Sea Grant Hard Clam Selective Breeding Collaborative

The National Sea Grant Hard Clam Selective Breeding Collaborative is a three-year project funded under 2019's National Sea Grant Advanced Aquaculture Collaborative Programs. This project is the first step to establishing a regional aquaculture hub using advanced genomic technology to conduct selective breeding for hard clam (Mercenaria mercenaria) to benefit the aquaculture industry throughout the Atlantic Coast.

In order to achieve this ambitious plan, Sea Grant has coordinated a team with complementary research expertise to identify broodstock lineage to use in planned technology transfer education programming.

This collaborative effort will also benefit from input via an advisory panel to bridge the gap between research, Sea Grant administration and the aquaculture industry. This organizational framework guarantees this technology will be efficiently integrated in hard clam hatchery operations to support the growth of hard clam production.

There are several interim steps necessary to establish this selective breeding program. Researchers will complete the sequencing of the hard clam genome and characterize the genetic diversity of the species throughout its natural range. This information will be used to create low cost genotyping tools to identify and selectively breed clams that are resistant to QPX disease and heat stress. 

Even though the focus of this project is on QPX resistance and heat tolerance, the developed technologies are adaptable to various traits, allowing future development of breeding programs that fit different regions. Selected stocks will be distributed through the Broodstock Hub Network.

The Brookstock Hub (Hub) is supported by a network of research hatcheries (nodes) strategically situated along the Atlantic Coast. These nodes are located in New York (Stony Brook University Experimental Hatchery located at Flax Pond and Cornell Cooperative Extension of Suffolk County Shellfish Hatchery), New Jersey (Rutgers University Haskin Shellfish Research Laboratory), and Florida (University of Florida Molluscan Shellfish Aquaculture Restoration Laboratory) — click the "Members" section in navigation above for more details.

Each node is responsible for maintaining a superior broodstock bred line for their specific region. Broodstocks are available from each node, upon request. Each node has trained staff who will work with Sea Grant and Cooperative Extension professionals to transfer this technology to the industry.

The Sea Grant Hard Clam Selective Breeding Collaborative mission is to use research to establish an accelerated selective breeding program for the hard clam (M. mercenaria), in order to increase resiliency throughout the growing range along the Atlantic seaboard.

This overarching goal will be achieved through the following specific objectives:

1. Complete the hard clam genome to develop an efficient and cost-effective genotyping platform to be used as a diagnostic tool.
2. Apply this tool to identify QPX-resistant and heat-tolerant clams, so that these animals can be selectively bred to produce resistant seed (validated during field trials).
3. Use the research accomplishments to build the National Sea Grant Hard Clam Hub network, linking scientists, Sea Grant and Cooperative Extension, and the hard clam aquaculture industry.

By using resilient seed produced by the Sea Grant Hard Clam Breeding Hub, the industry will actively mitigate at least two barriers that contribute to production loss.

Genomic technologies that are applied under this Collaborative to produce the superior broodstock strains do not involve genetic engineering, and these seeds must not be confused with genetically modified organisms (GMO).

Readers who wish to learn about GMO and other genetic terminologies can use the list of educational resources that is provided at the end of the "Selective Breeding vs. GMO" subheading, or contact your local Sea Grant or Cooperative Extension professional for additional information — click the "Members" section in navigation above for more details.

Selective Breeding vs. GMO: What’s the Difference?

Use of the terms, “selective breeding” and “GMO” are becoming common in food sciences, especially agriculture, however, they are different processes and it is important to make this distinction.

Selective breeding allows a brood stock comprised of organisms possessing genes that control specific desired traits to pass these genes to the next generation (or progeny). Selectively bred organisms are natural and while breeders may use genetic technology as a diagnostic tool, there is no enhancement of the organism.

A genetically modified organism (GMO) is created when technology is used to change the genetic material (usually the DNA). Different methods are used to conduct gene modification and scientists collectively refer to them as “genetic engineering”. More recently, “bioengineered” is used to label these food products to inform the consumer.

Scientists never use “genetic engineering” or “bioengineered” with organisms that are produced by selective breeding, such as the hard clams (M. mercenaria) being produced under the National Sea Grant Hard Clam Selective Breeding Collaborative — click the "Acknowledgments" section in navigation above for more details about our collaborators and partners.

This website contains a list of educational resources about GMO if you wish to learn about this practice, and it will be updated during the project implementation.

GMO Educational Resources List

 Clemson University: A Quick Look at Genetically Modified Organisms 

 Clemson University: Genetically Modified Organisms 

 U.S. Food & Drug: Agriculture Biotechnology 

 U.S. Department of Agriculture: Agricultural Biotechnology Glossary 

The hard clam, M. mercenaria, (also known locally as quahog), is one of the most economically valuable species in the United States, especially on the eastern seaboard where it’s valued at $136 million annually.

This shellfish is cultivated from Florida to Massachusetts, with potential expansion for expansion into Maine, and hatcheries produce billions of seed to supply private growers and managers involved with restoration efforts in this region. Seeds are an expensive investment and growers must wait for a minimum of 18 months (often much longer) before they can harvest clams to sell to consumers at retail. Seeds must be able to tolerate harsh conditions (such as excessive heat, changes in salinity, and diseases) during growout to sustain economic viability in the aquaculture community. This goal can be achieved by providing seed distributors with access to brood stocks that are resistant to biological and environmental conditions known to exist in this geographical range.

Selective breeding is a common practice being applied for different purposes, including to produce: better yielding agricultural crops; flowering plants with a particular color, shape, or scent; better meat quality in livestock, etc.

This method of breeding allows organisms to pass on specific characteristics (or traits) to their offsprings. For example, a farmer operating in an area that is prone to severe drought may decide to keep seeds from crops that survive to plant the next season. Continuing this practice over several generations ultimately leads to drought tolerant plants that reduces crop loss and ultimately increases the profitability in the business venture. Unfortunately, using this approach to produce the desired brood stocks requires consistent drought conditions and patience to be successful – this method is extremely slow. While this was the approach used for centuries, technological advancement makes it possible to accomplish this goal using more efficient and reliable tools.  

So you might be asking what does growing agricultural crops have to do with clams? While hard clam is a relatively “hardy” species compared to other shellfish (e.g., eastern oyster), clams can still succumb to biological and environmental conditions that significantly impact production and economic profits in the aquaculture industry. Substantial losses in hard clam production have been reported since the 1990s after a lethal pathogen known as quahog parasite unknown (QPX) wreaked havoc in the aquaculture industry from Massachusetts to Virginia, with stock mortality reaching epic proportion (90-95%), and aquaculture extension professionals provide assistance to producers who experience this substantial loss that can lead to job and revenue loss, and bankruptcy in extreme cases. 

Evidence suggests this susceptibility to QPX is hereditary (Figure 2, below), which makes selective breeding a feasible strategy to solving this problem.

Unfortunately, disease isn’t the only impediment to hard clam aquaculture. Harsh environmental conditions e.g. temperature and salinity extremes, have been attributed to mortality in this industry. In southern regions, extreme and persistent summer heat elevates water temperature in growout sites can exceed 35°C (95°F), especially during low tide. This condition creates high mortality in clams that are just about ready for the retail market size, and results in heavy financial loss to growers. This problem is particularly relevant in Florida, where the industry has access to heat-tolerant strains such as triploid strain with faster growth rates, and cross bred northern-southern strain. Unfortunately, these management strategies achieve limited success and it is unfeasible to scale-up these technologies to supply the demands in the Southeast region. Evidence suggests that intolerance to extreme heat is hereditary, and this also makes selective breeding a feasible solution to alleviate this bottleneck.

Advances in genetic technology over the years have enabled more sophisticated and affordable diagnostic tools to use in selective breeding programs, and technology that was once reserved for prime livestock and agricultural crops are accessible to other sectors. Farmers seeking drought tolerant seeds are benefiting from this genetic technology to achieve the same results (or better) in less time, and reduce the risk of financial loss for the business. The Sea Grant Hard Clam Selective Breeding Collaborative enables researchers to use genomics to revolutionize hard clam aquaculture production, and leverages the resources and expertise at research hatcheries across the region.

Outcomes

Research conducted under this collaborative will ultimately help to build and expand capacity in the East Coast hard clam industry.

The technologies to conduct genomic selection have been successfully applied to improve production and yield across multiple agricultural crops, and similar results will be achieved for hard clams. Outcomes of this project, including the sequenced M. mercenaria genome, and the tools developed, including the genetic markers associated with clam resistance to biological (QPX) and environmental (heat) stressors, will be used collectively, to transform the aquaculture industry to produce superior heat and parasite resistant clams. 

Furthermore, this capability will create the basis for additional research to identify other traits that restrict clam production in the Atlantic region, with future funding.

Eventually, private farmers who purchase seeds from hatcheries that distribute these resistant strains will benefit from this collaborative effort. This distribution chain will include shellfish farmers and restoration managers up and down the East Coast, from Massachusetts to Florida, who will be able to purchase clams that are genetically resistant to QPX and heat stress, to better achieve their business and conservation goals. This technology and information transfer will lead to a robust and resilient hard clam aquaculture industry.

Implementation

2020 Project Inauguration Meeting (Stony Brook University)

Coming soon - Powerpoint Materials, notes, etc.

2021 Project Mid-Term Meeting (Virtual)

This collaborative functions as a partnership involving Sea Grant College Programs: New York Sea Grant, New Jersey Sea Grant, Woods Hole Sea Grant, Virginia Sea Grant, and Florida Sea Grant), Stony Brook University’s Marine Animal Disease Laboratory and other research institutions, Cooperative Extension, not-for-profits, an advisory panel, and private sector. 

The collaborative involves scientists, Sea Grant Extension professionals from Massachusetts, New York, New Jersey, Virginia, and Florida, Cooperative Extension, public, and the private sector.

Sea Grant Extension professionals assist with the field experiments to provide broodstock for researchers to conduct genetic studies, and validate the strains that are produced. 

Sea Grant Extension also leads other efforts to engage aquaculture industry representatives who will use these seeds.

Click through the map provided for locations of research and extension members (as well as local industry partners) and their contact information You can also view the full contact list via  PDF . Advisory panel members are listed below the map.

Advisory Members

An advisory panel was appointed to assist this Collaborative, to provide input and perspective on the research, and identify strategies for technology transfer to the aquaculture industry.

The panelists possess a wide range of expertise including shellfish genetics, Sea Grant administration and extension, resource management, shellfish hatchery, and private growers.

•  Peter Rowe , Ph.D. (Chair) - Acting Director & Associate Director, New Jersey Sea Grant Consortium
•  Rebecca Shuford , Ph.D. - Director, New York Sea Grant 
• Wade Carden - Biologist, NYS DEC Bureau of Shellfisheries, Division of Marine Resources
•  Dina Proestou , Ph.D. - Animal Geneticist, USDA Agricultural Research Service 
•  Brent Vadopalas , Ph.D. - Aquaculture Specialist, Washington Sea Grant
• Joseph Vinarski - Manager, Frank M. Flowers & Sons Inc.
• Karen Rivara - President, East Coast Shellfish Association/Manager, Aeros Cultured Oyster Company 
• Craig Strong, Hatchery Manager, Town of Brookhaven
• Martin Byrnes, Hatchery Manager, Town of Islip

Resources for Members

For our members, below are several versions of the Hard Clam Selective Breeding Collaborative logo that you can include to the left of your institutional or program logo for presentations or any other ways in which you might help promote this project and its findings:

Logo: Transparent background —  TIF  |  PNG 

Logo: White background —  TIF  |  PNG 

Brochure: Sea Grant Hard Clam Selective Breeding Collaborative (2022) ( pdf )

Journal Articles

Allam B, Pales Espinosa E, Farhat S, Tanguy A, Reece K, Yang H, Rivara G, Reitsma J, Clemetson A, Guo X. (2020). East Coast clam selective breeding collaborative. National Shellfisheries Association 113th annual meeting. Virtual.

Allam B, Pales Espinosa E, Farhat S, Tanguy A, Reece K, Yang H, Rivara G, Reitsma J, Clemetson A, Guo X. (2020). East Coast clam selective breeding collaborative. Milford Aquaculture Seminar, CT, January

Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot J-F, Allam B. (2022). Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 23:192.  doi: 10.1186/s12864-021-08262-1 

Farhat S, Tanguy A, Pales Espinosa E, Guo X, Boutet I, Smolowitz R, Murphy D, Rivara G, Allam B. (2020). Identification of variants associated with hard clam, Mercenaria mercenaria, resistance to Quahog Parasite Unknown disease. Genomics 112(6): 4887-4896.

Media Articles

 Virginia’s Historic Clam Industry Gains New Genetic Insights  (May 2021)

 Researchers Closing in on Solution to Clam QPX  (March 2021)

 SBU Researcher Discusses Clam Genome Project  (June 2020)

 Project Seen Transformative for Hard Clam Industry in U.S. East Coast  (March 2020)

 Advancing East Coast Aquaculture: NYSG Contributes to Several Marine Aquaculture Research Projects  (November 2019)

 Funding helps researchers clam up  (November 2019) 

 NY Sea Grant Contributes to Marine Aquaculture Research Projects  (November 2019) 

Stories in  NYSG's "Hard Clam" News Archive  ...

 The Hard Clam Selective Breeding Collaborative Offers Support for Stressed Clams  (May 2022)

 On YouTube: Stopping the Disease that has Wracked the New York Hard Clam Fishery  (December 2018)

 SBU Researchers Receive Funding to Study Effects of Ocean Changes on Marine Life  (September 2016) 

 NOAA and Sea Grant Fund $800K in Ocean Acidification Research  (September 2016)

 Investigating Hard Clam Resistance Against QPX Infection  (April 2014)

Our collaborators are available to provide information and interact with representatives in the hard clam industry, and we encourage questions, comments and suggestions about the work being conducted under the Sea Grant Hard Clam Selective Breeding Collaborative.

Kindly direct all inquiries to  HardClamHub@gmail.com  and we look forward to hearing from you.