Journal Search Engine
Download PDF Export Citation PMC Previewer
ISSN : 1225-5009(Print)
ISSN : 2287-772X(Online)
Flower Research Journal Vol.32 No.1 pp.14-20
DOI : https://doi.org/10.11623/frj.2024.32.1.02

Search Using Text Mining in R on Botrytis cinerea in Horticulture

Yong Kyun Lee1, Young Boon Lee2*
1Institute of Future Convergence Technologies, Korea East-West Power Co., Ltd., Ulsan 44543, Korea
2Department of Horticulture, Chonnam National University, Gwangju 61186, Korea


Correspondence to Young Boon Lee Tel: +82-62-530-2062 E-mail: floral@jnu.ac.kr
15/01/2024 24/03/2024

Abstract


This study utilized text mining analysis to identify keywords used in the research of gray mold (Botrytis cinerea), taking into account horticultural crops, environmental or physical treatments, and chemical or material factors. Data spanning from 1980 to 2021 was gathered from ScienceON and interpreted using word cloud visualization analysis following post-processing. Morphological analysis and coding were conducted using the text mining packages library tm provided by the R program. Our review of B. cinerea included and analyzed 7,342 papers. Among the extracted words, those related to crops and ranking in the top 10 were tomato, strawberry, grape, apple, cucumber, bean, kiwifruit, rose, pepper, and pear. roses were the only flower in the top 10 horticultural crops. Research has explored environmental or physical treatment factors such as storage, temperature, cold, seasons, humidity, heat/hot UV-C, sprays, films, and coatings. Chemical or material words included fungicide, chitosan, ethylene, oil, ROS, ABA, VOC, glucose, carbon, and ethanol.




초록


    Introduction

    Gray mold is a primary postharvest disease in floriculture crops (Ha et al. 2021), with Botrytis cinerea ranking second among the top 10 fungal pathogens affecting plants, following Magnapor theoryzae (Dean et al. 2012). Gray mold causes economic losses of millions of dollars worldwide (Lee and Kim 2019). During the distribution of cut flowers in Dutch flower auctions, gray mold causes losses in the market share of roses, gerberas, and lisianthus of 8-10%, 22-33%, and 50%, respectively (Vrind 2005). In Colombia and Kenya, economic losses due to gray mold in export-quality roses are 1.6% and 10-20%, respectively (Salgado-Salazar et al. 2018). Greenhouse-grown crops are especially at risk, particularly in Spain, Italy, Turkey, South Korea, and Japan (Rosslenbroich and Stuebler 2000).

    Infection is frequently facilitated by high relative humidity (> 93%) and temperatures of 15-20°C during postharvest storage and transportation (Fanourakis et al. 2013;Williamson et al. 1995). The physical control of B. cinerea may include low-temperature storage, hot-water or heat treatment, radiofrequency and microwave exposure, low and high-pressure treatments, UV-C treatment, or the use of a controlled and modified atmosphere (Nicot et al. 1996;West et al. 2000). Physical control methods are easy to implement because they are not harmful to humans and demand no technological innovations or regulations, so many studies have been conducted using these methods in recent years (Fallik 2004).

    Alternatively, chemical control involves treating plants with fungicides and pesticides (Roberts et al. 2003;van Jaarsveld 2018), while biological control options use Bacillus subtilis, Cladosporium cladosporioides, and Cladosporium oxysporum (Simone et al. 2020). Chemical control is relatively inexpensive, easily applied, and generally effective in preventing and controlling pathogens (Usall et al. 2016). However, the cost of chemical control to suppress gray mold on horticulture crops was in the millions of dollars, accounting for 10% of the global antifungal market share (Dean et al. 2012).

    Although many review papers have been published on gray mold, no studies have used the R program to code for text mining analysis and have considered the thesis according to a specific Korean site in analyzing (Krasnow and Ziv 2022; Table 1). In this study, we conducted a study to identify what keywords the study of gray mold (Botrytis cinerea) was studied a lot using a text mining in R analysis that considered horticultural crops, environmental or physical treatments, and chemical or material factors.

    Materials and Methods

    Search and article selections

    This study used text-mining techniques to understand domestic and international research trends on gray mold (Do et al. 2020). The data were collected from papers on B. cinerea in ScienceON (https://scienceon. kisti.re.kr). Data, including international and domestic articles, reports, and patents, could be sorted by year, journal name, researchers, research institutes, tables and graphs, and countries. Article abstracts comprised shorter sentences and succinct text, presenting only the most essential findings (Westergaard et al. 2018). These abstracts were extracted to form text from papers published between 1980 and 2021 and saved as Excel files. A total of 36,626 words were recognized in 7,342 paper abstracts.

    Data analysis

    Lim et al. (2014) proposed an unstructured data-cleaning model for text mining. To analyze the data related to B. cinerea, we conducted word extraction and preprocessing to analyze the 1,000 most common words, classifying inappropriate words, such as idioms, prepositions, adverbs, and units, into dictionaries and eliminating them (Lee 2020). With this model, the final dataset consisted of data not in the dictionary, and unnecessary words were removed using heuristic post-processing methods with R. The collected and post-processed data was interpreted through word cloud visualization (Fig. 1). Morphology analysis was performed through the text-mining package tm, provided by R (version 4.1.1, Sun et al. 2017).

    The final dataset was created through heuristic post-processing of words from morpheme analysis, and the results were visualized through the R wordcloud package. Words with similar meanings were grouped and treated as one word. Words with higher frequencies were displayed in larger fonts and positioned closer to the center (Do et al. 2020). A word cloud was created using the dplyr and stringr packages, which extracted 500 words that were identified more than 100 times (Lu 2018).

    Results and Discussion

    The top 10 keywords on B. cinerea of horticultural crops were tomato, strawberry, grape, apple, cucumber, bean, kiwifruit, rose, pepper, and pear (Tables 2 and Fig. 1). The roses on horticultural crops were in the top 10. Ha et al. (2021) studied chemical control approaches, radiation, biological controls, resistance inducers, and ethylene inhibitors to control B. cinerea in rose flowers. Roses, gerberas, and chrysanthemums account for a high proportion of plants affected by gray mold due to environmental factors such as distribution time, temperature, relative humidity, ethylene, dry and wet transportation methods, the accumulation of bacteria in preservation solutions, and airborne spores (Hoogerwerf et al. 1989).

    Previous research on B. cinerea through text mining analysis has been conducted to study environmental or physical factors. It included storage, temperature, cold, seasons, humidity, heat/hot, UV-C, sprays, films, and coatings (Table 2). The leading causes of B. cinerea postharvest losses are physical damage, poor packing, and issues related to transportation, storage, and handling (Nxumalo et al. 2021). The environmental and physical treatments to control gray mold that involves eco-friendly and residue-free technologies are particularly valued by consumers (Simone et al. 2020). However, these treatments could have low persistence, adversely affecting crop quality when commercially applied (Usall et al. 2016). Heat treatment is the most well-known physical treatment, typically involving hot water dips or rinsing and hot air (Usall et al. 2016). 50°C hot water dip treatment for 20-40 s was effective against gray mold in roses (Lee et al. 2016). Ultraviolet (UV) light is divided into long-wavelength UV-A (400-315 nm), medium-wavelength UV-B (315-280 nm), and short-wavelength UV-C (280-100 nm), which can be used to improve antioxidants and for sterilization purposes in horticultural crops (Lee and Kim 2018;Song and Lee 2012). The appropriate UV-C dosage for suppressing gray mold has been determined for roses (1.08 kJ·m-2) (Vega et al. 2020). Coatings inhibiting B. cinerea have been studied mainly with edible coatings in fruits rather than flowers.

    Chemical or material words included fungicide, chitosan, ethylene, oil, ROS, ABA, VOC, glucose, carbon, and ethanol (Table 2). Fungicide applications are the easiest method to control gray mold in many horticultural crops. Lee et al. (2006) confirmed the importance of post-harvest fungicide treatment because gray mold is likely to occur after harvest if only pre-harvest fungicide treatments are made. Fillinger and Elad (2016) reviewed the significant fungicides active against gray mold, and these fungicides are divided by their mode of action on respiration, cytoskeleton integrity, osmoregulation, amino-acid synthesis, and the synthesis of sterols such as dichlofuanid, fluazinam, and carbendazim. Some alternative fungicides have been studied for controlling gray mold in horticultural crops, including treatment with NaOCl, ClO2, CaSO4, CO2, plant extracts, hot water dips, and hot air on cut flowers (Fillinger and Elad 2016;Ha et al. 2021;Lee and Kim 2020;Usall et al. 2016). Pulsed treatments of 400 μM methyl jasmonate (C13H20O3) provided systemic protection against Botrytis rot by inducing resistance mechanisms in cut roses without impairing flower quality (Meir et al. 1998). Chitosan is a linear polysaccharide composed of D-glucosamine and N-acetyl-D-glucosamine linked by a β-(1→4) bond obtained by treating the exoskeleton of arthropods with alkaline solutions. It is the second most abundant biopolymer (Simone et al. 2020). Chitosan natural polymers are non-toxic, biodegradable, and active against B. cinerea, damaging hyphal cell walls (Ghaouth et al. 1994). Many ethylene inhibitors or action inhibitors, such as aminoethoxyvinylglycine (AVG), aminooxyacetic acid (AOA), silver thiosulphate (STS), 1-methylcyelopropene (1-MCP), and nano silver (NS) have been studied for their potential to control gray mold (Ha et al. 2021). Plant essential oils have the potential to replace synthetic fungicides in the management of postharvest diseases (Vitoratos et al. 2013). In a test of 49 essential oils, Wilson et al. (2007) found that palmarosa (Cymbopogon martini), red thyme (Thymus zygis), cinnamon leaf (Cinnamomum zeylanicum), and clove buds (Eugenia caryophyllata) had the most antifungal activity against B. cinerea occurring constituents of D-limonene, cineole, β-myrcene, α−pinene, β−pinene, and camphor. Reactive oxygen species (ROS), abscisic acid (ABA), and volatile organic compounds (VOCs) were also included in the materials identified through text mining (Table 2). The ROS levels of horticultural crops were related to the activities of antioxidant enzymes (Romanazzi et al. 2016). One paper analyzed VOCs influencing horticultural crop quality related to gray mold infection (Guigon-Lopez et al. 2021). Salts such as sodium potassium carbonate and ethanol were tested as control agents of gray mold, with both preharvest and postharvest applications (Romanazzi et al. 2010).

    In conclusion, the top 10 keywords on B. cinerea` of horticultural crops were tomato, strawberry, grape, apple, cucumber, bean, kiwifruit, rose, pepper, and pear. Roses were the only flower in the top 10 horticultural crops. Research has examined environmental or physical treatment factors such as storage, temperature, cold, seasons, humidity, heat, UV-C, sprays, films, and coatings. Chemical or material words included fungicide, chitosan, ethylene, oil, ROS, ABA, VOC, glucose, carbon, and ethanol.

    Acknowledgment

    This study was financially supported by Chonnam National University (Grant number: 2023-0518) and the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (No. 2021R 1G1A1094351).

    Figure

    FRJ-32-1-14_F1.gif

    Word cloud depicting the 100 most frequently utilized words within 7,342 article abstracts published after post-processing. The word cloud was created using the dplyr and stringr R packages (Lu 2018).

    Table

    Review papers on controlling Botrytis cinerea of environmental or physical treatments and chemical or material factors through text mining analysis since 2000.

    zUltraviolet-C.
    yReactive oxygen species.
    xModified atmosphere.
    wModified atmosphere packaging.
    vVolatile organic compounds.

    Top ten keywords on controlling Botrytis cinerea of environmental or physical treatments and chemical or material factors through text mining analysis.

    zRanked <i>Botrytis cinerea</i> keywords identified through text-mining analyses of 7,342 abstracts in articles on ScienceON. Morphology analysis was performed through the text mining package <i>tm</i> provided by R (version 4.1.1) (Sun et al. 2017).
    yReactive oxygen species
    xVolatile organic compounds.

    Reference

    1. Canito AD , Matro-Vargas MA , Mazzieri M , Cantoral J , Fosxhino R , Cordero-Bueso G , Vigentini I (2021) The role of yeasts as biocontrol agents for pathogenic fungi on postharvest grapes: A review. Foods 10:1650
    2. Dean R , van Kan JAL , Pretorius ZA , Hammond-Kosack KE , Pietro AD , Spanu PD , Rudd JJ , Dickman M , Kahmann R , Ellis J , Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414-430
    3. Do MS , Choi G , Hwang JW , Lee JY , Hur WH , Choi YS , Son SJ , Kwon IK , Yoo SY , Nam HK (2020) Research topics and trends of endangered species using text mining in Korea. J Asia Pac Biodivers 13:518-523
    4. Fallik E (2004) Prestorage hot water treatments (immersion: rinsing and brushing). Postharvest Biol Technol 32:125-134
    5. Fanourakis D , Pieruschka R , Savvides A , Macnish AJ (2013) Sources of vase life variation in cut roses: A reviews. Postharvest Biol Technol 78:1-15
    6. Fillinger S , Elad Y (2016) Botrytis – the fungus, the pathogen and its management in agricultural systems. Springer International Publishing, New York, NY, Retrieved from https://link.springer.com/book/10.1007/978-3-319-23371-0
    7. Ghaouth AE , Arul J , Benhamoun N (1994) Ultrastructural and cytochemical aspects of the effect of chitosan on decay of bell pepper fruit. Physiol Mol Plant Pathol 44:417-432
    8. Guigon-Lopez C , Holguín-Ibarra PD , Torres-Zapien JH , García-Cruz I , Villapando I , Salas-Salazare NA (2021) Metarhizium anisopliae reduces conidial germination and mycelium growth of the apple gray mold Botrytis cinerea. Biol Control 160:104660
    9. Ha STT , Choi B , In BC (2021) Nature and regulation of Botrytis cinerea in Rosa hybrida. Flower Res J 29: 129-137
    10. Hoogerwerf A , Pladdet FC , Kempkes MMJ , van Doorn WG (1989) Measurement of opinions on the relationship between environmental factors and keeping quality of ornamentals. Acta Hortic 261:240-248
    11. Jacometti MA , Wratten SD , Walter M (2010) Review: Alternatives to synthetic fungicides for Botrytis cinerea management in vineyards. J Grape Wine Res 16: 154-172
    12. Krasnow C , Ziv C (2022) Non-chemical approaches to control postharvest gray mold disease in bell peppers. Agronomy 12:216
    13. Lee JH , Choi JW , Hong YP , Kwon H (2016) Hot water dipping on reduction of grey mold (Botrytis cinerea) in cut rose ‘Antique Curl’. Flower Res J 24:304-311
    14. Lee JS , Han KS , Park JH , Cheong SR , Jang HI (2006) Control of gray mould (Botrytis cinerea) on roses by pre- and post-harvest treatment with agricultural chemicals. Res Plant Dis 12:249-253
    15. Lee WJ (2020) A study on word cloud techniques for analysis of unstructured text data. J Convergence Cult Technol 6:715-720
    16. Lee YB , Kim WS (2018) Effect of UV-B radiation timing on growth and antioxidants in edible flower pansy. Flower Res J 26:102-108
    17. Lee YB , Kim WS (2019) Effects on dipping treatment of chlorine dioxide to inhibitor Botrytis cinerea on exported cut rose flowers. Flower Res J 27:51-59
    18. Lee YB , Kim WS (2020) ClO2 dipping treatment inhibits gray mold on cut rose flowers during storage. Hortic J 89:496-501
    19. Lim SY , Lee MS , Jun SH , Shin DB (2014) A study on the research trends in the area of geospatial-information using text-mining technique focused on national R&D reports and theses. Spat Inf Res 22:11-20
    20. Lu Y (2018) Cybersecurity research: A review of current research topics. J Ind Integr Manag 3:1850014
    21. Ma PSC , Julia SC , Alitzel BGH , Georgina CD , Hortensia GV , Rubén OE , María CFM , Jorge YF (2021) Chitosan as a coating for biocontrol in postharvest products: A bibliometric review. Membranes 11:421
    22. Meir S , Droby S , Davidson H , Alsevia S , Cohen L , Horev B , Philosoph-Hadas S (1998) Suppression of Botrytis rot in cut rose flowers by postharvest application of methyl jasmonate. Postharvest Biol Technol 13:235-243
    23. Nicot PC , Mermier M , Vaissiere BE , Lagier J (1996) Differential spore production by Botrytis cinerea on agar medium and plant tissue under near-ultraviolet light-absorbing polyethylene film. Plant Dis 80:555-558
    24. Nxumalo KA , Aremu AO , Fawole OA (2021) Potentials of medicinal plant extracts as an alternative to synthetic chemicals in postharvest protection and preservation of horticultural crops: A review. Sustainability 13:5897
    25. Roberts AV , Debener T , Gudin S (2003) Encyclopedia of rose science (vol 1). Elsevier Academic Press, Cambridge, MA, pp 3-90
    26. Romanazzi G , Lichter A , Gabler FM , Smilanick JL (2012) Recent advances on the use of natural and safe alternatives to conventional methods to control postharvest gray mold of table grapes. Postharvest Biol Technol 63:141-147
    27. Romanazzi G , Gabler FM , Lichter A , Smilanick JL (2010) Natural and safe alternatives to conventional methods to control gray mold of table grapes in storage. Acta Hortic 905:161-167
    28. Romanazzi G , Sanzani SM , Bi Y , Tian S , Martínez PG , Alkan N (2016) Induced resistance to control postharvest decay of fruit and vegetables. Postharvest Biol Technol 122:82-94
    29. Rosslenbroich HJ , Stuebler D (2000) Botrytis cinerea — history of chemical control and novel fungicides for its management. Crop Prot 19:557-561
    30. Salgado-Salazar C , Shishkoff N , Daughtrey M , Plmer CL , Crouch JA (2018) Downy mildew: A serious disease threat to rose health worldwide. Plant Dis 102: 1873-1882
    31. Simone ND , Pace B , Grieco F , Chimienti M , Tyibilika V , Santoro V , Capozzi V , Colelli G , Spano G , Russo P (2020) Botrytis cinerea and table grapes: A review of the main physical, chemeical, and bio-based control treatments in postharvest. Foods 9:1138
    32. Song EK , Lee JH (2012) Plant responses to environmental stress. Expt Mol Med 32:36-43
    33. Sun H , Lim C , Lee YS (2017) Analysis of the yearbook from the Korea meteorological administration using a text-mining algorithm. J Korean Stat Soc 30: 603-613
    34. Usall J , Ippolito A , Sisquella M , Neri F (2016) Physical treatments to control postharvest diseases of fresh fruits and vegetables. Postharvest Biol Technol 122:30-40
    35. van Jaarsveld AJ (2018) Flower preservation method and device. United States Patent 9974309 B2.
    36. Vega K , Ochoa S , Patino LF , Herrera-Ramirez JA , Gomez JA , Qujano JC (2020) UV-C radiation for control of gray mold disease in postharvest cut roses. J Plant Prot Res 60:351-361
    37. Vitoratos A , Bilalis D , Karkanis A , Efthimiadou A (2013) Antifungal activity of plant essential oils against Botrytis cinerea, Penicillium italicum and Penicillium digitatum. Not Bot Horti Agrobot Cluj Napoca 41: 86-92
    38. Vrind TA (2005) The Botrytis problem in figures. Acta Hortic 699:99-102
    39. West JS , Pearson S , Hadley P , Wheldon AE , Davis FJ , Gilbert A , Henbest RGC (2000) Spectral filters for the control of Botrytis cinerea. Ann Appl Biol 136:115-120
    40. Westergaard D , Stærfeldt HH , Tønsberg C , Jensen LJ , Brunak S (2018) A comprehensive and quantitative comparison of text-mining in 15 million fulltext articles versus their corresponding abstracts. PLOS Comput Biol 14:1-16
    41. Williamson B , Duncan GH , Harrison JG , Harding LA , Elad Y , Zimand G (1995) Effect of humidity on infection of rose petals by dry-inoculated conidia of Botrytis cinerea. Mycol Res 99:1303-1310
    42. Wilson CL , Pathologist RP , Solar JM , EI Ghaouth A , Wisniewski ME (2007) Rapid evaluation of plant extracts and essential oils for antifungal activity against Botrytis cinerea. Plant Dis 81:204-210
    
    1. SEARCH
    2. Journal Abbreviation : 'Flower Res. J.'
      Frequency : Quarterly
      Doi Prefix : 10.11623/frj.
      ISSN : 1225-5009 (Print) / 2287-772X (Online)
      Year of Launching : 1991
      Publisher : The Korean Society for Floricultural Science
      Indexed/Tracked/Covered By :

    3. Online Submission

      submission.ijfs.org

    4. Template DOWNLOAD

      Original Research
      Articles
      국문 영문
      Review Articles 리뷰
      ★NEWTechnical Reports단보
      New Cultivar
      Introduction
      품종
    5. 논문유사도검사

    6. KSFS

      Korean Society for
      Floricultural Science

    7. Contact Us
      Flower Research Journal

      - Tel: +82-54-820-5472
      - E-mail: kafid@hanmail.net