Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/3146
Title: An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree
Contributor(s): Lee, Sang Hong (author); Van Der Werf, Julius Herman (author)orcid 
Publication Date: 2006
DOI: 10.1051/gse:2005025
Handle Link: https://hdl.handle.net/1959.11/3146
Abstract: Variance component (VC) approaches based on restricted maximum likelihood (REML) have been used as an attractive method for positioning of quantitative trait loci (QTL). Linkage disequilibrium (LD) information can be easily implemented in the covariance structure among QTL effects (e.g. genotype relationship matrix) and mapping resolution appears to be high. Because of the use of LD information, the covariance structure becomes much richer and denser compared to the use of linkage information alone. This makes an average information (AI) REML algorithm based on mixed model equations and sparse matrix techniques less useful. In addition, (near-) singularity problems often occur with high marker densities, which is common in fine-mapping, causing numerical problems in AIREML based on mixed model equations. The present study investigates the direct use of the variance covariance matrix of all observations in AIREML for LD mapping with a general complex pedigree. The method presented is more efficient than the usual approach based on mixed model equations and robust to numerical problems caused by near-singularity due to closely linked markers. It is also feasible to fit multiple QTL simultaneously in the proposed method whereas this would drastically increase computing time when using mixed model equation-based methods.
Publication Type: Journal Article
Source of Publication: Genetics, Selection, Evolution, 38(1), p. 25-43
Publisher: EDP Sciences
Place of Publication: France
ISSN: 0999-193X
Field of Research (FOR): 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Statistics to Oct 2018: Visitors: 176
Views: 177
Downloads: 0
Appears in Collections:Journal Article
School of Environmental and Rural Science

Files in This Item:
2 files
File Description SizeFormat 
Show full item record

SCOPUSTM   
Citations

32
checked on Nov 30, 2018

Page view(s)

108
checked on Jan 3, 2019
Google Media

Google ScholarTM

Check

Altmetric

SCOPUSTM   
Citations

 

WEB OF SCIENCETM
Citations

 

Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.