Population genetic analyses of Botrytis cinerea isolates from Michigan vineyards using a high-throughput marker system approach

Authors: Naegele, Rachel; Abdelsamad, Noor; ALZOHAIRY, S.A. - Michigan State University; Saito, Seiya; Delong, Jeffery - Jeff; MILES, T.D. - Michigan State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2021
Publication Date: 4/20/2021
Citation: Naegele, R.P., Abdelsamad, N.A., Alzohairy, S., Saito, S., Delong, J.A., Miles, T. 2021. Population genetic analyses of Botrytis cinerea isolates from Michigan vineyards using a high-throughput marker system approach. Frontiers in Microbiology. 12:660874. https://doi.org/10.3389/fmicb.2021.660874.
DOI: https://doi.org/10.3389/fmicb.2021.660874

Interpretive Summary: Plant pathogens can vary greatly in their genetic diversity, and pathogen populations need to be genetically profiled to better develop durable management strategies. One way to do this is via molecular markers (e.g. tags) that naturally occur in each organism. Differences in these molecular "tags" can help identify differences between individuals. Different types of molecular tags can be used, and depending on the genetic diversity of the organism and the genome size more or less tags may be needed. In this study, we compare single nucleotide polymorphism (SNP)-based markers (496) to microsatellite (e.g. simple sequence repeat) (9) markers for their ability to tease apart genetic signatures associated with fungicide resistance, geography of origin and year of collection for the fungal pathogen Botrytis cinerea. Both marker systems were able to find positive genetic signatures associated with fungicide resistance, but differed in their ability to distinguish signatures based on other characteristics. Either marker system should be useful for profiling genetic signatures in this fungal pathogen.

Technical Abstract: As sequencing costs continue to decrease, new tools are being developed for assessing pathogen diversity and population structure. Traditional marker types, such as microsatellites, are often more cost effective than SNP panels when working with small numbers of individuals, but may not allow for fine scale evaluation of low or moderate structure in populations. Botrytis cinerea is a necrotrophic plant pathogen with high genetic variability that can infect more than 200 plant species worldwide. A panel of 52 amplicons were sequenced for 82 isolates collected from four Michigan vineyards representing two years of collection and varying fungicide resistance. A panel of nine microsatellite markers previously described was also tested across 74 isolates from the same population. A microsatellite and SNP markers analysis of B. cinerea populations was performed to assess the genetic diversity and population structure of Michigan vineyards, and the results from both marker types were compared. Genetic diversity and population structure of the isolates were evaluated using microsatellite and SNP markers, and the results compared. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and resistance to multiple fungicides (MFR). Microsatellites were also able to differentiate population structure associated with another fungicide, fluopyram, while SNPs were able to additionally differentiate structure based on year. For both methods, AMOVA results were similar, with microsatellite results explaining a smaller portion of the variation compared to the SNP results. The SNP-based markers presented here were able to successfully differentiate population structure similar to microsatellite results. These SNP markers represent new tools to discriminate B. cinerea isolates within closely related populations.