Population genetic diversity and structure of Venturia carpophila on peach and almond in the U.S.A.

Authors: Bock, Clive; Chen, Chunxian; YOUNG, CAROLYN - North Carolina State University; CHARLTON, NIKKI - Noble Research Institute; SCHNABEL, GUIDO - Clemson University; LALANCETTE, NORMAN - Rutgers Agriculture Research & Extension Center; PITTS, JAMES - Auburn University; ADASKAVEG, JAMES - University Of California, Riverside; BRANNEN, PHILLIP - University Of Georgia

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2025
Publication Date: 4/15/2025
Citation: Bock, C.H., Chen, C., Young, C.A., Charlton, N.D., Schnabel, G., Lalancette, N., Pitts, J., Adaskaveg, J.E., Brannen, P.M. Population genetic diversity and structure of Venturia carpophila on peach and almond in the U.S.A.. Phytopathology. 2025. https://doi.org/10.1094/PHYTO-11-24-0361-R.
DOI: https://doi.org/10.1094/PHYTO-11-24-0361-R

Interpretive Summary: Scab of peach and almond is caused by the plant pathogenic fungus Venturia carpophila. Scab can result in yield losses to both crops. Isolates of V. carpophila were sampled from peach orchards in the eastern U.S.A. and from almond orchards in California. The aims of the research were to determine the population genetic diversity and structure of V. carpophila on peach and almond, compare populations of the pathogen from various orchards of each host in each location, and determine mating type ratios in the orchard populations of the two hosts. Results showed that genetic diversity was higher for peach compared to almond populations. Mating types of V. carpophila were consistently at equilibrium for peach, but not for almond. The genetic diversity was structured such that most of it was represented at the scale of the tree but also a substantial quantity attributable to location (crop type). Other analyses confirmed this structure. Taken as a whole the results suggest that on peach in the southeastern U.S.A., V. carpophila is genetically diverse and has characteristics of a sexually reproducing pathogen, but on almond in California, the lower diversity, and low frequency of a mating type suggests a predominance of asexual reproduction. Differences in the lifecycle of the pathogen may occur in the two crop production areas.

Technical Abstract: Scab of peach and almond is caused by Venturia carpophila, and the disease can result in yield losses to both crops. A total of 735 isolates of V. carpophila were sampled from different peach orchards (411 isolates) in the eastern U.S.A. and from almond orchards (324 isolates) in California. The aims of the research were to determine the population genetic diversity and structure of V. carpophila on peach and almond, compare populations of the pathogen from various orchards of each host in each location, and determine mating type ratios in the orchard populations of the two hosts. Results showed that the allelic richness for the peach populations (2.67 to 3.15) was higher compared to almond populations (2.13 to 2.33). Other measures of gene and genotypic diversity including the Shannon-Wiener index, and Evenness showed similar trends. Based on clone corrected data, mating types of V. carpophila were consistently at equilibrium for populations from peach, but none of the populations from almond were at equilibrium, with the MAT1-1-1 idiomorph being at low frequency or absent from almond populations. All populations exhibited linkage disequilibrium, but when based on mating type, the MAT1-1-1 peach population loci were at equilibrium, although MAT1-2-1 peach population showed some evidence of linkage disequilibrium. Both mating type populations from almond had significant linkage disequilibrium. Analysis of molecular variance showed structure, and the greatest proportion of variance was at the level of the tree (71.8%) with a large portion of variance also at the level of the location (crop) (25.3%). A discriminant analysis of principal components and a dendrogram based on Nei’s genetic distance showed that the peach and almond orchard populations clustered separately as independent groups. The results suggest that on peach in the southeastern U.S.A., V. carpophila is genetically diverse and has characteristics of a sexually reproducing pathogen, but on almond in California, the lower diversity, more extensive linkage disequilibrium, and low frequency or absence of the MAT1-1-1 mating type suggest a predominance of asexual reproduction. Differences in the lifecycle of the pathogen may occur in the two crop production areas, and the confounded factors of location and crop host resulted in readily differentiated populations.