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

• DOI: 10.1371/journal.pone.0239221
• Publication Date: 2020-11-11T18:28:00Z
• Authors: Michelle Y. Pepping; Sean M. O’Rourke; Connie Huang; Jacob V. E. Katz; Carson Jeffres; Michael R. Miller
• Keywords: Chinook wind; Hatchery

Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management migratory salmonid populations, which important health many economies, ecosystems, indigenous cultures, is particularly dependent on data gathered from tagged fish. However, physical tagging currently used have challenges including cost, variable marker retention, information limited individuals. Genetic combat problems associated with tags, but their own high potentially difficult design, incompatibility markers across species. Here we show feasibility a new genotyping method parent-based (PBT), where tracked through inherent genetic relationships parents. We found that Rapture sequencing, combination restriction-site DNA capture provides sufficient parentage assignment. Additionally, same bait set, targets specific loci, can be both Rainbow Trout Oncorhynchus mykiss Chinook Salmon tshawytscha . input 248 single nucleotide polymorphisms 1,121 samples assignment software compared parent-offspring spawning pairs recorded in hatchery. Interestingly, our results suggest sperm contamination during hatchery occurred production 14% offspring, further confirming need accurately PBT successfully assigned progeny parents 98.86% accuracy data. Cost this pilot study was approximately $3 USD per sample. As costs vary based number sequenced, expect when implemented at large-scale, sample could decreased. conclude cost-effective accurate alternative coded wire other genetic-based methods.