• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of gseBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleGenetics, Selection, Evolution : GSEJournal Front Page
Genet Sel Evol. 2001; 33(6): 605–634.
Published online Nov 15, 2001. doi:  10.1186/1297-9686-33-6-605
PMCID: PMC2705394

Prediction of identity by descent probabilities from marker-haplotypes

Abstract

The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (i.e. all information came from the marker genotypes), and the situation where, say T, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.

Keywords: identity by descent, haplotype analysis, coalescence process, linkage disequilibrium, QTL mapping

(To access the full article, please see PDF)


Articles from Genetics, Selection, Evolution : GSE are provided here courtesy of BioMed Central

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...