The Role of Pedigree Information in Combined Linkage Disequilibrium and Linkage Mapping of Quantitative Trait Loci in a General Complex Pedigree

Title
The Role of Pedigree Information in Combined Linkage Disequilibrium and Linkage Mapping of Quantitative Trait Loci in a General Complex Pedigree
Publication Date
2005
Author(s)
Lee, Sang Hong
Van Der Werf, JH
( author )
OrcID: https://orcid.org/0000-0003-2512-1696
Email: jvanderw@une.edu.au
UNE Id une-id:jvanderw
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Genetics Society of America
Place of publication
United States of America
DOI
10.1534/genetics.104.033233
UNE publication id
une:501
Abstract
Combined linkage disequilibrium and linkage (LDL) mapping can exploit historical as well as recent and observed recombinations in a recorded pedigree. We investigated the role of pedigree information in LDL mapping and the performance of LDL mapping in general complex pedigrees. We compared using complete and incomplete genotypic data, spanning 5 or 10 generations of known pedigree, and we used bi- or multiallelic markers that were positioned at 1- or 5-cM intervals. Analyses carried out with or without pedigree information were compared. Results were compared with linkage mapping in some of the data sets. Linkage mapping or LDL mapping with sparse marker spacing (5 cM) gave a poorer mapping resolution without considering pedigree information compared to that with considering pedigree information. The difference was bigger in a pedigree of more generations. However, LDL mapping with closely linked markers (1 cM) gave a much higher mapping resolution regardless of using pedigree information. This study shows that when marker spacing is dense and there is considerable linkage disequilibrium generated from historical recombinations between flanking markers and QTL, the loss of power due to ignoring pedigree information is negligible and mapping resolution is very high.
Link
Citation
Genetics, 169(1), p. 455-466
ISSN
1943-2631
0016-6731
Start page
455
End page
466

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