Use of Molecular Genetic Data to Manage Salmon Conservation Programs: Snake River Sockeye Salmon Captive Broodstock Program

The Snake River Sockeye Salmon Captive Broodstock Program was initiated in 1991 following the listing of the species as endangered under the Endangered Species Act.  The goals of the program are to:  1) Conserve the population in the short-term by reducing demographic, genetic, and environmental risks that could lead to extinction 2) Re-introduce and re-build the wild population.   Since this population is closed, one of the challenges has involved selecting the most representative broodstock and pairing males and females for spawning to ensure that inbreeding is minimized and effective population size is maximized. Pedigree data were tracked through 2004 and used to guide breeding decisions.  After 2004, it became too difficult to track pedigrees and an inbreeding avoidance matrix was generated from a molecular genetic pairwise relatedness estimator each year.   During 2006, we began to genotype all broodstock with microsatellites and in 2010, parentage analyses were used to estimate relatedness and build first-generation pedigrees.  In this study, we discuss the utility of using parentage analyses to estimate relatedness and select broodstock.  Parentage analyses also enabled us to evaluate different release strategies in the wild and reproductive success of hatchery fish in captive and wild environments.