Pair-wise linkage disequilibrium decay among linked loci suggests meiotic recombination in natural populations of Sclerotinia sclerotiorum

Abstract

Both clonal and recombining population structures have been reported in Sclerotinia sclerotiorum populations around the world. Association of independent and putatively unlinked markers indicates clonal population structure, whereas random association of the markers suggests recombination and outcrossing. However, high mutation rates of markers used for inference, like certain microsatellite markers, could interfere and compromise the inferences of recombination and outcrossing. To test if the recombination is due to outcrossing or mutation, we used 12 microsatellite loci distributed over four chromosomes to genotype 230 isolates sampled from seven populations in the USA and China from a variety of crops. All the isolates produced single alleles for each of the loci tested, indicating all the isolates were homokaryotic for the microsatellite loci in consideration. Pair-wise linkage disequilibrium (LD) tests (Hedrick?s D, Fishers exact test and IA) between physically linked loci showed relationships ranging from linked to random association with increasing distance between loci on three chromosomes. For the three loci on chromosome four, LD decay with increasing physical distance between loci was found in six of the seven populations.