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

Authors: Bock, Clive; CHARLTON, NIKKI - Noble Research Institute; SHILLER, JASON - Noble Research Institute; RANDALL, JENNIFER - New Mexico State University; YOUNG, CAROLYN - Noble Research Institute

Submitted to: Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2022
Publication Date: 3/2/2022
Citation: Bock, C.H., Charlton, N.D., Shiller, J., Randall, J.J., Young, C.A. 2022. Population genetic diversity and structure of the pecan scab pathogen, Venturia efffusa, on cv. Desirable and native seedings, and the impact of marker number. Plant Pathology. 71:1103-1119. https://doi.org/10.1111/ppa.13551.
DOI: https://doi.org/10.1111/ppa.13551

Interpretive Summary: Scab (caused by the plant pathogenic fungus Venturia effusa) is the major biotic cause of economic loss in pecan in the southeastern U.S.A. The pathogen population is genetically diverse. We explored population genetic diversity and structure among the cultivars. We also compared the ability of 30, 15 and 7 previously developed molecular markers to characterize the population genetic diversity and structure. Genetic diversity of V. effusa was found to be structured dependent on cultivar. Among orchards of cv. Desirable, geographic distance was strongly related to the pairwise genetic divergence of the populations. There was discernible difference between some tree populations within orchards, but there was little difference in measures of genotypic or genic diversity when using 30, 15 or 7 markers. Thus, future studies may be based on 15 or 7 markers without losing ability to discern population genetic diversity or structure. Knowledge of population genetics of V. effusa in relation to host cultivar, native tree and wild host populations of pecan scab is urgently needed to understand pathogen population interactions and gene flow, knowledge which will help underpin future breeding efforts to develop durable resistance in this long-lived orchard tree.

Technical Abstract: Scab (caused by the plant pathogenic fungus Venturia effusa) is the major biotic cause of economic loss in pecan in the southeastern U.S.A. The pathogen population is characterized as genetically diverse with some limited population differentiation, high gene flow, with mating types in equilibrium indicating regular recombination. We explored population genetic diversity and structure among the cultivars sampled, and within orchard variability among trees of each cultivar. We also compared the ability of 30, 15 and 7 previously developed microsatellites to characterize the population genetic diversity and structure of V. effusa in the 11 pecan orchards previously analyzed, as using fewer microsatellites will be more efficient. Genetic diversity of V. effusa was found to be structured dependent on cultivar. Within cv. Desirable, which was represented by 6 orchard populations, a Mantel test showed that the geographic distance was strongly related to the pairwise genetic divergence of the orchard populations (R2 = 0.83). Based on individual orchard analyses of molecular variance, three orchards showed between tree population structure. There was little discernible difference in measures of genotypic or genic diversity using 30, 15 or 7 markers. Although population structure based on analysis of molecular variance was similar, regardless of number of markers, there were some minor differences in population structure when viewed using a minimum spanning network, when using discriminant analysis of principal components, or when comparing genetic distance using a dendrogram. Thus, future studies may be based on 15 or 7 markers without losing ability to discern population genetic diversity or structure. However, more populations exhibited linkage disequilibrium when using 15 or 30 markers compared to when using 7 markers. Knowledge of population genetics of V. effusa in relation to host cultivar, native tree and wild host populations of pecan scab is urgently needed to understand pathogen population interactions and gene flow, knowledge which will help underpin future breeding efforts to develop durable resistance in this long-lived orchard tree.