Toward detection of quantitative trait loci and marker‐assisted selection in fish

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Abstract
Genes affecting aquaculture performance, or quantitative trait loci (QTLs), can be mapped in relation to naturally occurring genetic markers. Knowledge of linkages between marker and QTL alleles can be used for marker‐assisted selection (MAS), increasing the rate of genetic progress above that for selective breeding alone. Although fish may provide an attractive system for detecting QTLs and executing MAS, QTL detection and MAS have not yet been practiced on an aquaculture species. We review the technical literature on QTL detection and MAS in other species in order to advance critical discussion of how best to pursue QTL detection and MAS in fish. Over 100 highly polymorphic markers would be needed for complete genome coverage, although a subset of QTLs might be detected with fewer markers. The need for cost‐effectively screening markers suggests polymerase chain reaction‐based screening of a collection of microsatellite loci or RAPDs (random amplified polymorphic DNAs). Experimental power calculations suggest that because markers will have to be screened within large progeny groups, selective or sequential genotyping or screening of bulked DNA samples are needed for cost‐effective detection of QTLs. With well‐designed experiments, QTL detection and MAS might prove an effective adjunct to conventional selective breeding in fishes.