Development and characterization of microsatellite markers of the fungal plant pathogen Sclerotinia trifoliorum

Abstract

Sclerotinia trifoliorum is an important pathogen of forage legumes and some grain legumes. Attempts to study its population biology using microsatellite markers developed for Sclerotinia sclerotiorum and Sclerotinia subarctica resulted in no amplification or low levels of polymorphism. This study reports the development and characterization of 33 microsatellite loci developed from a microsatellite-enriched library of S. trifoliorum. Based on a population of 42 isolates of S. trifoliorum, these microsatellite markers are highly polymorphic, with a mean of 6.5 alleles per locus (range 3-12) and a mean expected heterozygosity of 0.63 (range 0.26-0.9). Based on locations of these marker sequences in the S. sclerotiorum genome, these microsatellite loci are dispersed throughout the genome. However, 50% (265 of 528) of pairwise comparisons of the 33 microsatellite loci had significant linkage disequilibrium, which could be explained by the mixed mating systems (homothallism and heterothallism) and clonal reproduction of S. trifoliorum. Thirty of the 33 loci were successfully applied to S. sclerotiorum, and 28 loci were polymorphic. However, only 10 loci are applicable to Sclerotinia minor and 1 locus to Sclerotinia homoeocarpa. These markers are therefore useful for population structure assessment, QTL mapping, and ecological analyses in S. trifoliorum and potentially in other Sclerotinia species.

Spatial Patterns of Brown Rot Epidemics and Development of Microsatellite Markers for Analyzing Fine-Scale Genetic Structure ofMonilinia fructicolaPopulations Within Peach Tree Canopies

“…Although previous cytological studies have shown that fungi in the genus Monilinia are multinucleate (~5 to 10 nuclei per conidium) (13,15,31), only one peak was detected for each locus, which is consistent with the haploid-monokaryotic state of other fungi in the Sclerotinaceae (17,25,32). The number of alleles per locus ranged from 2 to 16, with an average of 9 alleles per locus.…”

Development of polymorphic microsatellite markers issued from pyrosequencing technology for the medicinal mushroom Agaricus subrufescens

“…Our results supported the poor, but not null, transferability of the microsatellite markers across species in fungi (Dutech et al ., ). As previously reported, this level of transferability was in agreement with phylogenetic relatedness (Njambere et al ., ).…”

Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California

“…PCR conditions for amplification were the same as those described by Njambere et al . (). Analysis of fragment sizes was done using a LI‐COR 4300 gel‐based sequencer (LI‐COR Biosciences), and allele sizes were determined using the gene Imag IR v. 4.05 software (LI‐COR Biosciences).…”

“…Each genotyping run was performed with independently isolated genomic DNA to confirm the reproducibility and accuracy of the results. Allele sizes were sequenced to confirm that size differences were due to different numbers of respective microsatellite repeats (Njambere et al ., ).…”

“…Seven microsatellite loci (Table ) that were previously shown to detect polymorphisms in S. trifoliorum populations (Njambere et al ., ) were selected for this study. PCR conditions for amplification were the same as those described by Njambere et al .…”