Fungicide Resistance and Host Influence on Population Structure in Botrytis spp. from Specialty Crops in California

Abstract

Botrytis is an important genus of plant pathogens causing pre- and post- harvest disease on diverse crops worldwide. This study evaluated Botrytis isolates collected from strawberry, blueberry, and table grape berries in California. Isolates were evaluated for resistance to eight different fungicides, and 60 amplicon markers were sequenced (neutral, species-identification, and fungicide-resistance associated) distributed across 15 of the 18 B. cinerea chromosomes. Fungicide resistance was common among the populations, with resistance to pyraclostrobin and boscalid being most frequent. Isolates from blueberry had resistance to the least number of fungicides, while isolates from strawberry had the highest number. Host and fungicide resistance-specific population structure explained, 12% and 7 to 26%, respectively of the population variability observed. Fungicide resistance was the major driver for population structure with select fungicides explaining up to 26% and resistance to multiple fungicides (MFR) explaining 17% of the variability observed. Shared and unique significant SNPs associated with host and fungicide resistance (fluopyram, thiabendazole, pyraclostrobin, and fenhexamid) associated population structure were identified. While overlap between host and fungicide-resistance SNPs were detected, unique SNPs suggest that both host and fungicide resistance play an important role in Botrytis population structure.

Multiple and multidrug resistance in Botrytis cinerea: molecular mechanisms of MLR/MDR strains in Greece and effects of co-existence of different resistance mechanisms on fungicide sensitivity

“…Thus, in the current study, we documented a further increase in MLR frequencies within the fungal population. Multiple resistance to fungicides in B. cinerea is a rapidly expanding problem in the fungal populations worldwide, reported in several studies during the last decade ( Leroch et al., 2011 ; de Miccolis Angelini et al., 2014 ; Fernandez-Ortuno et al., 2014 ; Li et al., 2014 ; Lu et al., 2016 ; Campia et al., 2017 ; Rupp et al., 2017 ; Cosseboom et al., 2020 ; Makris et al., 2022 ; Naegele et al., 2022 ). The observed increased frequencies of MLR strains in populations from crops heavily treated with fungicides are obviously associated with the high number of sprays required to successfully control the disease, the application of pre-packed mixtures of different active ingredients that are of high risk for resistance development, or the absence of effective alternative control methods that could contribute to a reduction of selection pressure.…”

“…Such problems have been faced in the past in B. cinerea populations that have developed resistance worldwide to all site-specific fungicides, associated with target site modifications due to mutations’ presence in genes encoding the target site of the fungicides ( Brent and Hollomon, 2007 ; Hahn, 2014 ; Fernandez-Ortuno et al., 2017 ; Fillinger and Walker, 2016 ; Shao et al., 2021 ). More recent studies have shown that in pathogen populations throughout the world, strains have been selected possessing more than one target-site alternation conferring resistance to the respective fungicides and leading to multiple resistance (MLR) to fungicides ( de Miccolis Angelini et al., 2014 ; Rupp et al., 2017 ; Naegele et al., 2022 ).…”

Microscopic and Transcriptomic Analyses to Elucidate Antifungal Mechanisms of Bacillus velezensis TCS001 Lipopeptides against Botrytis cinerea

“…It has been ranked as a high-risk plant pathogen in developing fungicide resistance . In fact, B. cinerea populations resistant to single-site inhibitors or to multiple fungicides with different modes of action have been reported throughout the world. ,− More seriously, public concerns have been rising promptly for the negative effects posed by conventional fungicides on humans and the environment …”