Bioscience Method 2026, Vol.17 http://bioscipublisher.com/index.php/bm © 2026 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Bioscience Method 2026, Vol.17 http://bioscipublisher.com/index.php/bm © 2026 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. BioSci Publisher is an international Open Access publisher specializing in bioscience methods, including technology, lab tool, statistical software and relative fields registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher BioSci Publisher Editedby Editorial Team of Bioscience Methods Email: edit@bm.bioscipublisher.com Website: http://bioscipublisher.com/index.php/bm Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Bioscience Methods (ISSN 1925-1920) is an open access, peer reviewed journal published online by BioSci Publisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of bioscience, the range of topics including (but are not limited to) technology review, technique know-how, lab tool, statistical software and known technology modification. Case studies on technologies for gene discovery and function validation as well as genetic transformation. All the articles published in Bioscience Methods are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BioSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Bioscience Methods (online), 2026, Vol.17, No.1 ISSN 1925-1920 https://bioscipublisher.com/index.php/bm © 2026 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Biocontrol Agents for Managing Potato Pests and Diseases Hangshun Dong Bioscience Methods, 2026, Vol.16, No.1, 1-8 Application of Genome Editing in Pineapple Disease Resistance Breeding: CRISPR/Cas9 Strategies Chuchu Liu, Zhonggang Li Bioscience Methods, 2026, Vol.16, No.1, 9-22 The Effects of Different Harvesting Periods on the Moisture Content, Whole Kernel Rate and Eating Quality of Rice YuwenTu Bioscience Methods, 2026, Vol.16, No.1, 23-31 The Effects of Different Winter Pruning Intensities on The Proportion of Fruiting Branches and Fruit Quality of Kiwifruit ShudanYan Bioscience Methods, 2026, Vol.16, No.1, 32-42 The Effects of Different Potassium Fertilizer Application Rates on Sweet Potato Yield, Dry Matter Content and Sugar Accumulation Yanhong Zhong Bioscience Methods, 2026, Vol.16, No.1, 43-56 Recent Advances in Cucumber Cultivation for Maximizing Yield Wenzhong Huang, Kaiwen Liang Bioscience Methods, 2026, Vol.16, No.1, 57-66
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 1 Case Study Open Access Biocontrol Agents for Managing Potato Pests and Diseases Hangshun Dong Dongyang Crop Production Technology Extension Center (Plant Protection and Quarantine Station), Dongyang, 322100, Zhejiang, China Corresponding email: 805026882@qq.com Bioscience Methods, 2026, Vol.17, No.1 doi: 10.5376/bm.2026.17.0001 Received: 21 Dec., 2025 Accepted: 07 Jan., 2026 Published: 14 Jan., 2026 Copyright © 2026 Dong, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Dong H.S., 2026, Biocontrol agents for managing potato pests and diseases, Bioscience Methods, 17(1): 1-8 (doi: 10.5376/bm.2026.17.0001) Abstract Potato cultivation faces significant challenges from various pests and diseases, including insect infestations, fungal infections, and viral diseases, which can severely impact yield and crop quality. This study provides a systematic review of the application of biological control agents (BCAs) as sustainable alternatives to chemical pesticides in managing potato pests and diseases. It outlines the types of microbial control agents (such as fungi, bacteria, and viruses), natural predators and parasitoids, with a focus on their mechanisms of action, including antagonism, induction of systemic resistance, and competitive exclusion. The study also evaluates the effectiveness of integrating BCAs into integrated pest management (IPM) programs through field trials and case studies. The research highlights the importance of biological control agents in promoting sustainable potato cultivation and provides practical recommendations to enhance crop resilience and reduce dependence on chemical pesticides. Keywords Biocontrol agents; Potato pests and diseases; Integrated pest management (IPM); Antibiosis; Sustainable agriculture 1 Introduction Potato (Solanum tuberosum) is a staple crop worldwide, but its production is significantly hampered by various pests and diseases. Among the most notorious pathogens are Phytophthora infestans, causing late blight, and Rhizoctonia solani, responsible for black scurf and stem canker (Wang and Long, 2023). Other significant pathogens include Streptomyces scabies, which causes common scab, and Fusarium species, which lead to dry rot (Steglińska et al., 2022). These diseases not only reduce yield but also affect the quality of the tubers, leading to substantial economic losses. The conventional approach to managing potato pests and diseases has heavily relied on synthetic chemical pesticides and fungicides. While effective, these chemicals pose several challenges. They can lead to the development of resistant pathogen strains, negatively impact human health, and cause environmental degradation. Moreover, the stringent regulations and removal of various fungicides from the market further complicate disease management (Gush et al., 2023). The over-reliance on chemical control methods is increasingly seen as unsustainable, necessitating the exploration of alternative strategies (Cray et al., 2016; Feng et al., 2021). Biocontrol agents (BCAs) offer a promising alternative to synthetic chemicals, aligning with the principles of sustainable agriculture. These agents, including bacteria, fungi, and their metabolites, can effectively suppress potato pathogens through various mechanisms such as competition, antibiosis, and induction of plant resistance. For instance, Bacillus subtilis EG21 has shown antagonistic potential against P. infestans and R. solani, while Bacillus velezensis K-9 has been effective against Streptomyces scabies (Ma et al., 2023). Pseudomonas fluorescens LBUM223 has demonstrated efficacy in controlling common scab through the production of phenazine-1-carboxylic acid (Arseneault et al., 2016). The integration of BCAs into pest management strategies not only reduces the dependency on harmful chemicals but also promotes environmental health and sustainability. This study aims to explore the potential of biocontrol agents (BCAs) in managing potato pests and diseases, focusing on their mechanisms of action, efficacy, and practical applications. It seeks to provide a comprehensive understanding of how BCAs can be integrated into sustainable potato cultivation practices, including evaluating the effectiveness of various biocontrol agents and examining their interactions with pathogens to ensure the long-term viability of potato production.
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 2 2 Types of Biocontrol Agents in Potato Pest Management 2.1 Microbial biocontrol agents Microbial biocontrol agents are microorganisms such as bacteria, fungi, and oomycetes that can suppress or inhibit the growth of potato pathogens. These agents work through various mechanisms, including the production of antimicrobial compounds, competition for nutrients and space, and induction of plant resistance. Bacillus subtilis strains have shown significant potential in controlling potato pathogens. For instance, Bacillus subtilis EG21 has demonstrated strong antagonistic effects against Phytophthora infestans and Rhizoctonia solani through the production of cyclic lipopeptides and extracellular enzymes like cellulase, pectinase, and chitinase. Similarly, Bacillus velezensis K-9 has been effective in managing potato scab caused by Streptomyces scabies, reducing disease symptoms and increasing potato yield (Ma et al., 2023). Lactic acid bacteria (LAB) such as Lactiplantibacillus plantarum KB2 LAB 03 have also been identified as effective biocontrol agents. This strain has shown a significant reduction in the infestation of multiple potato pathogens, including Pectobacterium carotovorum and Rhizoctonia solani, by producing organic acids and other antimicrobial metabolites (Steglińska et al., 2022). Arbuscular mycorrhizal fungi (AMF) and endophytic fungi like Epicoccum nigrumASU11 have been used to control blackleg disease caused by Pectobacterium carotovora. These fungi enhance plant growth and induce systemic resistance, reducing disease severity and improving potato yield (Bagy et al., 2019). 2.2 Natural predators and parasitoids Natural predators and parasitoids are another group of biocontrol agents that can help manage potato pests. These organisms prey on or parasitize pest species, thereby reducing their populations and the damage they cause to potato crops. Various insects and mites can serve as biological control agents. For example, lady beetles (Coccinellidae) and lacewings (Chrysopidae) are known to prey on aphids, which are common pests in potato fields (Volynchikova and Kim, 2022). Similarly, parasitoid wasps can target and parasitize the larvae of potato tuber moths, reducing their impact on potato crops. 3 Mechanisms of Action of Biocontrol Agents 3.1 Antagonism and competition Biocontrol agents (BCAs) often employ antagonism and competition to suppress potato pests and diseases. This involves the production of antimicrobial compounds, competition for nutrients and space, and direct parasitism of pathogens. For instance, Bacillus subtilis EG21 produces cyclic lipopeptides such as surfactins, which exhibit strong anti-oomycete and zoosporecidal effects against Phytophthora infestans. Rhizosphere bacteria isolated from resistant potato plants, including Streptomyces and Pseudomonas species, have shown significant inhibitory effects on the mycelium growth of P. infestans through the production of cellulase and catalase (Feng et al., 2021). These mechanisms highlight the potential of BCAs to outcompete and directly antagonize pathogens, thereby reducing disease incidence. 3.2 Induction of host plant resistance 3.2.1 Activation of systemic acquired resistance (SAR) in potato plants Systemic acquired resistance (SAR) is a plant defense mechanism that is activated in response to pathogen attack, leading to enhanced resistance throughout the plant. The co-treatment of potato plants with Bacillus thuringiensis B-5351 and salicylic acid (SA) has been shown to significantly increase the transcriptional activity of SAR-related genes such as PR1 and PAL, which are crucial for the plant's defense against P. infestans (Sorokan et al., 2021). This combined treatment not only enhances the plant's resistance to late blight but also increases the population of beneficial bacteria within the plant tissues, further contributing to disease suppression. 3.2.2 Enhancement of the plant’s immune response Biocontrol agents can also enhance the plant's immune response through the induction of induced systemic resistance (ISR) and mycorrhizal-induced resistance (MIR). For example, the dual inoculation of potato plants
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 3 with Pseudomonas sp. R41805 and Rhizophagus irregularis MUCL 41833 has been shown to elicit the expression of ethylene response factor 3 (ERF3), which plays a significant role in pathogen defense (Velivelli et al., 2015). This enhancement of the plant's immune response through complex signaling networks involving salicylic acid, jasmonic acid, and ethylene, provides a robust defense mechanism against various pathogens. 3.3 Direct pathogen and pest attack BCAs directly attack pathogens and pests through mechanisms such as hyperparasitism, production of lytic enzymes, and release of antimicrobial compounds. For instance, Bacillus subtilis EG21 produces extracellular lytic enzymes, including cellulase, pectinase, and chitinase. Cellulase degrades the cellulose components in the cell walls of pathogens, disrupting their structural integrity. Pectinase acts by breaking down pectin in plant cell walls, further weakening the pathogen's adhesion to plant tissues. Chitinase is particularly crucial for degrading the main chitin component of fungal cell walls, demonstrating significant effectiveness against fungal pathogens. These enzymes cause extensive damage to the hyphae of Rhizoctonia solani and inhibit the infection of Phytophthora infestans. Experimental results indicate that the lytic enzymes secreted by Bacillus subtilis EG21 significantly inhibited the growth of Rhizoctonia solani in vitro. Microscopic observations revealed marked deformation, swelling, and rupture of the pathogen's hyphae, further confirming the critical role of lytic enzymes in disrupting the structure of the pathogens (Figure 1) (Alfiky et al., 2022). Similarly, microbial biopesticides can produce antimicrobial compounds that inhibit pathogen growth and virulence factors, thereby directly reducing disease incidence. These direct interactions between BCAs and pathogens are crucial for effective biocontrol in potato crops. Figure 1 Representative images for A, potato tuber slices at 4 days postinoculation (dpi) as they were treated with bacterial cells (left), Bacillus subtilis EG21 culture filtrate (middle), and Luria Bertani broth as control (right), and then inoculated with Rhizoctonia solani. B, Lytic enzyme activities in EG21 for cellulase (left) and pectinase (right) (Adopted from Alfiky et al., 2022) 4 Application Strategies for Biocontrol Agents in Potato Cultivation 4.1 Soil and seed treatment Soil and seed treatments are critical strategies for the effective application of biocontrol agents in potato cultivation. These treatments involve the introduction of beneficial microorganisms directly into the soil or onto the seed tubers to suppress soil-borne pathogens and enhance plant health. For instance, Bacillus velezensis K-9 has been shown to significantly reduce potato scab caused by Streptomyces scabies when applied to the soil, leading to improved tuber quality and increased yields (Gush et al., 2023). Similarly, Brevibacillus laterosporus
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 4 BL12 has demonstrated the ability to colonize the tuberosphere and rhizosphere soils, altering the soil bacterial community to suppress potato common scab (Li et al., 2021). The use of Fusarium oxysporum strain Fo47 as a soil treatment has also been explored, with successful re-isolation from inoculated plants in field trials, indicating its potential for large-scale application (Constantin et al., 2020). These examples highlight the importance of soil and seed treatments in establishing a protective microbial environment around potato plants. 4.2 Foliar application Foliar application involves spraying biocontrol agents directly onto the leaves of potato plants to combat foliar pathogens. This method is particularly effective against diseases such as early blight caused by Alternaria solani. Azospirillum lipoferum AL-3, when applied as a foliar spray, significantly reduced early blight severity and increased tuber yield by inducing systemic resistance in potato plants (Mehmood et al., 2021). The foliar application of Bacillus subtilis EG21 has also shown promise, with its metabolites exhibiting strong anti-oomycete and zoosporecidal effects against Phytophthora infestans, the causative agent of late blight (Alfiky et al., 2022). These findings suggest that foliar application of biocontrol agents can be an effective strategy for managing foliar diseases in potato cultivation. 4.3 Integration with other pest management practices Integrating biocontrol agents with other pest management practices is essential for achieving sustainable and effective pest control in potato cultivation. This integrated approach, known as Integrated Pest Management (IPM), combines biological, cultural, and chemical methods to manage pests and diseases. For example, combining biocontrol agents such as Pochonia chlamydosporia and Purpureocillium lilacinum with trap cropping using Solanum sisymbriifoliumhas shown promise in managing potato cyst nematodes (PCN) (Mhatre et al., 2022). The use of biocontrol agents like Bacillus subtilis EG21 in conjunction with other IPM strategies can enhance disease suppression and reduce reliance on synthetic chemicals. The integration of biocontrol agents with other pest management practices not only improves efficacy but also promotes environmental sustainability and reduces the risk of pathogen resistance. 5 Case Studies of Successful Biocontrol Implementation 5.1 Control of potato late blight (Phytophthora infestans) Potato late blight, caused by Phytophthora infestans, is a devastating disease affecting potato crops worldwide. Traditional management relies heavily on synthetic fungicides, which pose environmental and health risks. Biocontrol agents offer a promising alternative. For instance, Bacillus subtilis H17-16 has shown significant potential in inhibiting P. infestans by producing protease, volatile compounds, and forming biofilms, which enhance plant resistance and promote growth. Field applications of H17-16, especially when combined with chitosan or chemical fungicides, have effectively reduced late blight incidence (Zhang et al., 2023). Trichoderma spp. have demonstrated multifaceted biocontrol strategies, including direct mycoparasitism, competition for nutrients, and antibiosis, significantly inhibiting P. infestans both in vitro and in planta (Alfiky et al., 2023). Essential oils (EOs) have also been explored for their anti-oomycete activities, showing promise as sustainable biopesticides (Martini et al., 2023). These biocontrol agents, when integrated into pest management programs, can significantly reduce the reliance on chemical fungicides and enhance sustainable agriculture practices. 5.2 Management of Colorado potato beetle (Leptinotarsa decemlineata) The Colorado potato beetle (CPB) is a major pest of potato crops, notorious for its resistance to multiple insecticides. Innovative biocontrol strategies are being developed to manage this pest. Ledprona, a sprayable double-stranded RNA biopesticide, targets the proteasome subunit beta type-5 in CPB, triggering the RNA interference pathway. Laboratory and greenhouse trials have shown that Ledprona can achieve up to 90% mortality in CPB larvae, demonstrating efficacy comparable to traditional insecticides like spinosad (Rodrigues et al., 2021; Dzedaev et al., 2023). Another approach involves the use of Bacillus subtilis 26DCryChS, which produces Cry1Ia toxin fromBacillus thuringiensis. A key advantage of Bacillus subtilis 26DCryChS is its ability to function as an endophytic bacterium, effectively colonizing the internal tissues of plants, particularly showing strong endophytic capabilities
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 5 in potato plants. This strain can persist stably within plant tissues and is less affected by external environmental factors, such as UV radiation and rain wash-off, thereby ensuring its continuous action within the plant. The strain not only inhibits Phytophthora infestans but also exhibits insecticidal activity against the Colorado potato beetle (CPB). By expressing the Cry1Ia toxin, the strain demonstrates potent insecticidal activity against pests. When insects feed on plant tissues containing the 26DCryChS strain, the Cry1Ia toxin disrupts the insect’s gut cells, causing severe intestinal damage and ultimately leading to insect death (Figure 2). Figure 2 Mesenteron structure of L. decemlineatabeetles 24 h after feeding of potato plants, which contained cells of Bacillus strains. Scale bars, 200 μm. (I) Healthy larva; (II) bacteriosis on alive larva on the 5th day after eating of plants containing Bacillus sp. (Adopted from Sorokan et al., 2020) 5.3 Control of rhizoctonia root rot Rhizoctonia root rot, caused by Rhizoctonia solani, is another significant disease affecting potato crops. Bacillus subtilis EG21 has shown strong antagonistic potential against both P. infestans and R. solani. The strain produces cyclic lipopeptides, such as surfactins, which exhibit antifungal and anti-oomycete activities. Microscopic examinations have revealed extensive damage to R. solani mycelium upon interaction with EG21. The cell-free culture filtrate (CF) of EG21 has been found to be chemically stable and effective in inhibiting the growth of both pathogens under various conditions (Alfiky et al., 2022). Field applications of EG21 have confirmed its disease-inhibiting effects, making it a promising candidate for integrated pest management strategies aimed at controlling Rhizoctonia root rot and other potato diseases. 6 Challenges and Limitations of Biocontrol Agents 6.1 Variability in field performance One of the primary challenges in the application of biocontrol agents for managing potato pests and diseases is the variability in their performance under field conditions. While laboratory and greenhouse experiments often show promising results, translating these findings to the field has proven problematic. For instance, biocontrol agents such as Bacillus sp. JC12GB43 have shown near-complete inhibition of pathogens in controlled environments but exhibited variable efficacy in the field due to differing environmental conditions (Cray et al., 2016; Yang, 2024). Similarly, the endophytic microbe Fusarium oxysporum 47 (Fo47) demonstrated effective biocontrol in laboratory settings, but its performance in large-scale field trials was inconsistent, highlighting the challenge of maintaining inoculum viability and effectiveness in diverse agricultural environments (Constantin et al., 2020). This variability necessitates extensive field trials and optimization of application methods to achieve reliable results.
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 6 6.2 Regulatory and commercialization hurdles The regulatory landscape for biocontrol agents poses significant hurdles to their commercialization and widespread adoption. The process of obtaining regulatory approval for new biocontrol agents is often lengthy and complex, involving rigorous testing to ensure safety and efficacy. This can be a deterrent for companies looking to invest in the development and commercialization of biocontrol products. Additionally, the economic feasibility of biocontrol agents is influenced by the costs associated with their development and regulatory approval. For example, the introduction of biocontrol for wireworms in potato cultivation has been found to be economically viable, but the high costs and regulatory hurdles can limit the adoption of such strategies (Benjamin and Wesseler, 2016; Naqqash et al., 2020). These challenges underscore the need for streamlined regulatory processes and economic incentives to promote the use of biocontrol agents in integrated pest management (IPM) programs. 6.3 Compatibility with conventional agricultural practices Integrating biocontrol agents into conventional agricultural practices presents another set of challenges. Biocontrol agents must be compatible with existing farming practices and other pest management strategies to be effective. For instance, the use of Bacillus subtilis EG21 and its metabolites has shown promise in controlling potato pathogens, but its integration into conventional farming systems requires careful consideration of its interactions with other agricultural inputs and practices (Alfiky et al., 2022). The success of biocontrol agents often depends on their ability to work synergistically with other methods in IPM programs. The combination of multiple biocontrol agents or their integration with chemical treatments can enhance efficacy, but this requires a thorough understanding of their modes of action and potential interactions (Wang and Long, 2023). Ensuring compatibility with conventional practices is crucial for the successful adoption and implementation of biocontrol strategies in potato cultivation. 7 Innovations in Biocontrol Agent Development And Deployment 7.1 Discovery of novel biocontrol strains The discovery of novel biocontrol strains has been pivotal in advancing sustainable agricultural practices. For instance, Bacillus subtilis EG21 has shown significant antagonistic potential against potato pathogens Phytophthora infestans and Rhizoctonia solani, producing stable antifungal metabolites such as cyclic lipopeptides. Similarly, Bacillus sp. JC12GB43 has demonstrated near-complete inhibition of Phytophthora and Fusarium species under specific environmental conditions, although it can also stimulate pathogen proliferation under certain stress conditions (Cray et al., 2016; Yang and Fu, 2024). Another promising strain, Bacillus velezensis K-9, has been effective in managing potato scab, significantly reducing disease symptoms and increasing potato yield (Ma et al., 2023). Brevibacillus laterosporus BL12 has been shown to suppress potato common scab by altering the soil bacterial community, promoting beneficial bacteria that aid in disease control. 7.2 Advanced formulation techniques Advanced formulation techniques are crucial for enhancing the efficacy and stability of biocontrol agents. The metabolites produced by Bacillus subtilis EG21, for example, have been found to be stable under high-temperature/pressure treatments and extreme pH values, making them suitable for various agricultural applications (Alfiky et al., 2022). The combination of arbuscular mycorrhizal fungi (AMF) and endophytic strain Epicoccum nigrum ASU11 has also been effective in controlling potato blackleg, with the biocontrol agents promoting systemic plant resistance and enhancing potato growth (Bagy et al., 2019). The complete genome sequencing of Streptomyces angustmyceticus CQUSa03 has provided insights into its potential for producing a variety of antagonistic compounds, providing a basis for the development of robust biocontrol formulations (Luo et al., 2022). 7.3 Data-driven optimization of biocontrol application Data-driven approaches are essential for optimizing the application of biocontrol agents. For instance, the population dynamics and gene expression of Pseudomonas fluorescens LBUM223 have been studied to understand its biocontrol efficacy against potato common scab. High populations of LBUM223 and increased expression of the phenazine-1-carboxylic acid biosynthetic gene were associated with effective disease control
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 7 (Arseneault et al., 2016). The use of multiple bacterial strains isolated from the rhizosphere of resistant potato plants has shown significant inhibition of Phytophthora infestans, with field trials indicating enhanced microbial diversity and reduced pathogen abundance (Feng et al., 2021). These findings underscore the importance of integrating biocontrol agents with data-driven strategies to achieve optimal pest and disease management in potato cultivation. Acknowledgments Thanks to Dr Chen for her assistance in references collection and discussion for this work completion. Conflict of Interest Disclosure The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Abd-Elgawad M., 2020, Biological control agents in the integrated nematode management of potato in Egypt, Egyptian Journal of Biological Pest Control, 30(1): 1-13. https://doi.org/10.1186/s41938-020-00325-x Alfiky A., Abou-Mansour E., Vrieze M., Haridon F., and Weisskopf L., 2023, Newly isolated Trichoderma spp. show multifaceted biocontrol strategies to inhibit potato late blight causal agent Phytophthora infestans both in vitro and in planta, Phytobiomes Journal, 7(3): 278-292. https://doi.org/10.1094/pbiomes-01-23-0002-r Alfiky A., L’Haridon F., Abou-Mansour E., and Weisskopf L., 2022, Disease inhibiting effect of strain Bacillus subtilis EG21 and its metabolites against potato pathogens Phytophthora infestans and Rhizoctonia solani, Phytopathology, 112(9): 1890-1901. https://doi.org/10.1094/PHYTO-12-21-0530-R Arseneault T., Goyer C., and Filion M., 2016, Biocontrol of potato common scab is associated with high Pseudomonas fluorescens LBUM223 populations and phenazine-1-carboxylic acid biosynthetic transcript accumulation in the potato geocaulosphere, Phytopathology, 106(9): 963-970. https://doi.org/10.1094/PHYTO-01-16-0019-R Bagy H., Hassan E., Nafady N., and Dawood M., 2019, Efficacy of arbuscular mycorrhizal fungi and endophytic strain Epicoccum nigrumASU11 as biocontrol agents against blackleg disease of potato caused by Pectobacterium carotovora subsp. atrosepticum, Biological Control, 134: 103-111. https://doi.org/10.1016/J.BIOCONTROL.2019.03.005 Benjamin E., and Wesseler J., 2016, A socioeconomic analysis of biocontrol in integrated pest management: A review of the effects of uncertainty, irreversibility and flexibility, NJAS: Wageningen Journal of Life Sciences, 77: 53-60. https://doi.org/10.1016/j.njas.2016.03.002 Constantin M., Lamo F., Rep M., and Takken F., 2020, From laboratory to field: applying the Fo47 biocontrol strain in potato fields, European Journal of Plant Pathology, 158(3): 645-654. https://doi.org/10.1007/s10658-020-02106-6 Cray J., Connor M., Stevenson A., Houghton J., Rangel D., Cooke L., and Hallsworth J., 2016, Biocontrol agents promote growth of potato pathogens, depending on environmental conditions, Microbial Biotechnology, 9(3): 330-354. https://doi.org/10.1111/1751-7915.12349 Dzedaev H., Gazdanova I., and Bekmurzov B., 2023, Biological control of Phytophthora infestans in potatoes, Agrarian Bulletin, 23(9): 2-10. https://doi.org/10.32417/1997-4868-2023-23-09-2-10 El-Hasan A., Ngatia G., Link T., and Voegele R., 2022, Isolation, identification, and biocontrol potential of root fungal endophytes associated with solanaceous plants against potato late blight (Phytophthora infestans), Plants, 11(12): 1605. https://doi.org/10.3390/plants11121605 Feng S., Jin L., Tang S., Jian Y., and Li Z., 2021, Combination of rhizosphere bacteria isolated from resistant potato plants for biocontrol of potato late blight, Pest Management Science, 77(10): 4586-4597. https://doi.org/10.1002/ps.6618 Gush S., Lebre P., Coutinho T., Cowan D., and van der Waals J., 2023, Disentangling shifts in the soil microbiome of potatoes infected with Rhizoctonia solani AG 3-PT in search of potential biocontrol agents, Phytobiomes Journal, 7(4): 365-379. https://doi.org/10.1094/pbiomes-06-23-0046-r Li C., Shi W., Wu D., Tian R., Wang B., Lin R., Zhou B., and Gao Z., 2021, Biocontrol of potato common scab by Brevibacillus laterosporus BL12 is related to the reduction of pathogen and changes in soil bacterial community, Biological Control, 153: 104496. https://doi.org/10.1016/j.biocontrol.2020.104496 Luo X., Qu J., and Ren M., 2022, Complete genome sequence data of a novel Streptomyces angustmyceticus strain CQUSa03, a potential biological control agent for potato oomycete and fungal diseases, Plant Disease, 106(12): 3531-3533. https://doi.org/10.1094/PDIS-08-22-1927-A Ma S., Wang T., and Wang Y., 2023, Bacillus velezensis K-9 as a potential biocontrol agent for managing potato scab, Plant Disease, 107(9): 2718-2726. https://doi.org/10.1094/PDIS-12-22-2829-RE
Bioscience Methods 2026, Vol.17, No.1, 1-8 http://bioscipublisher.com/index.php/bm 8 Martini F., Jijakli M., Gontier E., Muchembled J., and Fauconnier M., 2023, Harnessing plant’s arsenal: essential oils as promising tools for sustainable management of potato late blight disease caused by Phytophthora infestans—a comprehensive review, Molecules, 28(21): 7302. https://doi.org/10.3390/molecules28217302 Mehmood T., Li G., Anjum T., and Akram W., 2021, Azospirillum lipoferum strain AL-3 reduces early blight disease of potato and enhances yield, Crop Protection, 139: 105349. https://doi.org/10.1016/j.cropro.2020.105349 Mhatre P., Dandnaik L., Venkatesan P., Watpade S., Bairwa A., and Patil J., 2022, Management of potato cyst nematodes with special focus on biological control and trap cropping strategies, Pest Management Science, 78(9): 3721-3736. https://doi.org/10.1002/ps.7022 Naqqash M., Gökçe A., Aksoy E., and Bakhsh A., 2020, Downregulation of imidacloprid-resistant genes alters the biological parameters in Colorado potato beetle Leptinotarsa decemlineata, Chemosphere, 240: 124857. https://doi.org/10.1016/j.chemosphere.2019.124857 Rodrigues T., Mishra S., Sridharan K., Barnes E., Alyokhin A., Tuttle R., Kokulapalan W., Garby D., Skizim N., Tang Y., Manley B., Aulisa L., Flannagan R., Cobb C., and Narva K., 2021, First sprayable double-stranded RNA-based biopesticide product targets proteasome subunit beta type-5 in Colorado potato beetle (Leptinotarsa decemlineata), Frontiers in Plant Science, 12: 728652. https://doi.org/10.3389/fpls.2021.728652 Sorokan A., Benkovskaya G., Burkhanova G., Blagova D., and Maksimov I., 2020, Endophytic strain Bacillus subtilis 26DCryChS producing Cry1Ia toxin promotes multifaceted potato defense against Phytophthora infestans andLeptinotarsa decemlineata, Plants, 9(9): 1115. https://doi.org/10.3390/plants9091115 Sorokan A., Burkhanova G., Alekseev V., and Maksimov I., 2021, Influence of co-treatment with Bacillus thuringiensis B-5351 and salicylic acid on resistance of potato plants to Phytophthora infestans, Siberian Journal of Life Sciences and Agriculture, 53(6): 109-130. https://doi.org/10.17223/19988591/53/6 Steglińska A., Kołtuniak A., Berłowska J., Czyżowska A., Szulc J., Cieciura-Włoch W., Okrasa M., Kręgiel D., and Gutarowska B., 2022, Metschnikowia pulcherrima as a biocontrol agent against potato (Solanum tuberosum) pathogens, Agronomy, 12(10): 2546. https://doi.org/10.3390/agronomy12102546 Velivelli S., Loján P., Cranenbrouck S., Boulois H., Suárez J., Declerck S., Franco J., and Prestwich B., 2015, Induction of ethylene response factor 3 in potato as a result of co-inoculation with Pseudomonas sp. R41805 and Rhizophagus irregularis MUCL 41833, Plant Signaling & Behavior, 10(1): e988076. https://doi.org/10.4161/15592324.2014.988076 Vero S., Garmendia G., Allori E., Sanz J., Gonda M., Alconada T., Cavello I., Dib J., Díaz M., Nally C., Pimenta R., Silva J., Vargas M., Zaccari F., and Wisniewski M., 2023, Microbial biopesticides: diversity, scope, and mechanisms involved in plant disease control, Diversity, 15(3): 457. https://doi.org/10.3390/d15030457 Volynchikova E., and Kim K., 2022, Biological control of oomycete soilborne diseases caused by Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae in solanaceous crops, Mycobiology, 50(4): 269-293. https://doi.org/10.1080/12298093.2022.2136333 Wang W., and Long Y., 2023, A review of biocontrol agents in controlling late blight of potatoes and tomatoes caused by Phytophthora infestans and underlying mechanisms, Pest Management Science, 79(8): 3095-3110. https://doi.org/10.1002/ps.7706 Yang J.R., 2024, Molecular identification and breeding strategies of rice blast resistance genes, Rice Genomics and Genetics, 15(2): 69-79. https://doi.org/10.5376/rgg.2024.15.0008 Yang P.P., and Fu J., 2024, Pantoea ananatis: emerging bacterial pathogen in wheat fields, Molecular Pathogens, 15(2): 83-92. https://doi.org/10.5376/mp.2024.15.0009 Zhang J., Huang X., Yang S., Huang A., Ren J., Luo X., Feng S., Li P., Li Z., and Dong P., 2023, Endophytic Bacillus subtilis H17-16 effectively inhibits Phytophthora infestans and its potential application, Pest Management Science, 79(9): 3428-3440. https://doi.org/10.1002/ps.7717
Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 9 Research Insight Open Access Application of Genome Editing in Pineapple Disease Resistance Breeding: CRISPR/Cas9 Strategies ChuchuLiu 1,2 , Zhonggang Li 2 1 Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China 2 Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: chuchu.liu@cuixi.org Bioscience Methods, 2026, Vol.17, No.1 doi: 10.5376/bm.2026.17.0002 Received: 01 Dec., 2025 Accepted: 04 Jan., 2026 Published: 19 Jan., 2026 Copyright © 2026 Liu and Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Liu C.C., and Li Z.G., 2026, Application of genome editing in pineapple disease resistance breeding: CRISPR/Cas9 strategies, Bioscience Methods, 17(1): 9-22 (doi: 10.5376/bm.2026.17.0002) Abstract The three main causes of yield loss in pineapple crops include heart rot and black rot and leaf spot. Breeding new types in the usual way takes many years. The crop maintains a restricted genetic diversity because it cannot produce self-pollination and requires extended periods for growth and testing. The research evaluates CRISPR/Cas9 as a fast method to introduce disease resistance. We show the main defense routes, such as SA, JA/ET, and MAPK. We implement editing approaches which have proven effective in different plant species. The main ways are: (i) change promoters or switch on defense genes; (ii) remove susceptibility genes and genes that decrease defense; (iii) modify control sites such as miRNA binding sites; and (iv) edit multiple genes simultaneously to build resistance. Some problems remain. The regeneration rate is low and edited plants can be mosaic and pineapple has high heterozygosity and off-target hits can occur. The solutions for this problem include tissue culture improvement and morphogenic regulator addition and nuclease precision enhancement and RNP delivery without DNA. Our approach consists of three phases which begin with omics-based target selection followed by DNA-free multiplex editing and end with field testing and compliance with transgene-free plant regulations. The described methods enable pineapples to develop robust and extensive resistance that can be used by breeders to create new plant lines. Keywords Pineapple (Ananas comosus); CRISPR/Cas9; Disease resistance; Susceptibility genes; Promoter editing; Multiplex editing; DNA-free delivery 1 Introduction The tropical fruit pineapple (Ananas comosus) gains its popularity from its enjoyable taste and nutritious value and its essential role in global trade because of its multiple industrial uses. Bananas and citrus fruits join mangoes as the world's leading tropical fruits according to global production statistics (Tripathy, 2024). The FAO reports that worldwide production exceeds 28 million tonnes each year according to Gunawardena and Lokupitiya (2024). The cultivation of this plant species occurs in approximately 90 nations which span across Asia and Africa and the Americas. The majority of these products originate from Costa Rica and the Philippines and Brazil and Thailand and Indonesia because these countries produce more than 70% of the world supply (Li et al., 2022). Costa Rica alone produces close to 2.9 million tonnes annually. The pineapple trade is valued at several billion US dollars (Ming et al., 2015) and people use it both as a fresh product and in processed items including juice and canned fruit and confectioneries and bromelain. Given its high economic and nutritional importance, considerable efforts have been devoted to cultivar improvement. The continuous emergence of diseases results in decreased agricultural output and interrupted market operations (Sapak et al., 2021). The creation of resistant crop varieties has become essential because fungal diseases now endanger agricultural production at an unprecedented level. The protection of harvests and farmer incomes and export markets requires immediate development of resistant crop varieties. Pineapple farming faces its most critical challenge from disease pressure which includes heart rot as one of its most damaging diseases. The disease starts with small water-soaked spots in plant cores which then quickly lead to decay of inner leaf tissue. It is typically caused by Phytophthora spp. The disease results from fungal infections by Phytophthora infestans and bacterial infections by Dickeya zeae which can lead to total plantation destruction
Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 10 during major outbreaks (Sapak et al., 2021). Leaf spot which also goes by the names black spot or yellow spot represents a significant issue that usually results fromPenicillium funiculosum fungal infections. The pathogen causes damage to photosynthesis and creates harm to fruits while simultaneously degrading their quality (Serrato-Diaz et al., 2023). The postharvest black rot disease which Ceratocystis paradoxa causes damages crops at the same level by entering through fruit injuries to create a soft decay with foul odor (Hubert et al., 2014). The diseases affect pineapple cultivation throughout every pineapple-producing region worldwide. Phytophthora nicotianae-induced heart rot has been documented in Latin America Asia and Africa after heavy rainfall events (Ratti et al., 2018). Black rot has spread so widely that in some regions it has been designated a quarantine concern. Brazilian agricultural production faces major losses because fusariosis and black spot diseases continue to be major agricultural threats. The control strategies for disease management include disease-free seedlings and strict field hygiene and fungicides or antibiotics and quick removal of infected plants but these methods are not always effective (Sapak et al., 2021). The continued presence of these pathogens shows that breeding programs need to establish long-term resistance as their primary goal. Traditional breeding approaches, including hybridization and mutation breeding, have achieved only limited progress in improving pineapple resistance. The main challenge arises from the limited genetic diversity of commercial cultivars including 'Smooth Cayenne' and 'MD2' (Li et al., 2022). The limited availability of useful resistance genes exists because plant breeding operations face additional challenges due to the biological characteristics of the crop. Pineapple requires 2~3 years from planting to fruiting and because it is both self-incompatible and highly heterozygous, progeny populations show broad genetic variation that makes selection challenging. The execution of long-term field tests which extend across multiple years results in both high expenses and prolonged testing periods. The advancement of new crop varieties through chance seedlings and somaclonal variants has led to some progress yet the rate of improvement continues to be sluggish. Mutation breeding produces new traits but the process of screening big populations is time-consuming and unwanted genetic changes frequently emerge (Serrato-Diaz et al., 2023). The development of new hybrid cultivars requires 15–20 years but pathogens can adapt their resistance in less than this timeframe which creates a continuous challenge for plant breeders. In this context, CRISPR/Cas9 genome-editing technology represents a promising alternative. The system employs guide RNA together with Cas9 protein to generate precise double-strand breaks at predetermined positions in the genome. The plant cell fixes these breaks through its built-in cellular mechanisms which lead to minor genetic changes that result in gene inactivation (Guo et al., 2023). Scientists employ this method to disable disease-producing genes which makes plants more vulnerable to disease while maintaining their important agricultural characteristics (Wan et al., 2020). CRISPR technology enables scientists to evaluate edited lines within a single breeding cycle which results in faster breeding processes. The method allows scientists to turn on defense genes according to Han et al. (2025) and Rivera-Toro et al. (2025) or to edit multiple targets at once by using multiplexing approaches (Li et al., 2025; Oliva et al., 2019). Research studies show that CRISPR technology demonstrates potential for creating long-term disease resistance according to Langner et al. (2018), and its successful application in other crops strongly suggests that pineapple may also benefit from this technology. This study explores how CRISPR/Cas9 can help build disease-resistant pineapple. It reviews the pineapple genome and key defense routes, takes lessons from other crops, and puts forward editing plans for heart rot, black rot, and leaf spot. It also points out problems such as low transformation efficiency and off-target edits, and suggests possible fixes. The aim is to give clear scientific guidance for accurate breeding and to support lasting disease control and higher yields in tropical fruit crops. 2 Pineapple Genome and Disease-Related Gene Resources 2.1 Pineapple genome sequencing and annotation progress In the past ten years, research has made big progress in understanding the pineapple genome. This provides a base for using genome editing. The first draft genome of pineapple (‘F153’) was published in 2015 (Ming et al., 2015).
Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 11 It showed a genome size of about 526–563 Mb, with 25 chromosomes (2n = 50) (Figure 1) (Yow et al., 2021). Pineapple had fewer whole-genome duplication events than crops like grasses, so it has a smaller gene set. Around 27,000 protein-coding genes were found. The first genome gave useful data on traits such as CAM photosynthesis, but the sequence continuity was low (contig N50 < 100 kb). Figure 1 Karyotype structure and chromosome composition of the pineapple genome (Adapted from Ming et al., 2015) In 2022, researchers built a better genome assembly for the MD2 cultivar using PacBio long-read sequencing and Hi-C scaffolding. In the MD2 v2 version, 99.7% of the sequence was placed on 25 pseudochromosomes. The contig N50 was over 1 Mb. This work confirmed that the haploid genome size is about 563 Mb and that MD2 has high allelic heterozygosity (Yow et al., 2021). Genome annotation has also improved. Many genes now have predicted roles, and big gene families, such as transcription factors and enzymes, have been listed. Studies show that pineapple has kept many single-copy genes even though it did not have recent whole-genome duplications (Ming et al., 2015). RNA sequencing from different plant tissues has helped scientists predict gene models and spot genes linked to disease. At present, pineapple has a solid reference genome and detailed annotation data (Yow et al., 2021). These resources make it easier to find resistance genes and plan CRISPR strategies based on its genetic map. 2.2 Identified disease resistance genes in pineapple Research on pineapple disease-related genes is still limited, but some have been found. Pineapple carries NBS-LRR resistance (R) genes, which help recognize pathogen effectors. However, it has far fewer of these genes than many other crops. One study showed that pineapple has far fewer NBS-LRR genes than grasses, likely because it missed the whole-genome duplication events that expanded these genes in cereals (Chen et al., 2019). Pineapple may have only a few dozen, while rice and maize have hundreds (Zhou et al., 2024). Some pineapple R genes belong to known groups, such as coiled-coil NBS-LRRs, and are close to those in resistant monocots.
Bioscience Methods 2026, Vol.17, No.1, 9-22 http://bioscipublisher.com/index.php/bm 12 Another group is pathogenesis-related (PR) genes, which produce antimicrobial proteins. Transcriptome data show that pineapple can make chitinases and glucanases when attacked by pathogens (Sapak et al., 2021). The exact number of PRgenes is not well known, but pineapple probably has several PR1, PR2, and PR5 genes, which work in the salicylic acid defense pathway. Regulatory genes also play roles. Pineapple has 54 WRKY transcription factor genes, fewer than Arabidopsis (72) or rice (105) (Chen et al., 2019). This may also be largely due to its genome history without recent duplications. Some WRKY genes, such as AcWRKY28, have been studied and can improve stress tolerance when overexpressed (Zhou et al., 2024). Pineapple also carries genes for hormone pathways, such as salicylic acid and jasmonate, and for secondary metabolism, such as phenylpropanoid enzymes. For instance, phenylalanine ammonia-lyase (PAL) genes may help build stronger cell walls and improve resistance to pathogens (Rivera-Toro et al., 2025). In short, pineapple has fewer resistance genes overall, but important groups like NBS-LRR, PR, WRKY, and hormone regulators are present. These genes can be targets for CRISPR/Cas9, either to remove susceptibility genes or to boost positive defense genes. 2.3 Disease-related defense pathways in pineapple When pathogens attack, pineapple may turn on defense systems much like those in other plants. These include hormone signals and kinase chains. The main hormones are salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). In many plants, SA mainly fights biotrophic pathogens, while JA and ET defend against necrotrophs and insects (Li et al., 2019; Hou and Tsuda, 2022). Pineapple has genes such as NPR1 for SA signals and COI1/JAZ for JA signals. When SA is triggered, for example during Phytophthora infection, it can turn on PR genes like AcPR1 and cause systemic resistance (Sapak et al., 2021; Tian et al., 2025). Wounds or insect feeding can start the JA/ET pathways, leading to proteins such as protease inhibitors. These hormone pathways can affect each other. High SA may weaken JA defense, and high JA may reduce SA activity (Li et al., 2019). Pineapple also seems to use MAPK cascades to carry danger signals from the cell surface to the nucleus. In other plants, sensing pathogens turns on MAPKs, which then trigger defense gene expression (Hou and Tsuda, 2022; Zhang et al., 2025). The pineapple genome carries MAPKKK, MAPKK, and MAPKgenes. MAPK3/6-like genes may turn on WRKY transcription factors, which can boost defenses such as oxidative bursts or stronger cell walls. PAL genes in these pathways may raise lignin content, which in tomato has been linked to better resistance (Rivera-Toro et al., 2025). In short, pineapple makes use of common plant defense routes—SA, JA, and ET hormone signals, along with MAPK pathways. Genome editing can work on these points to improve resistance, either by removing blockers or by boosting helpers (Tian et al., 2025). Using knowledge of these pathways together with genome data can guide better strategies for stronger immunity. 3 Success Stories of CRISPR/Cas9 Disease Resistance in Other Crops 3.1Grape (Vitis vinifera) – resistance to powdery mildew via MLOgene knockout Powdery mildew, caused by Erysiphe necator, is a serious grape disease. CRISPR has been used to give grapes resistance by knocking out MLOgenes, which are susceptibility genes. In grape, VvMLO3 and VvMLO7 help the fungus infect plants. When these genes lose function, plants become resistant, as seen before in barley. Wan et al. (2020) used CRISPR/Cas9 to edit VvMLO3 and VvMLO4 in ‘Thompson Seedless’ grapes. They used Agrobacterium to deliver Cas9 and sgRNA into embryogenic callus, creating small indels. The edited plants had much better mildew resistance in greenhouse tests, with fewer lesions and spores than wild type (Figure 2). There were no major growth problems, apart from improved resistance.
RkJQdWJsaXNoZXIy MjQ4ODYzNA==