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MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses

Ronald M. Nelson, Carl Nettelblad, Mats E. Pettersson, Xia Shen, Lucy Crooks, Francois Besnier, José M. Álvarez-Castro, Lars Rönnegård, Weronica Ek, Zheya Sheng, Marcin Kierczak, Sverker Holmgren and Örjan Carlborg
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2147-2149; https://doi.org/10.1534/g3.113.008623
Ronald M. Nelson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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  • For correspondence: ronnnie.nelson@slu.se
Carl Nettelblad
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
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Mats E. Pettersson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Xia Shen
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, Sweden
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Lucy Crooks
Department of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, SwedenWelcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, United Kingdom
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Francois Besnier
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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José M. Álvarez-Castro
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenDepartment of Genetics, University of Santiago de Compostela, ES-27002 Lugo, Galiza, SpainInstituto Gulbenkian de Ciência, Evolutionary Genetics Group, Oeiras, Portugal
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Lars Rönnegård
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenStatistics Unit, Dalarna University, SE-791 88 Falun, Sweden
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Weronica Ek
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Zheya Sheng
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenState Key Laboratory for Agro-Biotechnology, China Agricultural University,100193, Beijing, People’s Republic of China
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Marcin Kierczak
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Sverker Holmgren
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
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Örjan Carlborg
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Abstract

MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7

  • QTL mapping
  • inbred line cross
  • outbred line cross
  • quantitative genetics
  • Received May 31, 2013.
  • Accepted September 26, 2013.
  • Copyright © 2013 Nelson et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Volume 3 Issue 12, December 2013

G3: Genes|Genomes|Genetics: 3 (12)

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MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses

Ronald M. Nelson, Carl Nettelblad, Mats E. Pettersson, Xia Shen, Lucy Crooks, Francois Besnier, José M. Álvarez-Castro, Lars Rönnegård, Weronica Ek, Zheya Sheng, Marcin Kierczak, Sverker Holmgren and Örjan Carlborg
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2147-2149; https://doi.org/10.1534/g3.113.008623
Ronald M. Nelson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
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  • For correspondence: ronnnie.nelson@slu.se
Carl Nettelblad
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mats E. Pettersson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
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Xia Shen
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, Sweden
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Lucy Crooks
Department of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, SwedenWelcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, United Kingdom
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Francois Besnier
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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  • Search for this author on this site
José M. Álvarez-Castro
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenDepartment of Genetics, University of Santiago de Compostela, ES-27002 Lugo, Galiza, SpainInstituto Gulbenkian de Ciência, Evolutionary Genetics Group, Oeiras, Portugal
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Lars Rönnegård
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenStatistics Unit, Dalarna University, SE-791 88 Falun, Sweden
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Weronica Ek
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
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  • Search for this author on this site
Zheya Sheng
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenState Key Laboratory for Agro-Biotechnology, China Agricultural University,100193, Beijing, People’s Republic of China
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Marcin Kierczak
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Sverker Holmgren
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
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Örjan Carlborg
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Citation

MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses

Ronald M. Nelson, Carl Nettelblad, Mats E. Pettersson, Xia Shen, Lucy Crooks, Francois Besnier, José M. Álvarez-Castro, Lars Rönnegård, Weronica Ek, Zheya Sheng, Marcin Kierczak, Sverker Holmgren and Örjan Carlborg
G3: Genes, Genomes, Genetics December 1, 2013 vol. 3 no. 12 2147-2149; https://doi.org/10.1534/g3.113.008623
Ronald M. Nelson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: ronnnie.nelson@slu.se
Carl Nettelblad
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mats E. Pettersson
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xia Shen
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lucy Crooks
Department of Cell and Molecular Biology, Uppsala University, BMC SE-75124 Uppsala, SwedenWelcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Francois Besnier
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
José M. Álvarez-Castro
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenDepartment of Genetics, University of Santiago de Compostela, ES-27002 Lugo, Galiza, SpainInstituto Gulbenkian de Ciência, Evolutionary Genetics Group, Oeiras, Portugal
  • Find this author on Google Scholar
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  • Search for this author on this site
Lars Rönnegård
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenStatistics Unit, Dalarna University, SE-791 88 Falun, Sweden
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  • Search for this author on this site
Weronica Ek
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zheya Sheng
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, SwedenState Key Laboratory for Agro-Biotechnology, China Agricultural University,100193, Beijing, People’s Republic of China
  • Find this author on Google Scholar
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  • Search for this author on this site
Marcin Kierczak
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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Sverker Holmgren
Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
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Örjan Carlborg
Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, SwedenDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden
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