Population genetic diversity and structure of the pecan scab pathogen, Venturia effusa, on cv. Desirable and native seedlings, and the impact of marker number

Scab (Venturia effusa) is the major cause of economic loss in pecan in the south‐eastern USA. We explored population genetic diversity and structure among orchards of cv. Desirable and native seedlings, and within‐orchard variability among trees of all cultivars sampled. We compared the ability of 30, 15 and 7 previously developed microsatellites to characterize the population genetic diversity and structure of V. effusa. Analyses of molecular variance (AMOVA) provided little evidence of structure dependent on cultivar, but there was some evidence of structure between orchards of a cultivar based on distance. Individual orchard AMOVA showed that three of 11 orchards had between‐tree population structure. Among six populations from cv. Desirable, a Mantel test showed that geographic distance was related to the pairwise genetic divergence (R2 = 0.84). Among 11 orchards of various cultivars there was little difference in diversity using 30, 15 or 7 markers, or population structure based on AMOVA. Some minor differences in population structure were seen based on discriminant analysis of principal components, or dendrograms. Thus, depending on the objectives, future studies may use as few as 15 or 7 markers without losing ability to discern population genetic diversity or structure. More populations exhibited linkage disequilibrium when using 15 or 30 markers compared to when using seven markers. Knowledge of population genetics of V. effusa in relation to host genotype is needed to understand pathogen population interactions and gene flow, knowledge that will help underpin future breeding efforts to develop durable resistance in this long‐lived orchard tree. There was cultivar‐based genetic structure among populations of Venturia effusa from pecan orchards of cv. Desirable and native seedlings; using 30, 15 or 7 SSRs resulted in the same conclusions on diversity and population structure.