Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices.

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.

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

Botrytis is an important genus of plant pathogens causing pre- and postharvest 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, whereas isolates from strawberry had resistance to 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 multiple fungicide resistance explaining 17% of the variability observed. Shared and unique significant single-nucleotide polymorphisms (SNPs) associated with host and fungicide (fluopyram, thiabendazole, pyraclostrobin, and fenhexamid) resistance-associated population structures were identified. Although 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.

Rotting Grapes Don't Improve with Age: Cluster Rot Disease Complexes, Management, and Future Prospects.

Cluster rots can be devastating to grape production around the world. There are several late-season rots that can affect grape berries, including Botrytis bunch rot, sour rot, black rot, Phomopsis fruit rot, bitter rot, and ripe rot. Tight-clustered varieties such as 'Pinot gris', 'Pinot noir', and 'Vignoles' are particularly susceptible to cluster rots. Symptoms or signs for these rots range from discolored berries or gray-brown sporulation in Botrytis bunch rot to sour rot, which smells distinctly of vinegar due to the presence of acetic acid bacteria. This review discusses the common symptoms and disease cycles of these different cluster rots. It also includes useful updates on disease diagnostics and management practices, including cultural practices in commercial vineyards and future prospects for disease management. By understanding what drives the development of different cluster rots, researchers will be able to identify new avenues for research to control these critical pathogens.

Population Genetics and Fungicide Resistance of Botrytis cinerea on Vitis and Prunus spp. in California.

Botrytis cinerea, the causal agent of gray mold, has high genetic diversity and a broad host range. In Vitis sp. and Prunus spp., B. cinerea causes pre- and postharvest diseases, and fungicides are routinely applied to prevent yield loss. In total, 535 isolates of B. cinerea collected from Vitis sp. and Prunus spp. in 2012, 2016, and 2017 were genotyped using 18 microsatellite markers and the transposable elements (TEs) Boty and Flipper. Only nine of the polymorphic markers and the two TEs were considered informative and retained for the final analyses. Of the 532 isolates, 297 were tested for resistance to seven fungicides representing six Fungicide Resistance Action Committee classes. After clone correction, 295 multilocus genotype groups were retained across the 3 years in 326 individuals, and four genetic subpopulations were detected. High levels of clonality were observed across the dataset. Significant pairwise differentiation was detected among years, locations, and TE composition. However, most of the diversity observed was within a subpopulation and not among subpopulations. No genetic differentiation was detected among resistant and sensitive isolates for individual fungicide classes. When resistance to the total number of fungicides was compared, regardless of the fungicide class, significant differentiation was detected among isolates that are resistant to two fungicide classes and those resistant to three or four fungicide groups. Fungicide resistance frequencies were stable for most chemistries evaluated with the exception of fluopyram, which increased from 2012 to 2016/2017.

Characterization, Virulence, Epidemiology, and Management of Anthracnose in Celery.

Leaf curling and petiole twisting of celery (Apium graveolens) were observed in several commercial fields in five Michigan counties in 2010 through 2012, causing significant crop damage and loss. Prior to this time, the pathogen Colletotrichum acutatum species complex had not been previously associated with celery in Michigan. In this study, the pathogen's genotype and phenotype were characterized, the influence of environmental conditions determined, and fungicides tested. Pathogen identification was based on conidial morphology and molecular identification using species-specific primers. Intersimple-sequence repeat (ISSR) banding patterns were similar between C. acutatum isolates from celery (n = 51) and blueberry (n = 1) but different from C. dematium and C. gloeosporioides. Four ISSR primers resulted in 4% polymorphism when tested on isolates from celery. Pathogenicity and virulence of C. acutatum sensu lato isolated from celery (n = 81), tomato (n = 2), and blueberry (n = 1) were evaluated in greenhouse experiments, which revealed differences in virulence among isolates but no significant differences specific to collection year, county, or field. In dew chambers and growth chambers, high temperatures (≥25°C) or long leaf wetness duration (>24 h) increased disease incidence. Twelve fungicides were tested in field studies over two growing seasons to determine their efficacy against celery anthracnose. The fungicides azoxystrobin, pyraclostrobin, mancozeb, and chlorothalonil reduced disease by 27 to 50% compared with the untreated control when disease pressure was moderate.

A New Method for Fractionation and Characterization of Polyphenols and Tannins from Grapevine Leaf Tissue.

Plants accumulate different types of phenolic material in their tissue as a response to biotic as well as abiotic stress. Monomeric polyphenols and smaller oligomers can serve as protection against ultraviolet radiation or prevent oxidative tissue damage, while larger molecules such as tannins can be the plant's reaction to an infection or physical damage. Therefore, characterization, profiling, and quantification of diverse phenolics can provide valuable information about the plant and the stress status at any given time. A method was developed that allows the extraction of polyphenols and tannins from leaf tissue, followed by fractionation and quantification. Extraction was performed with liquid nitrogen and 30% acetate-buffered ethanol. The method was tested with four cultivars under varying extraction conditions (solvent strength and temperature) and showed great improvements of the chromatography that would otherwise be impacted by tannins. The separation of tannins from smaller polyphenols was achieved by bovine serum albumin precipitation and resuspension in a urea-triethanolamine buffer. Tannins were reacted with ferric chloride and analyzed spectrophotometrically. Monomeric non-protein-precipitable polyphenols were then analyzed via HPLC-DAD from the supernatant of the precipitation sample. This way, a more complete spectrum of compounds can be analyzed from the same plant tissue extract. With the fractionation suggested here, hydroxycinnamic acids and flavan-3-ols can be separated and quantified with good accuracy and precision. Possible applications include the assessment of plant stress and response monitoring using the total concentrations of polyphenols and tannins, as well as the ratios between those compound classes.

Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera.

Macro and micro nutrient accumulation affects all stages of plant growth and development. When nutrient deficiencies or excesses occur, normal plant growth is altered resulting in symptoms such as leaf chlorosis, plant stunting or death. In grapes, few genomic regions associated with nutrient accumulation or deficiencies have been identified. Our study evaluated micro and macro nutrient concentrations in Vitis vinifera L. to identify associated SNPs using an association approach with genotype by sequencing data. Nutrient concentrations and foliar symptoms (leaf chlorosis and stunting) were compared among 249 F1 Vitis vinifera individuals in 2015 and 2016. Foliar symptoms were consistent (≥90%) between years and correlated with changes in nutrient concentrations of magnesium (r = 0.65 and r = 0.38 in 2015 and 2016, respectively), aluminum (r = 0.24 and r = 0.49), iron (r = 0.21 and r = 0.49), and sodium (r = 0.32 and r = 0.21). Single nucleotide polymorphisms associated with symptoms, sodium, and magnesium were detected on each chromosome with the exception of 5, 7 and 17 depending on the trait and genome used for analyses explaining up to 40% of the observed variation. Symptoms and magnesium concentration were primarily associated with SNPs on chromosome 3, while SNPs associated with increased sodium content were primarily found on chromosomes 11 and 18. Mean concentrations for each nutrient varied between years in the population between symptomatic and asymptomatic plants, but relative relationships were mostly consistent. These data suggest a complex relationship among foliar symptoms and micro and macro nutrients accumulating in grapevines.

Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach.

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.

Identification of Vitis Cultivars, Rootstocks, and Species Expressing Resistance to a Planococcus Mealybug.

Mealybugs cause economic loss to vineyards through physical damage, fouling fruit and leaves with honeydew, and the transmission of viruses. Planococcus ficus is one of several mealybug species in vineyards, and one that causes economic damage over a relatively large global range. To develop novel management tools, host resistance to P. ficus, which has not previously been identified for any grape cultivars, was studied. Ten grape lines (species, cultivars, and rootstocks) were evaluated for P. ficus resistance across two separate potted plant assays. Significant differences were detected among cultivars and rootstocks in the recorded number of P. ficus juveniles, adults, and egg sacs. Cabernet Sauvignon and Chardonnay were two of the most favorable grape cultivars for mealybug population growth, whereas rootstocks IAC 572, 10-17A, and RS-3 all demonstrated some level of resistance. Southern fire ant (Solenopsis xyloni) was positively associated with mealybug populations, but did not have a negative effect on the observed presence of other arthropod species including potential predators.

Genetic Diversity, Population Structure, and Heritability of Fruit Traits in Capsicum annuum.

Cultivated pepper (Capsicum annuum) is a phenotypically diverse species grown throughout the world. Wild and landrace peppers are typically small-fruited and pungent, but contain many important traits such as insect and disease resistance. Cultivated peppers vary dramatically in size, shape, pungency, and color, and often lack resistance traits. Fruit characteristics (e.g. shape and pericarp thickness) are major determinants for cultivar selection, and their association with disease susceptibility can reduce breeding efficacy. This study evaluated a diverse collection of peppers for mature fruit phenotypic traits, correlation among fruit traits and Phytophthora fruit rot resistance, genetic diversity, population structure, and trait broad sense heritability. Significant differences within all fruit phenotype categories were detected among pepper lines. Fruit from Europe had the thickest pericarp, and fruit from Ecuador had the thinnest. For fruit shape index, fruit from Africa had the highest index, while fruit from Europe had the lowest. Five genetic clusters were detected in the pepper population and were significantly associated with fruit thickness, end shape, and fruit shape index. The genetic differentiation between clusters ranged from little to very great differentiation when grouped by the predefined categories. Broad sense heritability for fruit traits ranged from 0.56 (shoulder height) to 0.98 (pericarp thickness). When correlations among fruit phenotypes and fruit disease were evaluated, fruit shape index was negatively correlated with pericarp thickness, and positively correlated with fruit perimeter. Pepper fruit pericarp, perimeter, and width had a slight positive correlation with Phytophthora fruit rot, whereas fruit shape index had a slight negative correlation.

Genetic diversity, population structure, and resistance to Phytophthora capsici of a worldwide collection of eggplant germplasm.

Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.