Mining and characterization of microsatellites from a genome of Venturia carpophila

Abstract

A total of 4021 microsatellites were mined from a genome of Venturia carpophila, and 192 were selected to screen 39 isolates of the fungus collected from peach and nectarine in the southeastern USA. Of the 192 selected, 32 primers consistently and reliably produced polymorphic amplicons. Subsequently, the genotyping data from these 32 primers were used for preliminary analysis of the genetic diversity among the 39 isolates. The number of alleles identified ranged from 2 to 9, and the polymorphic information content from 0.097 to 0.792. Over all isolates, Shannon’s information index was 0.914, indicating genetic diversity. Stoddart and Taylor’s index of diversity and Simpson’s index also indicated high diversity (32.4 and 0.969, respectively). Evenness within the sample was high (0.955), but there was strong evidence for haploid linkage disequilibrium (3.799, P = 0.001). Observations on diversity were supported by analysis of genetic distance, which showed little affinity for clustering based on isolate source population, location, or host. The microsatellites developed in this study should be useful in future research of the population genetic structure and dynamics of V. carpophila and evaluating the risks posed by the ability of the pathogen to adapt on peach and possibly other stone fruit hosts in the USA and elsewhere in the world.