References
- Adaskaveg JE, Förster H, Thompson DF. 2000. Identification and etiology of visible quiescent infections of Monilinia fructicola and Botrytis cinerea in sweet cherry fruit. Plant Dis. 84:328–333. doi:https://doi.org/10.1094/PDIS.2000.84.3.328.
- Agrios GN. 2005. Plant pathology. 5th ed. San Diego (CA): Elsevier Academic Press.
- Ahmad T, Liu Y. 2020. First record of Alternaria alternata causing postharvest fruit rot of sweet cherry (Prunus avium) in China. Plant Dis. 104:1–6. doi:https://doi.org/10.1094/PDIS-11-19-2322-PDN.
- Akbudak B, Tezcan H, Eris A. 2009. Evaluation of messenger plant activator as a preharvest and postharvest treatment of sweet cherry fruit under a controlled atmosphere. Int J Food Sci Nutr. 60:374–386. doi:https://doi.org/10.1080/09637480701712420.
- Akbulut M, Özcan M, Sökmen MA. 2008. Effects of postharvest treatments on physiological disorders and fungal rots of ’0900 Ziraat sweet cherry. Acta Hortic. 795:815–818. doi:https://doi.org/10.17660/ActaHortic.2008.795.131.
- Aktaruzzaman M, Afroz T, Kim B-S, Lee Y-G. 2017. Occurrence of postharvest gray mold rot of sweet cherry due to Botrytis cinerea in Korea. J Plant Dis Prot. 124:93–96. doi:https://doi.org/10.1007/s41348-016-0049-5.
- Almeida Da Silva G, Letícia Bernardi T, Dayane P, Schaker C, Agustini BC, Maria De Mello L, Valente P. 2016. Impact of fungicide residues on polymerase chain reaction and on yeast metabolism. Brazilian Arch Biol Technol. 59:1–7.
- Avenot HF, Michailides TJ. 2015. Detection of isolates of Alternaria alternata with multiple-resistance to fludioxonil, cyprodinil, boscalid and pyraclostrobin in California pistachio orchards. Crop Prot. 78:214–221. doi:https://doi.org/10.1016/j.cropro.2015.09.012.
- Barkai-Golan R. 2001. Postharvest diseases of fruits and vegetables: development and control. Amsterdam: Elsevier.
- BC Ministry of Agriculture. 2014. British Columbia agrifood industry year in review 2014. [accessed 2016 Dec 22]. http://www2.gov.bc.ca/assets/gov/farming-natural-resources-and-industry/agriculture-and-seafood/statistics/industry-and-sector-profiles/year-in-review/bcagrifood_yearinreview_2014.pdf.
- BC Ministry of Agriculture. 2017. Fast stats 2017: British Columbia’s agrifood and seafood sector. [accessed 2020 Apr 23]. https://www2.gov.bc.ca/assets/gov/farming-natural-resources-and-industry/agriculture-and-seafood/statistics/industry-and-sector-profiles/fast-stats/faststatsbc_2017.pdf.
- BC Ministry of Agriculture. 2018. 2018 British Columbia agrifood and seafood international export highlights. [accessed 2020 Apr 23]. https://www2.gov.bc.ca/assets/gov/farming-natural-resources-and-industry/agriculture-and-seafood/statistics/market-analysis-and-trade-statistics/2018_bc_agrifood_and_seafood_export_highlights.pdf.
- BC Tree Fruit Production Guide. 2017. Post-harvest rots. [accessed 2016 Dec 20]. http://www.bctfpg.ca/pest_guide/info/122/Post_Harvest_Rots.
- Bucher TB, Köppel R. 2016. Duplex digital droplet PCR for the determination of non-Basmati rice in Basmati rice (Oryza sativa) on the base of a deletion in the fragrant gene. Eur Food Res Technol. 242:927–934. doi:https://doi.org/10.1007/s00217-015-2599-3.
- Carmichael PC, Siyoum N, Jongman M, Korsten L. 2018. Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa. Sci Hortic (Amsterdam). 239:57–63. doi:https://doi.org/10.1016/j.scienta.2018.05.018.
- Cordova LG, Schnabel G. 2017. Meta-analysis of a web-based disease forecast system for control of Anthracnose and Botrytis fruit rots of strawberry in Southeastern United States. Plant Dis. 101:1910–1917. doi:https://doi.org/10.1094/PDIS-04-17-0477-RE.
- Delong JA, Saito S, Xiao C-L, Naegele RP. 2020. Population genetics and fungicide resistance of Botrytis cinerea on Vitis and Prunus spp. in California. Phytopathol. 110:694–702. doi:https://doi.org/10.1094/PHYTO-09-19-0362-R.
- Diguta CF, Rousseaux S, Weidmann S, Bretin N, Vincent B, Guilloux-Benatier M, Alexandre H. 2010. Development of a qPCR assay for specific quantification of Botrytis cinerea on grapes. FEMS Microbiol Lett. 313:81–87. doi:https://doi.org/10.1111/j.1574-6968.2010.02127.x.
- Dugan FM, Roberts RG. 1994. Etiology of preharvest colonization of Bing cherry fruit by fungi. Phytopathol. 84:1031–1036. doi:https://doi.org/10.1094/Phyto-84-1031.
- Elmer P, Michailides TJ. 2007. Epidemiology of Botrytis cinerea in orchard and vine crops. In: Elad Y, Williamson B, Tudzynski P, Delen N, editors. Botrytis: biology, pathology and control. Dordrecht (Netherlands): Springer; p. 243–272.
- Elmhirst J. 2006. Crop profile for sweet cherries in Canada. Ottawa, ON: Agriculture and Agri-Food Canada. http://www5.agr.gc.ca/resources/prod/doc/prog/prrp/pdf/cherry_e.pdf)
- Fairchild KL, Miles TD, Wharton PS. 2013. Assessing fungicide resistance in populations of Alternaria in Idaho potato fields. Crop Prot. 49:31–39. doi:https://doi.org/10.1016/j.cropro.2013.03.003.
- Fedele G, González-Domínguez E, Ammour MS, Languasco L, Rossi V. 2020. Reduction of Botrytis cinerea colonization of and sporulation on bunch trash. Plant Dis. 104:808–816. doi:https://doi.org/10.1094/PDIS-08-19-1593-RE.
- Gell I, De Cal A, Torres R, Usall J, Melgarejo P. 2009. Conidial density of Monilinia spp. on peach fruit surfaces in relation to the incidences of latent infections and brown rot. Eur J Plant Pathol. 123:415–424. doi:https://doi.org/10.1007/s10658-008-9378-y.
- Gillespie TJ. 1979. A predictive scheme for timing fungicide applications to control Alternaria leaf blight in carrots. Can J Plant Pathol. 1:95–99. doi:https://doi.org/10.1080/07060667909501469.
- Haddadderafshi N, Pósa TB, Péter G, Gáspár L, Ladányi M, Hrotkó K, Lukács N, Halász K. 2016. Characterization of community structure of culturable endophytic fungi in sweet cherry composite trees and their growth-retarding effect against pathogens. Acta Biol Hung. 67:269–285. doi:https://doi.org/10.1556/018.67.2016.3.5.
- Hahuly MV, Sumardiyono C, Wibowo A, Subandiyah S, Harper S. 2018. Identification of purple blotch pathogen of shallot by PCR using specific primer for Alternaria genus. Arch Phytopathol Plant Prot. 51:103–121. doi:https://doi.org/10.1080/03235408.2017.1384196.
- Hilje-Rodríguez I, Albertazzi FJ, Rivera-Coto G, Molina-Bravo R. 2020. A multiplex qPCR TaqMan-assay to detect fungal antagonism between Trichoderma atroviride (Hypocreaceae) and Botrytis cinerea (Sclerotiniaceae) in blackberry fruits using a de novo tef1-α- and an IGS-sequence based probes. Biotechnol Rep. 27:e00447. doi:https://doi.org/10.1016/j.btre.2020.e00447.
- Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, et al. 2011. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 83(22):8604–8610. doi:https://doi.org/10.1021/ac202028g
- Holz G, Gütschow M, Coertze S, Calitz FJ. 2003. Occurrence of Botrytis cinerea and subsequent disease expression at different positions on leaves and bunches of grape. Plant Dis. 87:351–358. doi:https://doi.org/10.1094/PDIS.2003.87.4.351.
- Hua SST, Palumbo JD, Parfitt DE, Sarreal SBL, O’Keeffe TL. 2018. Development of a droplet digital PCR assay for population analysis of aflatoxigenic and atoxigenic Aspergillus flavus mixtures in soil. Mycotoxin Res. 34:187–194. doi:https://doi.org/10.1007/s12550-018-0313-6.
- Iacomi-Vasilescu B, Avenot H, Bataillé-Simoneau N, Laurent E, Guénard M, Simoneau P. 2004. In vitro fungicide sensitivity of Alternaria species pathogenic to crucifers and identification of Alternaria brassicicola field isolates highly resistant to both dicarboximides and phenylpyrroles. Crop Prot. 23:481–488. doi:https://doi.org/10.1016/j.cropro.2003.10.003.
- Janisiewicz WJ, Korsten L. 2002. Biological control of postharvest diseases of fruit. Annu Rev Phytopathol. 40:411–441. doi:https://doi.org/10.1146/annurev.phyto.40.120401.130158.
- Kim TG, Jeong SY, Cho KS. 2014. Comparison of droplet digital PCR and quantitative real-time PCR for examining population dynamics of bacteria in soil. Appl Microbiol Biotechnol. 98:6105–6113. doi:https://doi.org/10.1007/s00253-014-5794-4.
- Kordalewska M, Brillowska-Dąbrowska A, Jagielski T, Dworecka-Kaszak B. 2015. PCR and real-time PCR assays to detect fungi of Alternaria alternata species. Acta Biochim Pol. 62:707–712. doi:https://doi.org/10.18388/abp.2015_1112.
- Larrabee MM 2019. Environmental effects on the presence and quantity of postharvest fungal pathogens on sweet cherry in the Okanagan Valley [MSc. Thesis]. Kelowna (BC): University of British Columbia.
- Lee HB, Patriarca A, Magan N. 2015. Alternaria in food: ecophysiology, mycotoxin production and toxicology. Mycobiology. 43:93–106. doi:https://doi.org/10.5941/MYCO.2015.43.2.93.
- Leiminger J, Bäßler E, Knappe C, Bahnweg G, Hausladen H. 2014. Quantification of disease progression of Alternaria spp. on potato using real-time PCR. Eur J Plant Pathol. 141:295–309. doi:https://doi.org/10.1007/s10658-014-0542-2.
- Ma Z, Felts D, Michailides TJ. 2003. Resistance to azoxystrobin in Alternaria isolates from pistachio in California. Pestic Biochem Physiol. 77:66–74. doi:https://doi.org/10.1016/j.pestbp.2003.08.002.
- Malarczyk D, Panek J, Frac M. 2019. Alternative molecular-based diagnostic methods of plant pathogenic fungi affecting berry crops—a review. Molecules. 24(7):1200. doi:https://doi.org/10.3390/molecules24071200
- McClellan WD, Hewitt WB. 1973. Early Botrytis rot of grapes: time of infection and latency of Botrytis cinerea Pers. in Vitis vinifera L. Phytopathol. 73:1151–1157.
- McDermott GP, Do D, Litterst CM, Maar D, Hindson CM, Steenblock ER, Legler TC, Jouvenot Y, Marrs SH, Bemis A, et al. 2013. Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR. Anal Chem. 85:11619–11627. doi:https://doi.org/10.1021/ac403061n
- Michailides TJ, Morgan DP, Luo Y, Prusky D, Gullino ML. 2010. Epidemiological assessments and postharvest disease incidence. In: Prusky D, Gullino ML, editors. Postharvest pathology. 1st ed. New York: Springer; p. 69–88.
- Miotke L, Lau BT, Rumma RT, Ji HP. 2014. High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR. Anal Chem. 86:2618–2624. doi:https://doi.org/10.1021/ac403843j.
- Mirmajlessi SM, Destefanis M, Gottsberger RA, Mänd M, Loit E. 2015. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev. 4:1–11. doi:https://doi.org/10.1186/2046-4053-4-9.
- Northover J, Biggs AR. 1990. Susceptibility of immature and mature sweet and sour cherries to Monilinia fructicola. Plant Dis. 75:280–284. doi:https://doi.org/10.1094/PD-74-0280.
- Palumbo JD, O ’Keeffe TL, Ho YS, Fidelibus MW. 2016. Population dynamics of Aspergillus Section Nigri species on vineyard samples of grapes and raisins. J Food Prot. 79:448–453. doi:https://doi.org/10.4315/0362-028X.JFP-15-437.
- Palumbo JD, O’Keeffe TL, Quejarro BJ, Yu A, Zhao A. 2019. Comparison of Aspergillus Section Nigri species populations in conventional and organic raisin vineyards. Curr Microbiol. 76:848–854. doi:https://doi.org/10.1007/s00284-019-01697-6.
- Pangga IB, Hanan J, Chakraborty S. 2011. Pathogen dynamics in a crop canopy and their evolution under changing climate. Plant Pathol. 60:70–81. doi:https://doi.org/10.1111/j.1365-3059.2010.02408.x.
- Pavón M, González I, Martín R, García Lacarra T. 2012. ITS-based detection and quantification of Alternaria spp. in raw and processed vegetables by real-time quantitative PCR. Food Microbiol. 32:165–171. doi:https://doi.org/10.1016/j.fm.2012.05.006.
- Pavón MÁ, González I, Rojas M, Pegels N, Martín R, García T. 2011. PCR detection of Alternaria spp. in processed foods, based on the internal transcribed spacer genetic marker. J Food Prot. 74:240–247. doi:https://doi.org/10.4315/0362-028X.JFP-10-110.
- Qiao X, Yin J, Yang Y, Zhang J, Shao B, Li H, Chen H. 2018. Determination of Alternaria mycotoxins in fresh sweet cherries and cherry-based products: method validation and occurrence. J Agric Food Chem. 66:11846–11853. doi:https://doi.org/10.1021/acs.jafc.8b05065.
- R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
- Roberts R, Reymond S, Andersen B. 2010. Alternaria cerasidanica sp. nov., isolated in Denmark from drupes of Prunus avium. Mycotaxon. 111:175–182. doi:https://doi.org/10.5248/111.175.
- Romanazzi G, Smilanick JL, Feliziani E, Droby S. 2016. Integrated management of postharvest gray mold on fruit crops. Postharvest Biol Technol. 113:69–76. doi:https://doi.org/10.1016/j.postharvbio.2015.11.003.
- Sanzani SM, Schena L, De Cicco V, Ippolito A. 2012. Early detection of Botrytis cinerea latent infections as a tool to improve postharvest quality of table grapes. Postharvest Biol Technol. 68:64–71.
- Selvaraj V, Maheshwari Y, Hajeri S, Chen J, Greg Mccollum T, Yokomi R. 2018. Development of a duplex droplet digital PCR assay for absolute quantitative detection of ‘Candidatus Liberibacter asiaticus’. PLoS One. 13:1–16. doi:https://doi.org/10.1371/journal.pone.0197184.
- Selvaraj V, Maheshwari Y, Hajeri S, Yokomi R. 2019. Droplet digital PCR for absolute quantification of plant pathogens. In: Khurana SMP, Gaur RK, editors. Plant biotechnology: progress in genomic era. Singapore: Springer; p. 583–595.
- Serrano M, Guillén F, Martínez-Romero D, Castillo S, Valero D. 2005. Chemical constituents and antioxidant activity of sweet cherry at different ripening stages. J Agric Food Chem. 53:2741–2745. doi:https://doi.org/10.1021/jf0479160.
- Si Ammour M, Fedele G, Morcia C, Terzi V, Rossi V. 2019. Quantification of Botrytis cinerea in grapevine bunch trash by real-time PCR. Phytopathol. 109:1312–1319. doi:https://doi.org/10.1094/PHYTO-11-18-0441-R.
- Suarez MB, Walsh K, Boonham N, O’Neill T, Pearson S, Barker I. 2005. Development of real-time PCR assays for the detection and quantification of Botrytis cinerea in planta. Plant Physiol Biochem. 43:890–899. doi:https://doi.org/10.1016/j.plaphy.2005.07.003.
- Tarbath MP, Measham PF, Glen M, Barry KM. 2014. Host factors related to fruit rot of sweet cherry (Prunus avium L.) caused by Botrytis cinerea. Australas Plant Pathol. 43:513–522. doi:https://doi.org/10.1007/s13313-014-0286-7.
- Taylor SC, Laperriere G, Germain H. 2017. Droplet digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep. 7:1–8. doi:https://doi.org/10.1038/s41598-017-02217-x.
- Wani AA, Singh P, Gul K, Wani H, Langowski HC. 2014. Sweet cherry (Prunus avium): critical factors affecting the composition and shelf life. Food Packag Shelf Life. 1:86–99. doi:https://doi.org/10.1016/j.fpsl.2014.01.005.
- Weerakoon KG, Gordon CA, Gobert GN, Cai P, Mcmanus DP. 2016. Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: a duplex approach with DNA binding dye chemistry. J Microbiol Methods. 125:19–27. doi:https://doi.org/10.1016/j.mimet.2016.03.012.
- Whale AS, Huggett JF, Tzonev S. 2016. Fundamentals of multiplexing with digital PCR. Biomol Detect Quantif. 10:15–23. doi:https://doi.org/10.1016/j.bdq.2016.05.002.
- White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T, editors. PCR protocols: a guide to methods and applications. New York: Academic; p. 315–322.
- Woudenberg JHC, Seidl MF, Groenewald JZ, De Vries M, Stielow JB, Thomma BPHJ, Crous PW. 2015. Alternaria section Alternaria: species, formae speciales or pathotypes? Stud Mycol. 82:1–21. doi:https://doi.org/10.1016/j.simyco.2015.07.001.
- Yin WX, Adnan M, Shang Y, Lin Y, Luo CX. 2018. Sensitivity of Botrytis cinerea from nectarine/cherry in China to six fungicides and characterization of resistant isolates. Plant Dis. 102:2578–2585. doi:https://doi.org/10.1094/PDIS-02-18-0244-RE.