2013 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.
Continued progress on Objective 1 was made through collaboration with University of Washington researchers. A large mixed-family breeding experiment was initiated with the assistance of Taylor Shellfish. The animals produced by this experiment will enable the estimation of covariance matrices for larval and field performance in response to exposure to acidified ocean water which is currently one of the most significant threats of global climate change to Pacific oyster production on the US West Coast. Adult oysters from nine separate families were conditioned and held in a hatchery and half were exposed to elevated carbon dioxide. They were then crossed and spawned with half of the resulting larvae also exposed to elevated carbon dioxide. Larval performance and survival to juvenile seed was assessed and conditions experienced in the both parental and larval phase appeared to carry over to the juvenile seed stage. Representative sub-samples of oysters are currently being genotyped at several time points over the course of the experiment to determine parentage, and assess potential differences in survival due to family, treatment, and life-history stages. To address objective three we conducted gene mapping experiments to identify genes that control the expression of previously identified traits related to reproductive effortin Pacific oysters. This research has been submitted for publication and is designed to enable marker-assisted selection to reduce reproductive effort and the associated metabolic disturbances that contribute to summer mortality in cultured Pacific oysters. We collaborated with University of Texas, Austin, researchers to analyze several individuals from a mapping family using next generation sequencing to identify gene expression differences between high-reproductive effort individuals and low-reproductive effort individuals. Preliminary results suggested that a different platform should be used, but genes identified by this work will provide candidate genes for subsequent qPCR analysis and QTL mapping, and will be informative for marker-assisted selection. In addition, several pools of larvae, challenged with Vibrio tubiashii, were re-analyzed using a second next-generation sequencing platform to identify differential gene expression between treatments as well as potential allele frequency changes before and after treatment.