Characterizing Uncertainty in High-Density Maps from Multiparental Populations

Ahfock, Daniel, Wood, Ian, Stephen, Stuart, Cavanagh, Colin R. and Huang, B. Emma (2014) Characterizing Uncertainty in High-Density Maps from Multiparental Populations. Genetics, 198 1: 117-128. doi:10.1534/genetics.114.167577

Author Ahfock, Daniel
Wood, Ian
Stephen, Stuart
Cavanagh, Colin R.
Huang, B. Emma
Title Characterizing Uncertainty in High-Density Maps from Multiparental Populations
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
Publication date 2014-09
Year available 2014
Sub-type Article (original research)
DOI 10.1534/genetics.114.167577
Open Access Status
Volume 198
Issue 1
Start page 117
End page 128
Total pages 12
Place of publication Bethesda, MD United States
Publisher Genetics Society of America
Collection year 2015
Language eng
Formatted abstract
Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.
Keyword Recombinant Inbred Lines
Genetic Linkage Maps
Model Selection
Mouse Genome
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Mathematics and Physics
Official 2015 Collection
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 2 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sun, 02 Nov 2014, 00:15:54 EST by System User on behalf of School of Mathematics & Physics