QTL mapping designs for aquaculture

Rapid development of genomics technology is providing new opportunities for genetic studies, including QTL mapping, in many aquaculture species. This paper investigates the strengths and limitations of QTL mapping designs for fish and shellfish under three different controlled breeding schemes. For each controlled breeding scheme, the potential and limitations are described for typical species and are illustrated by three different designs using interval mapping. The results show that, regardless of the species, the family structure is extremely important in experimental designs. The heritability of the QTL (controlled by its allele frequency and effect on the trait) also has an important impact on the power to detect QTL, while the overall polygenic heritability of the trait is less important. Marker density does not greatly affect the power when the distance between markers is less than 10 cM; but ideally spacing should not exceed 20 cM. For each of the systems studied, it is possible to design an experiment that would have an 80% power to detect a QTL of moderate effect (explaining between 1.5 and 5% of the trait variation) by genotyping 1000 or fewer individuals.