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doi:10.1534/genetics.104.040311
A more recent version of this article appeared on April 1, 2006.
REGULAR RESEARCH PAPERS |
Relative influences of crossing-over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana
Vincent Plagnol 1*, Badri Padhukasahasram 1, Jeffrey D Wall 1, Paul Marjoram 1 and Magnus Nordborg 1
1 University of Southern California
* To whom correspondence should be addressed. E-mail: vincent.plagnol{at}normalesup.org.
Submitted on December 22, 2004
Revised on March 15, 2005
Accepted on 1 November 2005
In this paper we infer the rates of conversion and crossing-over in Arabidopsis thaliana from population genetics data. Our data set is a genome-wide survey consisting of 920 fragments of length 600 bp sequenced in 95 accessions. It has several orders of magnitude more markers than any previous non-human study. This allows for more accurate inference as well as a detailed comparison between theoretical expectations and observations. Our methodology is specifically set to account for deviations such as recurrent mutations or skewed frequency spectrum. We found that even if some components of the model clearly do not fit, the pattern of LD conforms to theoretical expectations quite well. The ratio between crossing-over and conversion is estimated to be around three, which is significantly lower than previous estimates.We also find evidence for fine-scale variations of the crossing-over rate.
Key Words: Arabidopsis thaliana, crossing over, gene conversion, population genetics
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