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Study Explores Ways To Minimize Genetic Change In Chinook Salmon Caused By Hatchery Rearing
Posted on Friday, February 16, 2018 (PST)

Genetic testing is suggesting that hatchery-reared spring chinook salmon at segregated hatcheries may differ in traits with fish from integrated hatcheries in return and spawn timing, according to a recent study.


The study looked at six traits in adult chinook salmon from the same stream, but from captive brood programs that used two alternative management approaches, and evaluated how the two types of hatcheries affected variations in those traits – return timing, length and weight at return, age at maturity, spawn timing and a daily growth coefficient.


The two lines of fish had the same wild origin from the same era, but one line was from an integrated hatchery line and the other from a segregated hatchery line, both at the Cle Elum Supplementation and Research Facility in Cle Elum, Washington.


The integrated line uses only wild-born broodstock, and all hatchery-born fish from this line are allowed to spawn in the wild. In contrast, the segregated line uses only hatchery-born broodstock, and all hatchery-born fish from this line are removed from the river before reproduction.


By comparing these lines, the study is one of the first to utilize genomic approaches to determine the effectiveness of a conservation strategy -- managed gene flow – on trait-associated – and potentially adaptive – loci (chromosomal position of a gene), said Charles D. Waters, a PhD candidate in the School of Aquatic and Fishery Sciences at the University of Washington.


“These results suggest that some traits, particularly return and spawn timing, may be affected by hatchery rearing,” Waters said. “However, the results also suggest that integrated management reduces these effects. The ultimate, long-term goal of this and future research would be to inform management practices that minimize genetic change caused by hatchery rearing and, in turn, maximize the success of hatcheries to supplement wild populations.”


Previous studies have found that hatchery-reared salmon differ from their wild counterparts, including reduced reproductive success, differences in growth rate and morphology, and increased vulnerability to predation, the study says. Integrating wild or natural-origin fish into hatchery broodstock can counter those differences.


The study, “Genome-wide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies,” was published online Jan. 21, 2018, in the journal Evolutionary Applications (


Waters co-authors are Jeffrey D. Hard, supervisory research fishery biologist, Conservation Biology Division, Genetics & Evolution Program, NOAA Fisheries - Northwest Fisheries Science Center; Marine S.O. Brieuc, postdoctoral fellow, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway; David E. Fast, senior research scientist, Yakama Nation Fisheries; Kenneth I. Warheit, supervisor, Molecular Genetics and Fish Health Laboratories, Washington Department of Fish and Wildlife; Curtis M. Knudsen, research scientist, Oncorh Consulting; William J. Bosch, data manager, Yakama Nation Fisheries; Kerry A. Naish, professor, School of Aquatic and Fishery Sciences, University of Washington.


Waters said that the first goal of the study was to identify genetic markers that are associated with key traits in chinook salmon, such as return and spawn timing.


“Identifying these genetic markers is important because it would improve our understanding of how key traits in salmon are affected by genetic variation as opposed to environmental factors,” he said. “This information is also important because these markers would improve our ability to monitor hatchery and wild salmon populations to determine if genetic variation is changing over time and in response to management actions.”


Continuing, he said that there has been a lot of research that indicate that hatchery-origin fish from some systems are less fit after release into the wild compared to wild salmon, but what’s not known is if this fitness decline is pervasive or limited geographically by species.


“Furthermore, if fitness declines do occur, we do not know the exact mechanisms, and if certain management actions may mitigate potential negative effects of hatchery-rearing,” he said. Integrated hatcheries appear to be able to mitigate this risk.


In another recent study, collaborating with the Yakama Nation, WDFW, and NOAA Fisheries, Waters and his co-authors provided the first empirical evidence that integrated salmon hatchery management, when compared to segregated management, successfully reduces genetic divergence of hatchery from wild fish “This, in turn, is likely to reduce the genetic risks of hatchery production to the wild population,” Waters said.


In this study, as a second goal, they aimed to extend their previous work and “determine if integrated management, again relative to segregated management, successfully limited genetic change at markers associated with key fitness traits.”


“The ultimate, long-term goal of this and future research would be to inform management practices that minimize genetic change caused by hatchery rearing and, in turn, maximize the success of hatcheries to supplement wild populations,” Waters said.


He warned that there are caveats that could limit the applicability of the study’s findings:


--these are short-term findings (four generations in the case of this study), but the long-term is unknown.

--the Cle Elum integrated hatchery uses 100 percent wild-born salmon as broodstock. Other hatcheries may include both wild and hatchery broodstock.

--the study doesn’t investigate fitness directly, meaning the contribution that a wild-born or hatchery-born fish makes to the next generation.

--the study focused on chinook salmon and the results may not be applicable to other species of salmonids.

--hatchery objectives vary and what’s good management at one hatchery may not be so at another.


However, the results lay the foundation for the development of tools to better monitor hatchery and wild populations over time, he said.


“Furthermore, the genetic markers that we identified are starting points for more in-depth investigations that aim to identify both the specific traits and specific genes that are affected by hatchery rearing,” Waters said. “If we understand how the hatchery environment affects the fitness of salmon, then we can potentially adjust management practices to minimize these effects and improve supplementation efforts. The field is in its infancy, and geneticists are currently researching ways in which trait-linked markers might contribute to conservation efforts.”


The Yakama Nation, WDFW, NOAA Fisheries, Washington Sea Grant and U of W’s Hall Conservation Genetics Research Award, all contributed to this study, Waters said.


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