Quantitative Trait Loci (QTL) Mapping

QTL mapping identifies specific regions of the genome statistically associated with variation in a quantitative trait, one measured on a continuous numeric scale such as growth rate or body weight rather than a simple present-or-absent characteristic, by tracking how a trait's measured value co-varies with inherited genetic marker patterns across a structured family or population, a foundational genetic mapping technique that predates and in many ways set the methodological groundwork later built upon by genome-wide association studies using denser, genome-wide marker coverage. Traditional QTL mapping typically used a smaller number of genetic markers across a specifically designed breeding cross, offering lower genomic resolution, identifying only a broad chromosomal region likely containing the causal gene rather than pinpointing it precisely, than modern dense-marker GWAS approaches can achieve, meaning QTL mapping findings often required substantial additional fine-mapping work to narrow down from a broad identified region to an actual candidate gene or precise causal variant. Despite denser modern genomic tools largely superseding traditional QTL mapping as the primary discovery method for new trait associations in well-resourced breeding programs, the QTL mapping framework and its underlying statistical logic remain conceptually foundational to understanding genetic architecture, how many genomic regions influence a given trait and how large each region's individual effect is, information that directly shapes whether a trait is a good candidate for targeted marker-assisted selection using one or a few large-effect markers versus requiring broader genomic selection approaches better suited to traits influenced by many small-effect genomic regions. Many historically identified QTL regions for important aquaculture traits, disease resistance, growth, have since been refined and validated using modern GWAS and fine-mapping approaches, meaning current breeding program marker panels often incorporate findings that trace their discovery lineage back through decades of accumulated QTL mapping research even where the specific mapping technology itself has since been superseded.