The Seaweed Population Genetics program, led by the Alaska Department of Fish and Game’s (ADFG) Gene Conservation Laboratory, is conducting advanced genetic research on Alaska’s main kelp species to inform sustainable mariculture policies, protect wild kelp populations, and support responsible industry growth. This $2.2 million program is funded through Research & Development grant component of the Alaska Mariculture Cluster (AMC).

As Alaska’s mariculture industry continues to grow, data-driven policy decisions will be essential for balancing economic opportunity with ecological responsibility. The Seaweed Population Genetics program is contributing to the scientific foundation needed to secure Alaska’s leadership in sustainable kelp farming.

Why It Matters:

Kelp farming in Alaska has the potential to catalyze a viable and sustainable mariculture industry in Alaska for the long-term benefit of the state’s economy, environment, and communities. However, genetic interactions between farmed and wild kelp pose potential risks to the genetic diversity, fitness, and resilience of wild kelp populations.

To mitigate these risks while also supporting industry opportunities, the Seaweed Population Genetics program is conducting extensive research on three commercially important kelp species: Sugar (Saccharina latissima), Ribbon (Alaria marginata), and Bull (Nereocystis luetkeana). Research insights and benefits include:

• Policy Improvements: Providing scientific evidence to update Alaska’s 50-km drift zone and 50-broodstock rule on a regional basis for permitting kelp farms.
• Sustainable Industry Growth: Ensuring farmed kelp populations remain genetically diverse, which guards against inbreeding and genetic degradation.
• Economic Opportunities: Supporting responsible expansion of Alaska’s kelp industry, benefiting coastal communities and Indigenous mariculture entrepreneurs.
• Ecosystem Conservation: Protecting wild kelp forests while enabling sustainable commercial cultivation.

The Science Behind the Program:

 ADFG’s Gene Conservation Laboratory is employing state-of-the-art Whole Genome Resequencing (WGR) to:

• Identify genetic markers suitable for detecting population structure and assessing adaptive variation.
• Develop Genotyping-in-Thousands by Sequencing (GTseq) panels for rapid, cost-effective genetic screening of kelp populations.
• Determine how wild populations are connected on broad and fine spatial scales across Alaska’s vast coastal environment.
• Assess changes, if any, in genetic variation from hatchery broodstock to outplanted crops.

Achievements So Far:

DNA Extraction Breakthrough:

Extracting high-quality DNA from kelp has long been a challenge due to polysaccharides and polyphenols interfering with the enzymes necessary to use next-generation sequencing techniques. After rigorous testing, ADFG scientists have successfully co-opted and refined higher-throughput kelp DNA extraction and purification methods, allowing for large-scale genetic analysis.

High-Performance Computing (HPC) Cluster:

Processing massive genomic datasets requires robust computing power. AMC funding helped ADFG procure and install a dedicated HPC system that enables analysis to be performed in-house, which supports Alaska’s nascent mariculture industry as well as the seafood industry. Previously, ADFG had to partner with outside entities, even when projects required only a fraction of the data being processed for the Seaweed Population Genetics program.

Sampling & Industry Collaboration:

Working alongside local kelp farmers and ADFG permit holders, the team has expanded sample collections across Alaska, particularly in areas where kelp farming is more prevalent, such as Kodiak, Prince William Sound, in northern Southeast Alaska near Juneau, and in southern Southeast near Ketchikan. These partnerships ensure that scientific findings directly support industry needs.

Pilot Whole Genome Sequencing Underway:

A test batch of kelp samples has been extracted in preparation for low- to mid-coverage whole genome sequencing. The results, expected in early 2025, will validate genetic screening methods before moving into large-scale analyses, be used toward developing the GTseq panels mentioned above, and will help elucidate broad-scale neutral and adaptive population genetic structure.

What’s Ahead:

• Q1 2025: Receive and analyze pilot whole genome sequencing data.
• Q2-Q3 2025: Begin large-scale DNA extractions and GTseq panel development.
• Q4 2025-Q2 2026: Conduct finer-scale population genetic analyses to directly inform mariculture policy.
• Q3 2026: Publish final reports and recommendations for industry best practices.

Background

Southeast Conference (SEC) is the federally designated Economic Development District (EDD) for Southeast Alaska, as well as the state designated Alaska Regional Development Organization. SEC’s mission is to undertake and support activities that promote strong economies, sustainable communities, and a healthy environment in Southeast Alaska.

In September 2022, Southeast Conference was awarded a $49 million U.S. Economic Development Administration (EDA) Build Back Better Regional Challenge (BBBRC) grant to catalyze a viable and sustainable mariculture industry in Alaska, supporting the production of shellfish and seaweed, for the long-term benefit of the state’s economy, environment, and communities.

SEC leads the Alaska Mariculture Cluster (AMC) grant coalition, which includes members of Alaska’s mariculture industry, tribal organizations, regulatory agencies, university system, regional EDDs, trade organizations, and others. A Governance Body, composed of AMC coalition leaders and Tribal executives from each of the project regions, guides the grant’s work and equity metrics.

The AMC has complementary grant components designed to break down barriers and develop Alaska’s mariculture industry.  The Overarching Narrative explains how the grant components work together to grow the industry in an equitable and responsible manner. The full project period for the AMC BBBRC project is October 1, 2022 to September 30th, 2026.