Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice

Abstract

Understanding the genetic basis of complex traits in aquaculture species is a major research goal. Quantitative trait loci (QTL) mapping is a first step toward identification of the genes and the causal variants underlying these traits. Genetic markers linked to QTL can also be applied in selective breeding schemes to improve the accuracy of selection for economically important traits via marker-assisted selection (MAS) or genomic selection. This has been achieved for a limited number of species, using microsatellite and, latterly, single-nucleotide polymorphism (SNP) markers. In the era of high-throughput sequencing, the genomic resources available for most aquaculture species are rapidly expanding, and now include reference genome assemblies, high-density linkage maps, and SNP arrays for several farmed species. Further, features of the reproductive biology of many aquatic species are amenable to well-powered genetic mapping studies, such as large full-sibling family sizes and flexible mating structures. These tools and features can expedite the discovery and application of QTL, and progress toward the underlying causative mechanisms. In this chapter, the methods and software typically used for QTL mapping using linkage analysis are reviewed, and examples given. The influence of developments in genomic technology and the opportunities it offers to the field are highlighted. Finally, successful examples of QTL mapping and application to improve economically important traits are given, and future directions for QTL research are discussed.