NECC1901: Integrating Genomics and Breeding for Improved Aquaculture Production of Molluscan Shellfish

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Active

NECC1901: Integrating Genomics and Breeding for Improved Aquaculture Production of Molluscan Shellfish

Duration: 10/01/2019 to 09/30/2024

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Bivalve shellfish are a significant economic and biological resource for our nation’s coastal states. Over the past several decades, commercial landings from wild fisheries have declined while the proportion of seafood landings associated with shellfish culture, particularly in the northeastern U.S., has grown steadily. Nationwide, landings of oysters, mussels and scallops were valued at nearly $700 million in 2015 (GMRI 2016). In New England alone, over 1500 leases, permits and licenses have been issued for place-based shellfish culture (Lapointe 2013). The industry is predominantly comprised of small, often family-owned, businesses growing a variety of shellfish, including oysters, hard clams, bay scallops, and mussels. The annual gate value for cultured shellfish in New England is currently estimated to be between $45 and $50 million (Scuderi & Chen 2018) with the bulk of the production centered on culture of eastern oysters, Crassostrea virginica. Shellfish culture is sustainable and environmentally responsible; shellfish remove excess plankton from the water column, play a key role in nutrient reduction in coastal waters, and provide habitat for other species, including fish.

Selective breeding programs throughout the Northeast region have supported production increases in the shellfish culture industry. Genetic improvement through selective breeding is the foundation on which increases in agricultural production and the efficiency of production are based (Hedgecock 2011). Over centuries the purposeful selection of individuals with unique or high quality traits by terrestrial agronomists has led to the development of the myriad of crops and animals found in the market today. Shellfish, such as oysters, have been cultivated since at least Roman times (Castell 2000), typically through the capture of wild spat or “seed” that are subsequently held in productive waters until they reach harvest size. Artificial selection for improved traits in shellfish is still in its infancy relative to selection on terrestrial crops and animals, and several authors have argued that bivalve shellfish have not yet been truly domesticated (Clutton-Brock 1981, Hedgecock 2011). Nonetheless, relatively few generations of breeding have often generated substantial improvements of traits with commercial value and the potential is there to do much more. The development of hatchery technologies, starting with the pioneering work of Loosanoff over 80 years ago (e.g., Loosanoff 1954) paved the way for not only the reliable production of bivalve seed, alleviating the uncertainty in natural supplies, but has also facilitated the development of genetically improved lines of oysters with characteristics substantially different from their wild ancestors (e.g., Allen et al. 1993, Rawson et al. 2010).

A major focus of the selective breeding efforts for shellfish in the Northeast, as well as along the Atlantic and Gulf Coasts of the U.S., has been the development of disease-resistant stocks. Wild and cultured populations of oysters (C. virginica) and hard clams (Mercenaria mercenaria) have been hard hit by disease outbreaks. In hard clams, the disease QPX (quahog parasite unknown, cause by a protist) has been responsible for significant losses among cultured and wild stocks in several East Coast states (e.g., Kraeuter et al. 2011). At the same time, diseases such as MSX, SSO, and Dermo, caused by the protistan parasites Haplosporidium nelson, H. costale, and Perkinsus marinus, respectively, and Roseovarius Oyster Disease (ROD) caused by the bacterium Aliiroseovarius crassostreae have been associated with large mortality events in oysters. Selection for disease resistance in oysters and clams has typically relied on using the survivors from disease outbreaks as the founders for development of a line resistant to any particular disease. For example, early efforts to develop MSX-resistant eastern oysters capitalized on the survivors of an outbreak of MSX in Delaware Bay in the 1950s (Haskin and Ford 1979). Breeding programs in several states, including those at institutions such as Rutgers University’s Haskin Shellfish Laboratory, the University of Maine’s Darling Marine Center, and the Aquaculture Genetics and Breeding Technology Center at the Virginia Institute of Marine Science, as well as efforts by private industry, have more recently used family-based selective breeding to develop genetic stocks resistant to one or more of these diseases, leading to substantial increases in the production of cultured oysters and hard clams. The development of triploid oysters (Guo et al., 1995), which have gained wide popularity among growers in the Northeast and mid-Atlantic has also contributed to production gains.

For oysters and other shellfish, genetics and breeding programs seek further gains in production through selection on key commercial traits in what are still relatively wild species. A long history of genetic improvement in terrestrial crops suggests that continued gains in productivity for shellfish on the order of 5-10% per generation are achievable. Indeed, numerous examples of successful breeding programs with terrestrial species highlights the steps necessary for creating a comprehensive, stable, and integrative breeding program for the domestication of clams, oysters, and other shellfish. These steps include, surveying germplasm diversity, identifying distinct stocks and choosing the best candidates for further improvement, clearly identifying the traits to be improved and their economic value, determining the nature of genetic variation controlling these traits, and designing a long-term, sustainable breeding plan and sticking to it. Recent advances in genomics have facilitated acceleration in the pace of genetic improvement for terrestrial crops and livestock. Shellfish breeding, too, can already capitalize on the burgeoning availability of genomic resources for oysters and other species.

A diversity of state and federal funding agencies have supported the development of improved stocks of shellfish, particularly oysters and hard clams, that are available to hatcheries and growers on the U.S. Atlantic coast. Agencies such as the USDA Northeast Regional Aquaculture Center, state Sea Grant Programs, NOAA Saltonstall-Kennedy, USDA Northeast Sustainable Agriculture and Research, and USDA NIFA, as well as state agencies like the Maine Technology Institute have provided grant and other types of funding to public and private breeding programs. This diverse funding has been instrumental in building expertise and establishing breeding programs in nearly every state in the region over the past several decades; this selective breeding effort has resulted in improved growth and survival of eastern oysters leading to significant economic gain. However, industry needs and priorities can vary greatly across geographic regions and time, and the extant and relatively fragmented breeding programs have struggled to address the challenges faced by shellfish growers across the species range.

A major goal for the Coordinating Committee on Integrating Genomics and Breeding for Improved Aquaculture Production of Molluscan Shellfish is the development of integrated and coordinated breeding programs that use state of the art approaches to directly serve the needs of the shellfish culture industry. A framework for such coordination is the East Coast Shellfish Breeding Consortium (ECSBC). The ECSBC includes a diverse team of shellfish breeders and geneticists from institutions from Maine to Alabama. Together with the East Coast Shellfish Growers’ Association (ECSGA), the consortium has worked toward the development of tools and research to further improve production traits in bivalve shellfish. The initial vision of the ECSBC was to seek long-term support from the USDA-ARS to involve a core of ARS scientists with expertise in quantitative genetics, genomics, and bioinformatics in regional breeding centers throughout the region. This vision has been partially realized with the establishment of one ARS position, housed at the University of Rhode Island; the scientist in this position works closely with several regionally-based programs engaged in the development of improved genetic lines for the industry.

Shellfish breeding in the Northeast and beyond faces some significant challenges, not the least of which is that numerous estuaries along the mid-Atlantic and New England coasts where shellfish are cultured differ dramatically in habitat quality and disease pressure. Historically, breeding for disease resistance has occurred one disease at a time. Often, the development of resistance to one disease is not correlated with increased resistance to other diseases, although cross-breeding among stocks can bring about multi-resistance. Even so, the expansion of parasite ranges raises concern of disease outbreaks and the availability of disease resistant seed across regions. Similarly, habitat quality can change dramatically from one culture lease site to another. Outside of site selection, shellfish growers exert little to no control over habitat quality, including availability of food sources. Thus, it is not uncommon to observe genotype by environment interactions where lines developed in one area do not perform as well in other locations.

These challenges demand a coordinated, goal-oriented program in shellfish genetics and breeding for the cost-effective development of genetically superior shellfish lines to support the increased production of bivalve shellfish in the region. To address this need, the proposed coordinating committee will facilitate and enhance communication among consortium members and federal scientists, provide an avenue for drawing upon additional expertise, and build and strengthen ties to industry. Membership in the committee will be drawn from institutions associated with State Agricultural Experiment Stations (SAES), as well as expertise from participants from non-SAES institutions, and industry representatives.

The establishment of a coordinating committee comes at a critical juncture in the further development of industry-responsive breeding programs. Recent advances in transcriptomics and the sequencing of the C. virginica genome provides an opportunity to incorporate genomic assisted selection into shellfish breeding to accelerate the pace of improvement. Genomic selection has recently been used with line-breeding to enhance selection for yield in several terrestrial crops (Heffner et al. 2010). At the same time, there is a need for an enhanced capacity for shellfish breeding programs to respond to emerging issues in the shellfish aquaculture industry. For example, recent increased usage of triploid oysters has been accompanied by increased observation of what has been called “triploid mortality”. This phenomenon has been observed from Rhode Island to the Gulf of Mexico and investigations to date have failed to identify a specific pathogen or physiological mechanism that leads to elevated mortalities of triploid oysters in the spring, which is typically considered a favorable time for oyster health. Further, shellfish breeding programs have generally had success at selecting for disease resistance but have paid far less attention to improvement in physiological traits. Rapidly evolving environmental conditions due to ocean acidification, increased run-off during heavy precipitation events leading to changes in salinity, sediment load, water color and productivity, as well as pronounced changes in temperature and phenology (seasonality) can impart physiological stress. Thus, breeding strategies will be sought that deliver high yield while maintaining or bolstering physiological resilience.



  1. Provide a forum for shellfish breeders, geneticists, physiologists, and industry members to discuss ways of capitalizing on state of the art genomic tools in shellfish breeding programs.
  2. Provide a setting where committee participants can identify key targets of selection and assess how to design selection programs to bring about improvement for those traits.
  3. Identify research needs for the sustainable enhancement of shellfish production, particularly with respect to emerging issues such as ocean acidification, climate change, and new pathogens.
  4. Develop strategies for meaningfully involving industry partners in genetic research.
  5. Coordinate research efforts among researchers along the East Coast and with colleagues on the Gulf and Pacific coasts.
  6. Provide industry with up to date information on the progress of research on shellfish production and the development of shellfish stocks with improved yields.

Procedures and Activities

The Multistate Research Coordinating Committee on Integrating Genomics and Breeding for Improved Aquaculture Production of Molluscan Shellfish will meet annually, in person. These annual meetings will consist of research updates from committee participants and roundtable discussions of progress in integrating genomic techniques into shellfish breeding programs, industry needs, and emerging issues. Meetings, lasting one business day, will be scheduled in conjunction with  a major conference that brings research and industry participants together in order to maximize attendance and minimize costs.

For issues that arise in-between annual meetings and need rapid attention, the Chair of the committee will be responsible for organizing additional electronic meetings via platforms such as Skype, Zoom, or BlueJeans.


Expected Outcomes and Impacts

  • The coordinating committee will be a critical resource for clear and effective communication among molecular geneticists, bioinformaticists, breeders and industry to effectively incorporate genomic tools into breeding programs thereby accelerating the pace of genetic improvement in oysters and other shellfish species.
  • The committee’s efforts will bring increased attention on physiological traits to bring about sustainable gains in growth, survival and yield and lead to the development of well-coordinated multi-state projects that quickly and efficiently address emerging issues.
  • The committee’s efforts will expand and enhance the multi-disciplinary exchange of ideas and research opportunities leading to new directions of scientific inquiry while reducing duplication of effort.
  • Incorporating research on emerging issues into shellfish breeding programs will provide for increased resilience, growth and expansion in what is already a multi-million dollar, environmentally-responsible industry.
  • The committee will provide a conduit for clear two-way communication with industry so that breeding programs are efficient, cost-effective and best serve the needs of the shellfish culture industry.

Projected Participation

View Appendix E: Participation

Educational Plan

Shellfish Culture industry members will be encouraged to participate in this coordinating committee. A major goal of the committee is to establish strong collaborative research opportunities involving researchers in multiple states and industry partners. These collaborations will be critical for the design of efficient and appropriate breeding programs, the timely dissemination of research results, and for the broadest commercial use of any resulting selected broodstocks of shellfish.

In addition, graduate students will be encourage to participate in the committee meetings to discuss their research interests and help them network with established researchers and industry partners.


The governance structure for this Coordinating Committee will include a Chair, a Chair-elect, and a Secretary.

The Chair will initially be elected from among the committee membership and serve a one year term. Duties of the Chair include organizing the annual meeting of the committee, chairing the meeting, extending invitations to outside participants and developing special presentations and initiatives.

To provide continuity, each year a Chair-elect will elected from among the committee membership. When the committee Chair has completed their one-year term, the Chair-Elect will succeed them. If the committee Chair be unable to complete a one-year term for any reason, the Chair-Elect will assume the duties of the Chair. After completing the term of a vacated Chair, the Chair-Elect will serve a full term as Chair.

The Secretary of the Coordinating Committee will be elected from among the committee membership for a one-year term. Duties of the Secretary including recording the minutes of the annual meeting and disseminating them by electronic means to the committee membership and annual meeting external participants. The Secretary will also be responsible for collecting any donations necessary to cover the costs of meetings and maintaining the committee email contact list.

Literature Cited

Allen, S.K., Gaffney, P.M., Ewart, J.W., 1993. Genetic improvement of the eastern oyster for growth and disease resistance in the Northeast. Northeast Regional Aquaculture Center Fact Sheet #210,

Castell, J. 2000. Farming the waters: bringing aquatic plant and animal species to agriculture. Can J Animal Sci 80:235-242.

Clutton-Brock, J. 1981. Domesticated Animals from Early Times. University of Texas Press, Austin, TX.

Gulf of Maine Research Institute (GMRI) 2016. Maine Farmed Shellfish Market Analysis. Retrieved from cover_10.13.16.pdf

Guo, X., G. DeBrosse and S.K. Allen, Jr. 1996. All-triploid Pacific oysters (Crassostrea gigas Thunberg) produced by mating tetraploids and diploids. Aquaculture, 142:149-161.

Haskin, H. H. and S. E. Ford. 1979. Development of resistance to Minchinia nelsoni (MSX) mortality in laboratory reared and native oyster stocks in Delaware Bay. Mar Fish Rev 41:54-63.

Hedgecock, D. 2011. Genetics of shellfish on a human-dominated planet. Pp. 339-357 In: Shumway, S. (ed). Shellfish Aquaculture and the Environment. Wiley-Blackwell, Oxford, UK.

Heffner, E. L., A. J. Lorenz, J-L. Jannink and M. E. Sorrells. 2010. Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50:1681-1690.

Kraeuter, J. N., S. Ford, D. Bushek, E. Scarpa, W. C. Walton, D. C. Murphy, G. Flimlin, and G. Mathis. 2011. Evaluation of three northern quahog (hard clam) Mercenaria mercenaria (Linnaeus) strains grown in Massachusetts and New Jersey for QPX-resistance. J Shellfish Res 30:805-812.

Lapointe, G. 2013. Northeast Region Ocean Council White Paper: Overview of the Aquaculture Sector in New England. Retrieved from

Loosanoff, V. L. 1954. New advances in the study of bivalve larvae. American Scientist 42:607-624.

Rawson, P. D., S. Lindell, X. Guo, and I. Sunila. 2011. Cross-Breeding for Improved Growth and Disease-Resistance in the Eastern Oyster. NRAC Publication No. 206-2010,

Scuderi, B. and X. Chen. 2018. Production efficiency in New England’s oyster aquaculture industry. Aquaculture Economics and Management. DOI:10.1080/13657305.2018.1449272.


Land Grant Participating States/Institutions


Non Land Grant Participating States/Institutions

other, USDA, ARS
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