ARS | Publication request: Pair-wise linkage disequilibrium decay among linked loci suggests meiotic recombination in natural populations of Sclerotinia sclerotiorum

Submitted to: Fungal Genetics Reports
Publication Type: Abstract Only
Publication Acceptance Date: February 25, 2013
Publication Date: March 11, 2013
Citation: Attanayake, R., Chen, W. 2013. Pair-wise linkage disequilibrium decay among linked loci suggests meiotic recombination in natural populations of Sclerotinia sclerotiorum. Fungal Genetics Reports. 60 (Suppl): 680.

Technical 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 detect linkage disequilibrium and recombination of linked loci, 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. Likewise, LD decay was found for the three loci on chromosome six in four of the seven populations, and also for the loci on chromosome five in two of the populations. The reduced pair-wise linkage disequilibrium with increasing distance cannot be attributed to mutation alone, and thus the high intrachromosomal recombination is most likely due to meiotic recombination following outcross in these populations. Recombination hot spots and cold spots were detected. Mating type loci in 59 isolates of two populations were genotyped using PCR with allele-specific primers. About 40% of the isolates showed both MAT1-1 and MAT1-2 idiomorphs, as expected for a homothallic species. However, the remaining 60% of the isolates had only the MAT1-2 idiomorph detected by the allele-specific PCR. Although the nature of the absence of the MAT1-2 idiomorph remains to be determined, the results showed variations in mating type alleles in natural populations suggesting that some of the isolates may not be truly homothallic.