Use of molecular markers to maximise diversity of founder populations for aquaculture breeding programs

Summary

When designing base populations for aquaculture-breeding programs, securing genetic variability for long-term genetic response is necessary. In this paper, we investigated three different strategies using molecular marker information with the aim of maximizing genetic diversity in a hypothetical base population for an aquaculture-breeding program. The strategies were evaluated by assessing the amount of genetic variance for three quantitative traits they captured. Eighty-two broodstocks from a commercial Atlantic salmon (Salmo salar) breeding population were genotyped for 237 AFLP markers. Disease challenge tests with furunculosis and infectious salmon anemia (ISA) were performed on 4061 progeny and growth was measured on the broodstock themselves. In strategy RAND, 10 sires and 10 dams were randomly selected from the 82 parents to form the base population. There were 100 replicates for this strategy. In strategy HET, we chose the 10 sires and 10 dams with the highest average heterozygosity across all markers. For strategy KIN, 10 sires and 10 dams with the highest contributions to total genetic diversity were selected to form the base population. We found that HET and KIN strategies resulted in significantly higher genetic variances of breeding values for challenges with furunculosis and ISA than RAND, although there were no differences between the strategies in genetic variance for growth. Our results suggest genetic variation for some traits in base populations can be maximized by using molecular marker information and strategy KIN. (c) 2005 Elsevier B.V. All rights reserved.