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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #352328

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Mining and characterization of microsatellites from a genome of Venturia carpophila

Author
item Chen, Chunxian
item Bock, Clive
item Brannen, Phillip - University Of Georgia
item Adaskaveg, James - University Of California

Submitted to: Mycological Progress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2018
Publication Date: 4/25/2018
Citation: Chen, C., Bock, C.H., Brannen, P.M., Adaskaveg, J.E. 2018. Mining and characterization of microsatellites from a genome of Venturia carpophila. Mycological Progress. 17(8):885-895. https://doi.org/10.1007/s11557-018-1401-x.
DOI: https://doi.org/10.1007/s11557-018-1401-x

Interpretive Summary: Peach fruit infected with peach scab (a fungal disease) has little market value due to black freckles and spots on the fruit surface. Timely fungicide sprays are crucial for the disease control in commercial peach production. To facilitate better disease management and resistance breeding in peach, we need more knowledge of the fungal pathogen, Venturia carpophila. In this study, simple sequence repeat (aka microsatellite) DNA markers were developed from a genome of the fungus and an optimally selected subset were used to assess isolates of the fungus collected from peach and nectarine in the southeastern US. Genotyping and phylogenetic analysis were performed. Genetic diversity among these isolates was supported by genetic distance, but showed little affinity for clustering based on isolate source population, location or host. The simple sequence repeat DNA markers developed in this study should be useful in future research of the population genetics and dynamics between the pathogen and hosts in the US and world.

Technical Abstract: A total of 4,021 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.