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United States Department of Agriculture

Agricultural Research Service

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Research Project: Determine Genetic Diversity and Develop Tools for Genetic Improvement of Oyster Stocks for the Pacific Northwest

Location: Forage Seed and Cereal Research

2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Assess the potential for genetic gain, and trade-offs among economically important traits in currently available Pacific oyster germplasm in order to develop a framework for informed decisions regarding alternative selective breeding strategies.

Sub-objective 1.A. Estimate the additive genetic, non-additive genetic, and environmental covariance matrices for larval, nursery, and field performance in currently available germplasm of the Pacific oyster using a multi-year animal model approach.

Sub-objective 1.B. Use the estimates obtained in Sub-objective 1.A. to design an efficient genetic improvement strategy for Pacific oysters.

Objective 2: Evaluate and optimize mixed-family breeding strategies for Pacific oysters.

Sub-objective 2.A. Determine at which stage larval progeny derived from controlled crosses of Pacific oysters can be mixed in equal proportions and not have those proportions drastically skewed at the field plant-out stage.

Sub-objective 2.B. Compare the results and costs of mixed family selection protocols to current procedures in which families are reared separately from spawn to harvest.

Objective 3: Identify genetic markers for economically important traits in Pacific oysters to enable marker-assisted selection.

Sub-objective 3.A. Examine the relationship between among-family variance in the expression levels of previously identified candidate genes and family-specific growth and survival in the field.

Sub-objective 3.B. Use standard QTL mapping approaches and quantitative assays of the levels of expression of candidate genes to identify regions of the Pacific oyster genome that control the transcription of the most promising candidate genes from Objective 3.A.


1b.Approach (from AD-416)
Utilize quantitative and molecular genetics techniques to elucidate the genetic architecture of, map quantitative trait loci for, and identify expression QTL for candidate genes that control economically important traits in cultured Pacific oysters. Utilize this new information to integrate rigorously-estimated breeding values and marker-assisted selection into the NIFA-funded Molluscan Broodstock Program, which currently selects only on post-larval yield using among-family selection. Explore the utility of marker-based pedigree reconstruction from mixed-family evaluations to mitigate family-specific environmental effects on families reared separately without replication during the larval and nursery stages and family-specific density effects on growth during field trials caused by differential survival of families. FY02 Program Increase $216,000. Add 1 SY. FY04 Program Increase $120,783. Replacing 5358-31000-001-00D (2/05). Replacing 5358-31000-002-00D (2/10). Program Increase $120,000 (2/10) to identify genetic and non-genetic factors influencing immunity in Atlantic oysters.


3.Progress Report
Project 5358-31000-003-00D, approved through the OSQR process replaced project 5358-31000-002-00D which was terminated 2/28/10 (natural progression).

A new collaboration with the Molluscan Broodstock Program was established to test and evaluate second-generation families of Kumamoto oysters from the Ariake Sea to replace and/or revitalize existing contaminated and inbred Kumamoto germplasm used by industry.

As part of a coordinated effort to address catastrophic mortality in commercial oyster hatcheries, we established collaborations with ecologists and oceanographers to identify the causal factors so that we can re-create them under controlled conditions. Also, a new collaborative research effort was established with the Molluscan Broodstock Program (MBP) to study the genetic basis of larval and post-larval production traits to allow design of a more effective selective breeding strategy incorporating larval survival.

A new collaboration was established with colleagues at the University of Rhode Island to develop molecular tools to identify and characterize genes that impact complex traits of economic importance in Eastern oysters. The project uses deep DNA sequencing to identify a large number of genetic markers for gene discovery and mapping. This research will be used to develop high-throughput genotyping methods in Eastern oysters.

Laboratory stress challenge experiments were completed to enable the genotyping of samples from a large quantitative trait locus (QTL) mapping experiment to identify genes that control the expression levels of genes associated with stress tolerance in Pacific oysters.


4.Accomplishments
1. Development of partnership to improve oyster tolerance to ocean acidification. The ARS Shellfish Genetics Program developed a partnership with NIFA- supported Pacific oyster breeding program to develop genetically rigorous selective breeding protocols that address the emerging challenge of ocean acidification and its impact on oyster production. Scientists from the USDA-ARS Shellfish Genetics Program in Newport, Oregon worked closely with MBP to develop a collaborative plan of work to elucidate and accelerate the potential for genetic improvement for larval survival and trade-offs with other characters. This partnership established a new framework for scientists and industry partners that wish to improve the tolerance of west coast oyster stocks to ocean acidification and facilitated the transition from a single-trait breeding program to a genetically rigorous, multi-trait strategy that can address current problems and opportunities for the cultured oyster industry in the Pacific Northwest.


Last Modified: 12/25/2014
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