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Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example

Yanyan Liu, Sican Xiong, Wei Sun and Fei Zou
G3: Genes, Genomes, Genetics Early online December 18, 2017; https://doi.org/10.1534/g3.117.300483
Yanyan Liu
Wuhan University
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Sican Xiong
Wuhan University
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Wei Sun
Public Health Sciences Division, Fred Hutchinson Cancer Research Center
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Fei Zou
University of North Carolina at Chapel Hill
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Abstract

Multiparent populations (MPP) have become popular resources for complex trait mapping because of their wider allelic diversity, and larger population size compared to traditional two-way recombinant inbred (RI) strains. In Mice, the Collaborative Cross (CC) is one of the most popular MPP and is derived from eight genetically diverse inbred founder strains. The strategy of generating recombinant inbred intercrosses (RIX) from MPP in general and the CC in particular can produce a large number of completely reproducible heterozygote genomes that better represent the (outbred) human population. Since both maternal and paternal haplotypes of each RIX are readily available, RIX is a powerful resource for studying both standing genetic and epigenetic variations of complex traits, in particular, the Parent-of-Origin (PoO) effects, an important contributor to many complex traits. Furthermore, most complex traits are affected by more than one genes where multiple QTL mapping could be more advantageous. In this paper, for MPP-RIX data but taking CC-RIX as a working example, we propose a general Bayesian variable selection procedure to simultaneously search for multiple genes with founder allelic effects and PoO effects. The proposed model respects the complex relationship among RIX samples and the performance of the proposed method is examined by extensive simulations.

  • Bayesian variable selection
  • Parameter expanded Gaussian priors
  • imprinting
  • Received November 7, 2017.
  • Accepted December 3, 2017.
  • Copyright © 2017, G3: Genes, Genomes, Genetics
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PUBLICATION INFORMATION

Volume 8 Issue 4, April 2018

G3: Genes|Genomes|Genetics: 8 (4)

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Multiparental Populations
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Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example

Yanyan Liu, Sican Xiong, Wei Sun and Fei Zou
G3: Genes, Genomes, Genetics Early online December 18, 2017; https://doi.org/10.1534/g3.117.300483
Yanyan Liu
Wuhan University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sican Xiong
Wuhan University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wei Sun
Public Health Sciences Division, Fred Hutchinson Cancer Research Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fei Zou
University of North Carolina at Chapel Hill
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: feizou@email.unc.edu
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Citation

Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example

Yanyan Liu, Sican Xiong, Wei Sun and Fei Zou
G3: Genes, Genomes, Genetics Early online December 18, 2017; https://doi.org/10.1534/g3.117.300483
Yanyan Liu
Wuhan University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sican Xiong
Wuhan University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wei Sun
Public Health Sciences Division, Fred Hutchinson Cancer Research Center
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fei Zou
University of North Carolina at Chapel Hill
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: feizou@email.unc.edu

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