumulation.   Nursery Upweller   Shellfish Field Site   Planting Oyster Floats   Weighing Mature Oyster

Research Projects:   1.      Germplasm characterization of Pacific and Kumamoto oysters                                                                                                                    Commercial-level hatchery production of molluscan shellfish is relatively new, and the genetic consequences of developing closed germplasm populations have not always been anticipated, appreciated, or effectively managed. Population bottlenecks, inbreeding, inadvertent hybridization among species, and domestication selection in hatcheries have potentially led to the loss of beneficial genetic diversity and compromised performance.  As an initial step toward addressing these issues, the Shellfish Genetics Program is using highly polymorphic neutral molecular DNA markers (microsatellite DNA and Amplified Fragment Length Polymorphisms) to assess the levels of genetic variation within and among the various commercially available breeding stocks of both Pacific and Kumamoto oysters and to compare them to genetically healthy wild populations.        2.      Pedigree reconstruction in Pacific oysters   Most genetic analyses rely upon pedigree information in order to track genetic relationships among individuals. In most domesticated animal species, obtaining this information this relatively easy using individual marking such as leg bands, ear tags, or branding. In shellfish, however, offspring are microscopic and impossible to mark, and this requires that groups of relatives be reared in separate tanks in the hatchery and deployed in separate plots or bags in the field.  This “separate-family” approach is costly and necessitates extensive replication to avoid confounding environmental and genetic influences. The Shellfish Genetics Program is developing computer software and genetic markers that will allow large numbers of families to be reared together and pedigree information extracted from non-destructive DNA samples of the most desirable animals. With this information, top performers can be used to improve the stock without creating problems through inbreeding or population bottlenecks.     3.      Quantitative genetics in Pacific oysters   The success of selective breeding efforts depends critically on the degree to which the target traits are genetically determined and on the levels of genetic variation within the breeding stocks (heritability). In addition, if multiple traits are targeted for improvement, or improvement is desired in multiple environments, genetic trade-offs such as negative genetic correlations among traits and genotype-by-environment interactions can create serious complications. Evaluating groups of known relatives at several field sites allows the statistical partitioning of overall variation in desirable traits into genetic and environmental components, and thus estimates of the heritabilities of and genetic correlations among traits as well as any genotype/environment interactions. These estimates are critical to the design and implementation of effective selective breeding.       4.      Quantitative trait locus (QTL) mapping in Pacific oysters   A more precise level of genetic information can be obtained by analyzing the co-inheritance of neutral DNA markers (e.g. microsatellite DNA, single nucleotide polymorphisms [SNPs] and AFLPs) and phenotypes of interest. Such experiments can reveal the number, approximate location in the genome, and degree of influence of genes that contribute to specific traits: QTL. These types of analyses are one way to start to “zero in” on specific genes in order to allow selective breeding efforts to directly target these genes rather than relying on measurements of the traits themselves.  Such “marker-assisted selection” can considerably improve the efficiency of selective breeding, especially for traits that are difficult to measure or that depend upon specific environmental conditions to be expressed.     5.      Transcriptome Profiling in Pacific oysters   Many genes are only expressed under particular conditions, and this is particularly true of genes that confer resistance to disease, parasites, or stress. Because oyster farms frequently suffer massive mortalities caused by a combination of stress and disease, the Shellfish Genetics Program is using high-throughput assays of gene expression (transcriptome profiling) to identify genes for stress and disease resistance. We use simple laboratory assays to identify susceptible and tolerant genotypes and then look for differences in gene expression in response to challenges using DNA microrrays or other molecular methods such as serial analysis of gene expression (SAGE).  Once identified, these genes are also excellent candidates for marker-assisted selection.      6.      Population Genetics of Olympia oysters   Over-exploitation, habitat degradation, and pollution have reduced the once enormous populations of  the Olympia oyster, the only oyster native to the Pacific Northwest, to scattered remnants, and there is a great deal of interest in restoring this species. It is, however, critical, to understand the degree to which these remnant populations are specifically adapted to local conditions in order to design effective restoration programs.  The Shellfish Genetics Program, in close collaboration with the Confederated Tribes of the Siletz, NOAA’s South Slough Estuarine Research Reserve in Coos Bay, and Oregon Sea Grant is developing polymorphic molecular DNA markers capable of revealing patterns in the distribution of genotypes of Olympia oysters at scales ranging from the entire west coast to sub-estuaries of San Francisco Bay and Puget Sound.