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United States Department of Agriculture

Agricultural Research Service

Title: Evidence for Frequent Recombination in a Wheat Streak Mosaic Virus Population

Authors
item French, Roy
item STENGER, DRAKE

Submitted to: American Society for Virology Meeting
Publication Type: Abstract Only
Publication Acceptance Date: March 15, 2003
Publication Date: July 15, 2003
Citation: FRENCH, R.C., STENGER, D.C. EVIDENCE FOR FREQUENT RECOMBINATION IN A WHEAT STREAK MOSAIC VIRUS POPULATION. American Society For Virology Meeting. 2003. (Oral Presentation)

Technical Abstract: There are two types of recombination events of interest in RNA viruses. One is between divergent virus populations or virus species. The other is between members of the same population. The former is perhaps important for long-term virus evolution while the latter could serve as a mechanism to prevent fixation of deleterious mutants through genetic exchange. Recombination between diverged viruses may be detected by looking for gene segments with different apparent evolutionary histories. Frequent recombination between nearly identical viruses is more difficult to identify. One approach is to examine linkage disequilibrium among pairs of polymorphic sites. Relaxed linkage among several pairs of polymorphic sites in a population sample would suggest a history of recombination, but recurrent mutation (homoplasy) at the some of these sites would give similar results. Since it is impossible to know the past chain of events (mutation or recombination) that produced an observed set of sequences, one can only attempt to determine the relative probability of the observed pattern of polymorphism under population models with or without recombination. In recent years, tools have become available to calculate these relative probabilities using a theoretical framework known as the coalescent. We have determined the coat protein gene sequences of 49WSMV isolates from the U.S.A. In this data set there are 247 polymorphic sites of which 63 are phylogenetically informative. For 12 sites the least common nucleotide is present in nine or more isolates. Relative likelihoods of a range of population recombination rates were determined using these 12 intermediate-frequency (i.e. > 20%) polymorphic sites. The most probable recombination rate, given the data, was inferred to be one hundred times the population mutation rate. This suggests that genetic exchange has occurred frequently enough within the U. S. WSMV population such that it may well prevent fixation of deleterious mutants and overcome the problem of Muller's ratchet predicted for clonal populations.

Last Modified: 8/27/2014
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