A Comparison of Categorical vs. Fractional Parental Allocation Based on Microsatellite Markers to Estimate Reproductive Success and Inbreeding Levels Over Three Generations of Selective Breeding in a Closed Population of Rainbow Trout (Oncorhynchus mykiss)

Abstract

The aim of this project was to assess three DNA-marker based pedigree reconstruction approaches and their associated challenges, strengths and weaknesses by conducting a retrospective analysis of a real, three generation rainbow trout (Oncorhynchus mykiss) pedigree from the SPA hatchery. Molecular genetic data at as few as three or four loci was used to infer relatedness among individuals and between generations in the reconstruction of the three full pedigrees. Parentage and pedigree reconstruction was estimated, for the quasi-categorical (exclusion-based and LOD-based) approaches via the program CERVUS 3.0 and for the fractional approach via a software (PIPEDIGREE), developed for this project. The fractional pedigree method appeared superior, particularly for the estimation of inbreeding levels. This retrospective analysis was able to demonstrate, under different pedigree reconstruction approaches, that the semi-selective, on-farm breeding scheme implemented at the time was successful in limiting the level of inbreeding increase and identifying possibly superior broodstock.