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 single-nucleotide polymorphism (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 2 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 marker 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. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and multiple fungicide resistance (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 with 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 using multiple targeted sequences.
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.
Grape production and fruit quality traits such as cluster size, berry shape, and timing of fruit development are key aspects in selecting cultivars for commercial production. Molecular markers for some, but not all, of these traits have been identified using bi-parental or association mapping populations. Previously identified markers were tested for transferability using a test panel of commercially available grape cultivars. Markers had little to no ability to differentiate grape phenotypes based on the expected characteristics, except the marker for seedlessness. Using a biparental inter-specific cross, forty-three QTL, both previously identified and new genomic regions, associated with berry shape, number, size, cluster weight, length, and time to flower, veraison and full color were detected. KASP markers designed on newly identified QTL were tested for transferability using the same panel. Transferability was low when use types were combined, but varied when use type were evaluated separately. Comparison of a 4Mb region at the end of chromosome 18 revealed structural differences among grape species and use types. Table grape cultivars had the highest similarity in structure for this region (> 75%) compared to other grape species and commodity types.
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