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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #244677

Title: Genetic assessment tools for evaluating broodstock population structure and pedigree reconstruction in rainbow trout

item Palti, Yniv
item Vallejo, Roger
item JOHNSON, NATHAN - University Of Florida
item Rexroad, Caird

Submitted to: World Aquaculture Society Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 8/31/2009
Publication Date: 3/1/2010
Citation: Palti, Y., Vallejo, R.L., Johnson, N.A., Rexroad Iii, C.E. 2010. Genetic assessment tools for evaluating broodstock population structure and pedigree reconstruction in rainbow trout. World Aquaculture Society Meeting. San Diego, CA.

Interpretive Summary:

Technical Abstract: DNA markers are very useful for aquaculture and fisheries broodstock management, but the cost of these technologies remains prohibitive for some applications. DNA markers have been used for parentage assignment when families share a common environment, and for evaluating population structure and other genetic parameters in breeding populations. Previously, we developed a single-step assay of 10 co-amplifying microsatellite markers to reduce costs and improve efficiency of parentage assignments and estimation of F-statistics and population sub-structure in rainbow trout. The selective breeding program at the National Center for Cool and Cold Water Aquaculture (NCCCWA) provides a unique resource for assessing the use of genetic markers for accurate estimation of molecular co-ancestry coefficients and population statistics (FIT, FIS and FST) using molecular and pedigree data. The synthetic NCCCWA even- and odd-year broodstock populations were initiated in 2002 and 2003, respectively, from established domesticated strains, and the pedigree information has been recorded and maintained in a computerized pedigree database. In addition, every generation of breeders has been genotyped with the 10-microsatellite multiplex system. We used real and simulated marker genotype data to determine how many markers and what sample size will be needed for kinship prediction that is as accurate as the one calculated from pedigree information. We specifically need this information as kinship among the NCCCWA 2002 and 2003 broodstock founders is unknown, but it is also useful for most commercial aquaculture breeding programs where pedigree information from more than two generations has not been followed up and for evaluating relatedness within hatchery stocks and between hatchery and wild populations. Overall the number of simulated genotypes needed for accurate kinship prediction is still cost prohibitive, but anticipated future developments in DNA markers technology, namely the development of more affordable species-specific single nucleotide polymorphism (SNP) multi-locus assays, will likely make it a feasible option for rainbow trout aquaculture and fisheries broodstock management.