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PMID: 15677753 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree.

Genetics ·Vol. 169 ·No. 1 ·2005-01-00 ·Pages 455-66

Lee SH, Van der Werf JH

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 ( approximately 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 ( approximately 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.

MeSH Terms
Alleles Chromosome Mapping Female Genetic Markers Genotype Humans Likelihood Functions Linkage Disequilibrium Male Models, Genetic Pedigree Quantitative Trait Loci Recombination, Genetic
Chemicals
Genetic Markers
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lee S H
School of Rural Science and Agriculture, University of New England, New South Wales 2351, Australia. [email protected]
Van der Werf J H J
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1534/genetics.104.033233
Email
[email protected]
Published
2005-01-00
Pages
455-66
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1448885
Subset
IM
External Links
PubMed source DOI: 10.1534/genetics.104.033233 PMC Full Text View journal details
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