Mapping of imprinted quantitative trait loci using immortalized F2 populations

Yongxian Wen; Weiren Wu

doi:10.1371/journal.pone.0092989

Mapping of imprinted quantitative trait loci using immortalized F2 populations

PLoS One. 2014 Mar 27;9(3):e92989. doi: 10.1371/journal.pone.0092989. eCollection 2014.

Authors

Yongxian Wen¹, Weiren Wu²

Affiliations

¹ Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, Fujian, China; School of Computer and Information Science, Fujian Agriculture & Forestry University, Fuzhou, Fujian, China.
² Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, Fujian, China.

Abstract

Mapping of imprinted quantitative trait loci (iQTLs) is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM) and composite interval mapping (CIM) based on conventional low-density genetic maps and point mapping (PM) and composite point mapping (CPM) based on ultrahigh-density genetic maps, using an immortalized F2 (imF2) population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM) are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Chromosome Mapping*
Computer Simulation
Crosses, Genetic
Genomic Imprinting*
Models, Genetic
Quantitative Trait Loci*

Grants and funding

This work was supported by the National Natural Science Foundation of China (project no.: 31171448) and the Natural Science Foundation of Fujian Province (project no. 2012J01069). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.