title: Fifteen years of quantitative trait loci studies in fish: challenges and future directions.
abstract: Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine-mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage-based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype-phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future.
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited, 291 Akersten St, Port Nelson, Nelson, 7010, New Zealand.
authors.forename: David T
authors.identifier: http://orcid.org/0000-0002-0996-6368
authors.initials: DT
authors.lastname: Ashton
authors.affiliation: School of Biological Sciences, Victoria University of Wellington, Kelburn, Wellington, 6012, New Zealand.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Ritchie
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited, 291 Akersten St, Port Nelson, Nelson, 7010, New Zealand.|Molecular Ecology and Evolution Group, Department of Biology, Lund University, 223 62, Lund, Sweden.
authors.forename: Maren
authors.identifier: http://orcid.org/0000-0002-2764-8291
authors.initials: M
authors.lastname: Wellenreuther
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005399:Fishes / Q000235:genetics*; D008040:Genetic Linkage; D023281:Genomics / Q000639:trends*; D010641:Phenotype; D040641:Quantitative Trait Loci
keywords: association; fish; linkage mapping; phenomics; quantitative trait loci mapping; teleost