Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids

Area of Science:

• Fisheries Science
• Genetics
• Aquaculture

Background:

• Accurate individual tracking is vital for fisheries and aquaculture management, especially for migratory salmonids important to economies and ecosystems.
• Current physical tagging methods face challenges like cost, marker loss, and limited data, while existing genetic methods can be expensive and species-specific.

Purpose of the Study:

• To demonstrate the feasibility of a novel genotyping method, Rapture sequencing, for parent-based tagging (PBT) in fisheries management.
• To assess the accuracy and cost-effectiveness of Rapture PBT for tracking Rainbow Trout and Chinook Salmon.

Main Methods:

• Utilized Rapture sequencing, combining restriction-site associated DNA and capture sequencing, to genotype 1,121 samples.
• Applied parentage assignment software with 248 single nucleotide polymorphisms to analyze parent-offspring relationships in a hatchery setting.
• Confirmed marker compatibility across Rainbow Trout (Oncorhynchus mykiss) and Chinook Salmon (Oncorhynchus tshawytscha) using a single capture bait set.

Main Results:

• Rapture PBT achieved 98.86% accuracy in assigning progeny to parents.
• Identified sperm contamination in 14% of hatchery-produced offspring, highlighting the need for precise genetic tracking.
• The pilot study indicated a per-sample cost of approximately $3 USD, with potential for further reduction at scale.

Conclusions:

• Rapture PBT is a feasible, cost-effective, and accurate genetic method for tracking individuals in fisheries and aquaculture.
• This method provides a superior alternative to physical coded wire tags and other genetic approaches for managing migratory fish populations.