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

Abstract

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

Rapid Molecular Determination of Sex for Western North American Chub (Gila spp.)

“…Sex-identifying assays will allow for both genetic confirmation of previously sexed fish and rapid sex identification of individuals outside of the breeding season. In the event of successful reintroduction of Bonytail to the wild and subsequent recruitment, these assays would also facilitate the instigation of a parental-based tagging program (Beacham et al 2017;Steele et al 2019;Pepping et al 2020).…”

“…Sex data can also be useful for genetically tagging wild populations, which has proven to be a viable approach to population monitoring for decades (Palsbøll 1999;Schwartz et al 2007). More recently, this technique has gained traction as a cost-effective approach to monitoring the survival and offspring contribution of hatcheryproduced salmonids in the wild (Beacham et al 2017;Steele et al 2019;Pepping et al 2020). Although some informative population genetic parameters such as effective number of breeders (N b ) can be calculated accurately in the absence of candidate parents , including sex data can allow for accurate parentage inference with genetic marker panels that have low statistical power, as it reduces the number of parent-offspring trios to be considered.…”

Largemouth Bass Hatchery Contributions Quantified via Parentage‐Based Tagging

“…This genetic per-tag cost was in line with other tagging types (e.g., $0.20 per tag for coded wire tags; Clark 2004), although the cost of coded wire tags can vary widely as a function of program (Clark 2004). Technological advancements in DNA sequencing technologies have reduced genotyping costs, and recently developed PBT marker panels have been constructed, with per-sample genotyping costs between $3 and $4 (Campbell et al 2015;Pepping et al 2020). In the current study, a state management agency (NCWRC) partnered with an academic institution (University of Florida), which resulted in lower costs, as the university already had existing infrastructure.…”

“…2015; Pepping et al. 2020). In the current study, a state management agency (NCWRC) partnered with an academic institution (University of Florida), which resulted in lower costs, as the university already had existing infrastructure.…”

Parentage‐based tagging using mothers balances accuracy and cost for discriminating between natural and stocked recruitment for inland fisheries

“…Outside of the North American Pacific Coast, parentage‐based tagging has so far primarily been applied to populations that are dominated by wild fish with relatively small stocking programmes (<150 broodmothers; Ashton et al, 2016; Denson et al, 2012; Evans et al, 2018). While parentage‐based tagging would still be useful in such applications, the approach may be most advantageous as a marking technique for larger hatchery programmes for which conventional marking programmes are too costly to implement on an annual basis or monitoring programmes require non‐lethal methods of tag recovery (Meek & Larson, 2019; Pepping et al, 2020). To advance parentage‐based tagging as an effective mass‐marking technique for inland fisheries, it needs to be validated for augmentation programmes with large broodstocks that lack genetic distinctness between hatchery and wild‐origin fish.…”