Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Details

• Journal Title:
  Molecular Ecology
• Personal Author:
  Waters, Charles D. ; Hard, Jeffrey J. ; Fast, David E. ; Knudsen, Curtis M. ; Bosch, William J. ; Naish, Kerry A.
• NOAA Program & Office:
  NMFS (National Marine Fisheries Service) ; NWFSC (Northwest Fisheries Science Center)
• Description:
  Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as ?integrated? with the founding wild stock, with ongoing gene flow, and as ?segregated? with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2?F4; inbreeding F2). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.
• Keywords:
  Chinook Salmon Inbreeding Chinook Salmon
• Source:
  Molecular Ecology, 29(4)
• DOI:
  https://doi.org/10.1111/mec.15356
• Document Type:
  Journal Article
• Rights Information:
  Accepted Manuscript
• Rights Statement:
  The NOAA IR provides access to this content under the authority of the government's retained license to distribute publications and data resulting from federal funding. While users may legally access this content, the copyright owners retain rights that govern the reproduction, redistribution, and re-use of this work. The user is solely responsible for complying with applicable copyright law.
• Compliance:
  Submitted
• Main Document Checksum:
  urn:sha-512:1aa811de147fabaec654b437f401ff484f78acf08d92257ec19f91adc81104ec42e42eadef09233b5bd27dc2c65853081a9077175c2c8c18dafef744d5599158
• Download URL:
  https://repository.library.noaa.gov/view/noaa/28505/noaa_28505_DS1.pdf
• File Type:
  [PDF - 298.97 KB ]