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Fifteen years of quantitative trait loci studies in fish: challenges and future directions
Author(s) -
Ashton David T.,
Ritchie Peter A.,
Wellenreuther Maren
Publication year - 2017
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.13965
Subject(s) - quantitative trait locus , biology , family based qtl mapping , phenomics , genomics , genetic architecture , population , population genomics , genetics , trait , evolutionary biology , computational biology , gene mapping , genome , gene , demography , sociology , computer science , chromosome , programming language
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 QTL s. 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 QTL s and variance explained by QTL s 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 QTL s 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.