Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/752
Title: Efficient designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage
Contributor(s): Lee, Sang Hong  (author); Van Der Werf, JH  (author)orcid 
Publication Date: 2004
Open Access: Yes
DOI: 10.1051/gse:2003056
Handle Link: https://hdl.handle.net/1959.11/752
Abstract: In a simulation study, different designs were compared for efficiency of fine-mapping of QTL. The variance component method for fine-mapping of QTL was used to estimate QTL position and variance components. The design of many families with small size gave a higher mapping resolution than a design with few families of large size. However, the difference is small in half sib designs. The proportion of replicates with the QTL positioned within 3 cM of the true position is 0.71 in the best design, and 0.68 in the worst design applied to 128 animals with a phenotypic record and a QTL explaining 25% of the phenotypic variance. The design of two half sib families each of size 64 was further investigated for a hypothetical population with effective size of 1000 simulated for 6000 generations with a marker density of 0.25 cM and with marker mutation rate 4 x 10-4 per generation.In mapping using bi-allelic markers, 42~55% of replicated simulations could position QTL within 0.75 cM of the true position whereas this was higher for multi allelic markers (48~76%). The accuracy was lowest (48%) when mutation age was 100 generations and increased to 68% and 76% for mutation ages of 200 and 500 generations, respectively, after which it was about 70% for mutation ages of 1000 generations and older. When effective size was linearly decreasing in the last 50 generations, the accuracy was decreased (56 to 70%). We show that half sib designs that have often been used for linkage mapping can have sufficient information for fine-mapping of QTL. It is suggested that the same design with the same animals for linkage mapping should be used for fine-mapping so gene mapping can be cost effective in livestock populations.
Publication Type: Journal Article
Source of Publication: Genetic Selection Evolution, 36(2), p. 145-161
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
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: 216
Views: 218
Downloads: 12
Appears in Collections:Journal Article

Files in This Item:
5 files
File Description SizeFormat 
open/SOURCE02.pdfPublisher version (open access)216.08 kBAdobe PDF
Download Adobe
View/Open
Show full item record

SCOPUSTM   
Citations

25
checked on Nov 26, 2018

Page view(s)

124
checked on Mar 5, 2019

Download(s)

30
checked on Mar 5, 2019
Google Media

Google ScholarTM

Check

Altmetric


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