Independently founded populations of Sclerotinia sclerotiorum from a tropical and a temperate region have similar genetic structure

Abstract

Sclerotinia sclerotiorum populations from tropical agricultural zones have been suggested to be more variable compared to those from temperate zones. However, no data were available comparing populations from both zones using the same set of markers. In this study, we compared S. sclerotiorum populations from the United States of America (USA, temperate) and southeast Brazil (tropical) using the frequency of mycelial compatibility groups (MCGs) and 13 microsatellite (SSR) markers. Populations were sourced from diseased plants within leguminous crops in New York, USA (NY; n = 78 isolates), and Minas Gerais State, Brazil (MG; n = 109). Twenty MCGs were identified in NY and 14 were previously reported in MG. The effective number of genotypes based on Hill's number of order 0, which corresponded to the number of multilocus genotypes (MLGs) were 22 (95% CI = 15.6-28.4) and 24 (95% CI = 18.9-29.1) in NY and MG, respectively. Clonal fractions of MLGs were 71.8% (NY) and 78.0% (MG). The effective number of genotypes based on Hill's number of orders 1 and 2 in NY were 8.9 (95% CI = 5.2-12.6) and 4.4 (95% CI = 2.6-6.1), respectively. For MG these indices were 11.4 (95% CI = 8.7-14.1) and 7.1 (95% CI = 5.1-9.0), respectively. There were no significant differences of allelic richness, private allelic richness, gene diversity, effective number of alleles and genotype evenness between the NY and MG populations. The populations were differentiated, with 29% of total variance attributed to differences between them and G''ST and Jost's D indices higher than 0.50. Cluster analysis revealed dissimilarity higher than 80% among most MLGs from both populations. Different alleles segregated in the populations but both had similar levels of genotypic variability.

Fig 1. Frequency of the mycelial compatibility groupings (A and B) and multilocus genotypes (MLGs) (C and D) obtained from 13 microsatellite loci in the Sclerotinia sclerotiorum populations from New York, USA, and Minas Gerais, Brazil.

The asterisk indicates the sum of the frequencies of two closely related MLGs, with a difference at the 8–3 locus (dinucleotide repeats). The MLG 1 has a 250 base pair (bp) allele while the MLG 2 has a 252 bp allele.

Fig 2. Diversity accumulation curves for different sample sizes with 95% confidence intervals (shaded areas) of the Hill’s numbers or effective number of genotypes of orders 0 (N0), 1 (N1) and 2 (N2) estimated for the Sclerotinia sclerotiorum populations from New York, USA and Minas Gerais, Brazil.

The N0, N1 and N2 numbers correspond to genotype richness, the exponential of Shannon’s entropy, and the inverse of the Simpson’s concentration indices, respectively. Solid lines correspond to rarefaction (interpolation) and dashed lines to extrapolation curves up to the base sample size of 156 individuals which corresponds to double the smaller reference sample size (NY = 78). The 95% confidence intervals were obtained by a bootstrap method based on 200 replications.

Fig 3. Genotype accumulation curves for the Sclerotinia sclerotiorum populations from New York, United States (USA) and Minas Gerais, Brazil.

The number of loci was randomly sampled (1,000 times) without replacement up to n − 1 loci. The 90% of the number of multilocus genotypes identified in each population are indicated by dashed lines.

Fig 4. Hierarchical cluster analysis according to complete linkage method from a dissimilarity matrix reflecting the percentage of allelic differences among the Multilocus Genotypes (MLGs).

Clusters (G) were assigned for MLGs with at least 50% of similarity.