Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Authors: ATTANAYAKE, RENUKA - Washington State University; TENNEKOON, VIDHURA - University Of Oklahoma; JOHNSON, DENNIS - Washington State University; Porter, Lyndon; DEL RÍO-MENDOZA, LUIS - North Dakota State University; JIANG, DAOHONG - Huazhong Agricultural University; Chen, Weidong

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/27/2014
Publication Date: 4/30/2014
Citation: Attanayake, R., Tennekoon, V., Johnson, D., Porter, L., Del Río-Mendoza, L., Jiang, D., Chen, W. 2014. Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay. Heredity. 113:353-363. doi: 10.1038/hdy.2014.37.

Interpretive Summary: Fungi are either capable of mating with themselves (self mate) or must mate with others (outcross) in the laboratory. Whether the fungi that self mate in the laboratory also outcross in nature is an unresolved question. Such behavior of either self-mating or outcrossing determines the population genetic structure of the fungus and has important implications from understanding the pathogen biology to developing management strategies. A traditional technique for determining whether a fungus is self-mating or outcrossing in nature is to determine the rate of genetic recombination using molecular markers. Random recombination of molecular markers suggests outcrossing. The self-mating fungal pathogen Sclerotinia sclerotiorum, causal agent of diseases of more than 400 plant species, has for a long time been considered to be predominantly self-mating in nature. However, more recent studies using molecular markers demonstrated that recombination of genes does occur, which suggests outcrossing, although in these studies mutation could not be differentiated from recombination. A high mutation rate of the markers would confound the recombination analyses and increase falsehood of inference of outcrossing. In this study, an innovative approach was taken to use markers located on the same chromosomes and to measure the rate of recombination as the markers become further apart on the same chromosomes, which allowed us to detect mutation rate relative to recombination. The results showed that markers close to each other are more linked than markers that are further apart on the same chromosomes, providing strong evidence that S. sclerotiorum actually undergoes frequent outcrossing in nature. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.

Technical Abstract: The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, eight population samples comprised of 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for 12 microsatellite markers, resulting in multiple polymorphic markers on three chromosomes. Each isolate was homokaryotic for the 12 loci. Pair-wise LD was estimated using three methods, Fisher’s exact test, Index of association (IA) and Hedrick’s D'. For most of the populations, pair-wise LD decayed with increasing physical distance between loci in two of the three chromosomes. Therefore, the observed recombination of alleles cannot be simply attributed to mutation alone. Different recombination rates in various DNA regions (recombination hot/cold spots) and different evolutionary histories of the populations could explain the observed differences in rates of LD decay among the chromosomes and among populations. The majority of the isolates exhibited mycelial incompatibility, minimizing the possibility of heterokaryon formation and mitotic recombination. Thus, the observed high intrachromosomal recombination is due to meiotic recombination, suggesting frequent outcrossing in these populations, supporting the view that homothallism favors universal compatibility of gametes instead of traditionally believed haploid selfing in S. sclerotiorum. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.