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Fifteen years of quantitative trait loci studies in fish: challenges and future directions

Ashton, David T.; Ritchie, Peter A. and Wellenreuther, Maren LU (2017) In Molecular Ecology
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... (More)
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. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
in
Molecular Ecology
publisher
Wiley-Blackwell
external identifiers
  • scopus:85011650433
  • wos:000397494300003
ISSN
1365-294X
DOI
10.1111/mec.13965
language
English
LU publication?
yes
id
338ee184-0ea2-4654-9951-af989a6d07d9
date added to LUP
2017-02-16 13:39:58
date last changed
2018-03-25 04:34:16
@article{338ee184-0ea2-4654-9951-af989a6d07d9,
  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.},
  author       = {Ashton, David T. and Ritchie, Peter A.  and Wellenreuther, Maren},
  issn         = {1365-294X},
  language     = {eng},
  month        = {02},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology},
  title        = {Fifteen years of quantitative trait loci studies in fish: challenges and future directions},
  url          = {http://dx.doi.org/10.1111/mec.13965},
  year         = {2017},
}