At the National Center for Cool and Cold Water Aquaculture (US Department of Agriculture, Ag. Research Service) in Leetown, WV, we have a broodstock development program now entering the second generation of family-based selective breeding using expected breeding values (EBVs). Our major breeding objectives are faster growth and resistance to Flavobacterium psy- chrophilum, the causative agent of bacterial coldwater disease. For these traits we have devel- oped assays to evaluate phenotypic performance. In addition to our breeding program, we are participating in an international collaboration to develop a microsatellite marker linkage map for the rainbow trout with the intent of identifying quantitative trait loci (QTL) and using them in mark- er (MAS) or gene-assisted (GAS) selection. There are several possible approaches with regard to the types and numbers of markers to develop and the strategies and methods for implement- ing the markers in a selective breeding program. This paper describes the choices we made con- cerning QTL identification for traits of high, low, and unknown degrees of heritability. These traits are plasma cortisol response to a crowding stress (h2 = 0.4), feed intake (h2 = 0.1) and resis- tance to F. psychrophilum (0.3<h2<0.4). In order to identify QTL in a relevant commercially important rainbow trout line, we are making crosses from within our resource population. The development of research family crosses, choice of markers for genome scanning, and planned steps to implementation of these results are described
