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ARS Home » Pacific West Area » Newport, Oregon » Pacific Shellfish Research Unit » Research » Research Project #437220

Research Project: Identifying Genetic Factors Associated with the Expression and Regulation of Economically Important Traits in Cultured Pacific Oysters

Location: Pacific Shellfish Research Unit

Project Number: 2076-63000-005-002-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2019
End Date: Jul 31, 2024

The general objective of this cooperative research is to identify genetic factors associated with the expression and regulation of economically important traits in cultured Pacific oysters (Crassostrea gigas) and use this information to develop marker assisted selection techniques that enhance broodstock development with improved characteristics. Specific project objectives are to: 1) Improve resistance of Pacific Northwest (NW) oyster stocks to microvariants of the oyster herpes virus OsHV-1 and acidified high PC02 seawater without a reduction in farm yields; 2) Use quantitative and molecular data from on-going research data collected by the Oregon State University molluscan shellfish breeding program (MBP) at the Hatfield Marine Science Center (HMSC), and other data sources, to design and implement breeding strategies to improve traits of Pacific oysters of high value to industry.

Selected families will be produced from two recent annual cohorts (27 and 28) of oyster families that show the greatest resistance to OsHV-1 microvariants under laboratory conditions and in field tests carried out in Tomales Bay, California, where a less-pathogenic, “standard” variant is present. To prevent a loss in gains due to past selection for farm yields, preference will be given to families that show both resistance to OsHV-1 as well as possessing high yields in both Tomales Bay, California, and Willapa Bay, Washington. Willapa Bay is not currently infected with OsHV-1 and is the most important bay for Pacific oyster aquaculture on the West Coast. Appropriate controls will be included in cohort (29), consisting of spat from 1) crosses among naturalized (unselected) Pacific oysters collected from Willapa Bay, 2) crosses between highly inbred families that are genetically consistent across generations, and 3) crosses among randomly selected families from previous cohorts. Spat from a recent cohort (28) of families and controls will be tested against OsHV-1 microvariants under laboratory conditions. Samples of moribund and surviving spat from the lab studies will be sampled for DNA and RNA analysis in order to identify markers for OsHV-1 resistance. A sub-sample of spat will also be taken for qPCR quantification of OsHV-1 to validate that mortalities were due to viral infection. Researchers plan to continue to test families at both the Tomales Bay site (infected with standard OsHV-1) and the Willapa Bay site (free of OsHV-1 but impacted by OA and hypoxic upwelling events). Mortalities at the Tomales Bay site will be monitored during periods when water temperatures exceed 16oC when outbreaks of OsHV-1 are often observed. When high mortalities of planted spat are observed, samples of moribund and surviving spat will be taken to confirm the presence of OsHV-1 in tissues using qPCR, and for DNA and RNA analysis in order to identify markers for OsHV-1 resistance. Data will be analyzed using a pedigree-based animal model to determine various genetic parameters, such as heritabilities and breeding values. Development of accurate genetic markers discovered via QTL mapping or GWAS approach requires a fully assembled Pacific oyster genome that is currently lacking. Scientists will combine long-read PacBio sequencing and HiC chromosome capture for long-range chromosome information retrieval.