Molecular Pathogens 2025, Vol.16 http://microbescipublisher.com/index.php/mp © 2025 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher.
Molecular Pathogens 2025, Vol.16 http://microbescipublisher.com/index.php/mp © 2025 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher. Publisher MicroSci Publisher Edited by Editorial Team of Molecular Pathogens Email: edit@mp.microbescipublisher.com Website: http://microbescipublisher.com/index.php/mp Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Molecular Pathogens (ISSN 1925-1998) is an open access, peer reviewed journal published online by MicroSciPublisher. The journal is committed to publishing and disseminating all the latest and outstanding research articles, letters and reviews in all areas of molecular pathogens. The range of topics including isolation and identification of emerging pathogens viruses, pathogen-host interactions, genetics and evolution, genomics and gene regulation, proteomics and signal transduction, glycomics and signal recognition, virulence factors and vaccine design and other topical advisory subjects. All the articles published in Molecular Pathogens 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. MicroSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights. MicroSci Publisher is an international Open Access publisher specializing in microbiology, bacteriology, mycology, molecular and cellular biology and virology registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada.
Molecular Pathogens (online), 2025, Vol. 16, No. 6 ISSN 1925-1998 http://microbescipublisher.com/index.php/mp © 2025 MicroSci Publisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher. Latest Content The Role of Resistance Genes in Potato Virus Defense Hangming Lin, Dandan Huang Molecular Pathogens, 2025, Vol. 16, No. 6, 257-265 Rhizosphere Microbiome-Assisted Breeding: Integrating Microbial Induction and Host Variety Improvement for Enhanced Disease Resistance Jin Wang, Chunyang Zhan Molecular Pathogens, 2025, Vol. 16, No. 6, 266-275 Response of Maize Root Rot Pathogenic Communities and Mechanisms of Disease Resistance under Soil Salinization Conditions Qian Li, Shiying Yu Molecular Pathogens, 2025, Vol. 16, No. 6, 276-284 Restoration of Cotton Disease Resistance by CRISPR-Mediated Disruption of Key Genes in Drug-Resistant Pathogens Shujuan Wang, Jiong Fu Molecular Pathogens, 2025, Vol. 16, No. 6, 285-293 Mechanistic Study of Rhizosphere Microbial Amendment Regulating Wheat Root Responses to Leaf Spot Disease Guiping Zhang, Wei Wang Molecular Pathogens, 2025, Vol. 16, No. 6, 294-302
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 257 Research Insight Open Access The Role of Resistance Genes in Potato Virus Defense Hangming Lin, Dandan Huang 1 Tropical Legume Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding author: dandan.huang@hitar.org Molecular Pathogens, 2025, Vol.16, No.6 doi: 10.5376/mp.2025.16.0026 Received: 20 Sep., 2025 Accepted: 30 Oct., 2025 Published: 12 Nov., 2025 Copyright © 2025 Lin and Huang, 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: Lin H.M., and Huang D.D., 2025, The role of resistance genes in potato virus defense, Molecular Pathogens, 16(6): 257-265 (doi: 10.5376/mp.2025.16.0026) Abstract Potato virus infections, especially those caused by potato Y virus (PVY), X virus (PVX), and leaf curl virus (PLRV), pose a serious threat to the global yield and quality of potatoes. In recent years, disease resistance strategies centered on resistance genes have become a sustainable and efficient approach to dealing with viral diseases. This study systematically reviewed the types of major potato viruses, their infection mechanisms, and the physiological response processes of host plants. It also classified and functioned the identified resistance genes, especially NB-LRR genes, revealing their key roles in virus recognition, signal transduction, and immune activation. Furthermore, it explored the molecular mechanisms by which resistance genes mediate virus defense. The application effectiveness of resistance genes in virus prevention and control was demonstrated through typical cases, such as the successful application of Ry genes in PV-resistant breeding, the promotion of Rx genes in commercial PVX-resistant varieties, and the comparison of the application of PLRV resistance genes in breeding projects in Europe and China. This study aims to provide a theoretical basis and practical guidance for building a sustainable potato virus defense system. Keywords Resistance gene; Potato virus; Effector triggers immunity; RNA silencing; Molecular breeding 1 Introduction The potato (Solanum tuberosum L.) can be regarded as one of the basic foods worldwide, especially being of great significance to the dining tables in developing countries. It is not only a matter of filling the stomach, but also a guarantee of nutrient intake. But this seemingly "plain and unadorned" crop has actually been plagued by viruses all along. Familiar faces like the potato Y virus (PVY), X virus (PVX), and leaf curl virus (PLRV) have long been common sources of trouble in many regions. It is not uncommon for the output to drop by 20% to 30% all at once. In severe years, the loss may even exceed 80% (Kolychikhina et al., 2021). And the impact brought by these viruses is not merely a headache for the fields. In Europe, the annual economic loss caused by PVY alone approaches 187 million euros (Dupuis et al., 2023), and this amount is sufficient to illustrate the severity of the problem. What's more troublesome is that the virus issue has not come to a standstill. Climate change has made things even more complicated. The warming trend not only makes vector insects more active but also contributes to the emergence of new strains. The situation that could have been stabilized through vector control is now becoming increasingly difficult to manage. Pesticides, although useful, have limited effects and also face resistance issues and environmental pressure. Against this backdrop, it seems quite natural to turn one's attention to resistant breeding. After all, allowing potatoes to withstand the virus on their own is the fundamental solution to the problem (Liu et al., 2023). When it comes to resistance, the R gene has always been a key focus of research, especially those genes encoding the NLR protein, which have demonstrated decent antiviral capabilities. Star members like the Ny and Ry genes can not only "precisely strike" specific strains, but some can also provide broad-spectrum protection. They have been successfully applied in some commercial varieties (Lucioli et al., 2022). In terms of breeding methods, from molecular markers to gene editing techniques such as CRISPR/Cas9, many breakthroughs have indeed been brought in recent years, accelerating the discovery and functional verification of resistance genes significantly.
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 258 This study reviews the global impact of viral diseases on potato production, with a focus on epidemiological trends and economic consequences. It discusses the molecular basis of resistance gene-mediated defense, including the latest progress in gene discovery and biotechnology applications, and outlines the current challenges and future development directions in the deployment of resistance genes. Focus on the integration of new technologies and addressing climate-driven threats. By advancing research on resistance genes, this study aims to contribute to global food security and the resilience of potato production systems in response to evolving viral threats. 2 Major Potato Viruses and Their Infection Mechanisms 2.1 Characteristics and impact of key viruses: PVY, PVX, PLRV, etc. Potato Y virus (PVY) is the most headache-inducing type for growers. The losses it causes are not just numerical - yellowing leaves, mottled leaves, necrosis, and growth stagnation - these symptoms immediately reveal the problem. Especially the necrotic strains such as PVYNTN and PVYN-Wi are more virulent and troublesome (Manasseh et al., 2023). While PVX is relatively milder, it still cannot be taken lightly. Solitary infection is still acceptable, but once combined with other viruses, the synergistic effect becomes a disaster, and the output can sometimes drop by 80% (Gajimuradova et al., 2023). PLRV is also a common "partner", usually mixed with other viruses to cause illness, which is unfavorable for both quality and yield (Kenzhebekova et al., 2025). However, the epidemic situation varies from region to region. Mixed infections are the norm and more difficult to control. 2.2 Virus infection process: from entry and replication to systemic spread Viruses entering potatoes are not always as violent as a "home invasion robbery". They might be brought in by aphids, such as PVY and PLRV. It could also be due to accidental mechanical propagation during operation, such as PVX (Figure 1) (Bhoi et al., 2022). Once inside, they will shed their shells and start replicating. Then it spreads through intercellular filaments and then spreads throughout the entire plant with the help of the phloem. Like coronaviruses, they rely on the TGB1 protein, which can cooperate with the plant's own stress sensing mechanism to help the virus spread over long distances (Cowan et al., 2018). However, environmental factors are not just for show. For instance, temperature can influence the replication rate of viruses and the severity of symptoms (Glushkevich et al., 2022). Figure 1 Interaction between potato and potato virus Y depicting incompatible and compatible resistance and susceptibility reaction in different potato varieties (Adopted from Bhoi et al., 2022)
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 259 2.3 Molecular and physiological responses of potato to viral stress The potato is not a plant that "stands and gets beaten". In the face of viruses, it has several sets of defense mechanisms. The first step is the intervention of the R gene. Like the Ny gene, once it recognizes the virus, it will trigger local cell death, which is known as an allergic reaction (HR). The Ry gene is even more potent, directly blocking the replication and spread of the virus without even showing any symptoms. Secondly, there is a major adjustment in gene expression. Once infected, pathogen-associated proteins (PR), various stress regulatory factors, and genes related to the salicylic acid signaling pathway will all be "awakened". Meanwhile, the cell walls of plants will also be "reinforced" - synthesizing more glycoproteins and regulating the activity of cellulase to prevent the further spread of viruses (Otulak-Koziel et al., 2018). Furthermore, the antioxidant system also comes into play. For instance, enzymes like SOD, POD, and CAT, which act as "scavengers", rapidly enhance their activity during an infection, thereby alleviating oxidative stress. In addition, the metabolism of carbohydrates, amino acids and fatty acids in plants will also change. Behind these changes, there are actually genetic differences in resistance among different varieties. Some reactions are evident in strongly resistant varieties, while others are only temporary regulatory responses. The final outcome can also vary depending on the virus strain and environmental conditions, ranging from completely sensitive to highly resistant. 3 Classification and Characteristics of Potato Resistance Genes 3.1 NBS-LRR type resistance genes and their virus recognition mechanisms These NB-LRR genes, in essence, are a type of receptor that "stands guard" in cells, capable of recognizing specific viral proteins and triggering an immune response. The Rx and Rysto genes in potatoes can be regarded as the "stars" in this regard. The former works against PVX, and the latter has a significant resistance effect against PVY (Kondrak et al., 2019; Torrance et al., 2020; Liu et al., 2021). But how do they identify viruses? Structurally speaking, the NBS section is responsible for energy operations (in combination with ATP/GTP), while the LRR segment is more like a "face recognition expert", determining which pathogens can be identified. Once matched, plants may choose to "cut off one arm of their own", that is, trigger an allergic reaction (HR) to cause local cell death to prevent the spread. There is also a more straightforward approach, which is to directly prevent the virus from replicating (ER) in the body, with almost no symptoms throughout the process. It should be noted that even minor sequence changes in the LRR region can affect the recognition range - this can also be seen from the domain swap experiments. Therefore, the "adaptability" of such genes is actually very strong and they can keep up with the changing rhythm of the virus. 3.2 Distribution of natural resistance resources in ecotypes and cultivars The "origin" of resistance genes is actually mainly concentrated in wild Solanaceous plants. These resources, after breeding, were transferred into cultivated potatoes, such as Rysto from the creeping tomato and Ry(o)phu from the Phureja group, which are located on chromosomes 12 and 9 respectively, and can provide broad-spectrum resistance to PVY (Akai et al., 2023). However, many commercial varieties do not carry these resistance genes at present, which can be seen from the results of molecular marker screening. On the other hand, the latest research also shows that more than 55 different Rysto-like sequences can be found in some wild relatives (Guo and Wang, 2025), and their genetic diversity far exceeds that of cultivated species. This also explains why they are often regarded as an important "gene pool" for resistance breeding (Paluchowska et al., 2024). 3.3 Expression regulation and signal transduction of resistance genes Genes not only need to be "present", but also "utilized". The expression of the R gene is not as simple as a light switch. It is regulated at multiple levels, including the joint participation of transcription, post-transcription and even epigenetic mechanisms. Some promoter regions carry cis-elements related to stress, such as sequences involved in salicylic acid or abscisic acid pathways, which become active when viruses invade (Karimipour et al., 2025). Once the R gene is activated, it will trigger a long series of signaling pathways, including protein kinases, transcription factors, and a cascade reaction involving multiple hormones. These pathways will eventually activate
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 260 defense genes and induce systemic resistance (Yan et al., 2022; Li et al., 2025). Co-expression analysis further identified many regulatory nodes and key modules, providing valuable targets for resistance breeding (Hajibarat et al., 2024). However, the expression of the R gene is not necessarily the stronger the better. When there is no illness, it should be kept "low-key", otherwise the adaptation cost will be too high and it will instead hinder growth. 4 Molecular Mechanisms of Resistance Gene–Mediated Virus Defense 4.1 ETI (Effector-triggered immunity) mechanisms based on gene recognition Not every time a virus invades, plants can immediately launch a full-scale counterattack. Usually, it is not until R proteins (such as NLR) recognize the "suspicious molecules" of a specific virus - that is, effector proteins - that cells will initiate the ETI immune process. The Ny-1 gene in potatoes operates in this way, specifically responding to PVY infection. Its reaction mode is a bit "ruthless": it directly triggers an allergic reaction (HR), causing the cells around the infected area to die voluntarily, thereby confining the virus within a local area. This reaction is not random. Salicylic acid (SA) plays a key role in timing and regional control. Molecules like NADPH oxidase RBOHD are activated at the edge of the lesion, releasing reactive oxygen species (ROS), which in turn guide SA to accumulate at the appropriate location. If there is a problem with the signaling link of this RBOHD-SA, the defense line will be easily broken through and the virus will spread (Gouveia et al., 2017). 4.2 RNA silencing and its interaction with viral suppressors In addition to protein recognition, potatoes have another "silencing mechanism" to deal with viruses - RNA silencing. This process relies on Dicer-like enzymes to cut the double-stranded RNA produced by the virus into siRNA fragments, and then the Argonaute protein is responsible for using these SiRnas as "navigation" to precisely remove the virus's RNA. However, viruses are not easy to deal with. They have evolved a class of inhibitors called VSR to fight back, such as the P25 protein of PVX, which specifically interferes with the normal operation of the AGO protein and can even promote its degradation. However, the host also has countermeasures. For instance, type I protease inhibitors can target these VSRS, thereby "unblocking" RNA silencing channels and restoring the antiviral mechanism to normal (Shen et al., 2025). This is a back-and-forth contest. Who gains the upper hand largely determines the outcome of this infection (Lopez-Gomollon and Baulcombe, 2022). 4.3 Crosstalk between resistance genes and hormone signaling (SA/JA/ET) After viral infection, the resistance response does not rely solely on a single pathway. The signaling pathways of salicylic acid (SA), jasmonic acid (JA), and ethylene (ET), these three hormones, often work together and cooperate with each other at different stages and sites. Sometimes, this kind of coordination relies on feedback loops like RBOHD-SA. For example, the participation of SA can be seen in the local defense strategy mentioned earlier (Yu, 2025). The problem is that viruses also know how to target from the hormonal level. For instance, some inhibitory factors can directly interfere with the recognition or signal transduction of SA, thereby weakening resistance internally. The pathway on the JA side is more inclined to enhance RNA silencing, which can increase the expression of key factors such as AGO protein (Yang et al., 2020). Hormones are not completely harmonious with each other either. Sometimes, there is even a phenomenon of "competing for resources". So, when dealing with viruses, plants, on the one hand, have to rely on the combined response of these pathways, but on the other hand, they also need to prevent pathogens from exploiting the loopholes in them. 5 Functional Validation and Genetic Tools for Resistance Genes 5.1 Cloning of resistance genes and development of molecular markers To figure out whether a resistance gene is useful or not, it is necessary to first identify and clone it. Genes like Ryadg, Rysto and Rychc were gradually identified through linkage analysis, and then precisely tracked with molecular markers such as RFLP, SNP or KASP (Caruana et al., 2021; Asano and Endelman, 2023). Nowadays, molecular marker-assisted selection (MAS) has become a "standard configuration" for many potato breeding projects. It can quickly introduce resistance genes from wild varieties into commercial varieties, saving a lot of time and manpower (Saidi and Hajibarat, 2021). Some laboratories have also developed multiplex PCR methods that can detect multiple genes at once, which are quite practical tools for breeders (Elison et al., 2020). However,
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 261 to be fair, although markers are useful, they are not omnipotent. Under different genetic backgrounds, some markers may not be so "accurate", so the verification step cannot be skipped. 5.2 Application of gene editing (CRISPR/Cas) in improving virus resistance In recent years, CRISPR/Cas has frequently appeared in research on potato disease resistance. Especially those Cas13 systems that can directly target RNA, such as Cas13a and Cas13d, have been successfully tested in multiple transgenic strains. They can directly cut viral RNA and have good inhibitory effects on PVY, PVX, PVS and even PLRV (Adilbayeva et al., 2025). However, the strength of this resistance is often related to the expression level of CRISPR; the stronger the expression, the more obvious the protection. Some people have also attempted to combine multiple guide Rnas to develop a "multi-pronged" strategy, hoping to combat multiple viruses simultaneously (Zhan et al., 2023). To bypass the regulatory challenges of genetically modified organisms, some people are now exploring ways to directly package Cas proteins and guide Rnas into cells without using DNA. This approach seems more suitable for the development of non-genetically modified products (Taliansky et al., 2021; Tiwari et al., 2022). 5.3 Transgenic and antisense RNA strategies to enhance viral resistance Before CRISPR became popular, traditional transgenic methods had already achieved many results in the prevention and control of potato viruses. For instance, by introducing the virus's capsid protein gene or replication enzyme fragment into potatoes, the plants can "recognize the enemy" in advance and interfere with the virus. RNA interference (RNAi) and antisense RNA techniques have also been used for a long time. By designing constructs that can block the accumulation of viral RNA, the symptoms of the disease have been alleviated significantly (Khoo et al., 2024). Although these methods are not new, when combined with CRISPR technology, they can still produce some synergistic effects, especially in terms of resistance stacking or long-term control, providing a sustainable and less pesticide-dependent solution (Taliansky et al., 2021). 6 Case Studies: Application of Resistance Genes in Potato Virus Management 6.1 Successful application of Ry gene in PVY-resistant breeding Many breeding projects have regarded the Ry gene as the core means to control PVY in practice, especially the types Rysto, Ryadg and Rychc, which have strong resistance to almost all PVY strains (Elison et al., 2020; Paluchowska et al., 2024). Rysto originally originated from Solanum stoloniferum. The TIR-NLR protein encoded by it can stably function at different temperatures. Whether the material is selected through transgenic methods or molecular labeling, it basically shows no symptoms (Torrance et al., 2020). Nowadays, multiplex PCR and molecular markers have made the detection and combination of these genes much simpler. Some new varieties in Europe, Russia and Asia have basically used these methods to select materials resistant to PVY (Figure 2). It is worth mentioning that these Ry genes have also helped farmers reduce their reliance on pesticides, and the yield has become more stable. They are now a "main option" for sustainable control of PVY. 6.2 Functional identification of Rx gene for PVX resistance and its commercialization Although PVX itself is not as harmful as PVY, it has relatively high requirements for the quality of seed potatoes. Therefore, the role of the Rx gene in breeding cannot be ignored. It was first found in the Solanum tuberosum ssp. andigena subspecies of potato. It can effectively prevent the spread of PVX, and the process does not trigger cell death. The Rx1 allele demonstrated the ability to block the transmission of viruses from leaves to tubers in experiments, which is particularly crucial for virus-free seed potatoes. At present, in some countries including China, there are already multiple varieties carrying Rx1 or Rx2. Precise breeding is achieved through molecular marker methods, and these varieties show relatively persistent resistance to PVX (Shaikhaldein et al., 2018; Liu et al., 2021). However, a current issue is that the genetic diversity of such genes in commercial varieties is still insufficient, and in the long term, it may plant the hidden danger of resistance decline. 6.3 Comparative analysis of PLRV resistance gene breeding projects in the Netherlands and China When it comes to resistance breeding of PLRV, although the approaches of the Netherlands and China have their own focuses, the basic paths are quite similar: both first search for genes from wild Solanum plants and then
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 262 screen materials through molecular markers and genomic association analysis. The International Potato Center (CIP) and relevant national research institutions have made significant contributions in this regard. They have not only provided abundant germplasm resources but also participated in promoting resistance breeding projects of multiple viruses (including PLRV, PVY, and PVX) (Jiang et al., 2020). At present, some multi-resistant varieties that can adapt to the local environment have already been developed. However, in the area of PLRV, the specific resistance genes and their mechanisms of action are not yet particularly clear, and more research is needed to make up for this shortcoming. Figure 2 Potato leaves showing blue staining produced after manual inoculation with PVY-GUS. Blue patches of β-glucuronidase stain, indicating virus replication, are visible (Adopted from Torrance et al., 2020) Image caption: a cv Tacna; b cv Corine; and clones c DB375(1); d 84.2P.75; e HB171(13) and f 99.FT.1b5 (Adopted from Torrance et al., 2020)
Molecular Pathogens, 2025, Vol.16, No.6, 257-265 http://microbescipublisher.com/index.php/mp 263 7 Conclusion and Future Perspectives In recent years, the breeding of potato virus resistance has actually advanced quite rapidly, especially in the discovery and application of resistance genes such as Rysto, Ryadg, and Rx. With them, problem viruses like PVY and PVX are no longer so troublesome in some varieties. It is precisely with the help of these resistance genes, along with the accelerated intervention of molecular markers and genotyping technologies, that marker-assisted selection has transformed from an "idea" into a "tool", making the introduction and superposition of resistance less complicated. Nowadays, RNA interference, transgenic techniques, and CRISPR/Cas systems have also come in. The toolbox is indeed getting larger and larger, and the resistance spectrum is gradually broadening. However, there are still some problems, especially the situation where resistance disappears without a trace is not uncommon. Some virus strains mutate at an extremely fast rate, and a single resistant gene often cannot withstand them. Especially when a resistant variety is planted in large numbers and too concentrated, the risk will be magnified. Furthermore, the genetic basis of potato varieties themselves is not broad, which instead leaves a breakthrough for pathogens. Moreover, even if resistance is introduced, there are sometimes situations where "it works well on this variety but not so well on that one", mainly due to the background of the host. Another reality is that the acceptance of gene editing and genetic modification in some regions is still relatively low, and their promotion will also encounter problems such as policies or public awareness. When it comes to the next step, to make resistance more stable, gene aggregation is an inevitable direction - putting multiple resistance genes together is always better than fighting risks alone. Precision breeding methods, whether genomics, gene editing, or in combination with high-throughput phenotypic analysis, are gradually providing practical and feasible paths for this kind of aggregation. Of course, genetic resistance is not a panacea. In the future, the strategy for potatoes to resist viruses may have to shift from "individual combat" to "multi-line coordination", and measures such as strengthening vector management and optimizing field cultivation methods also need to keep pace. Meanwhile, it is necessary to continue to explore new resistance genes from wild germplasm, verify their functions and develop corresponding molecular markers. These fundamental tasks still need to be advanced continuously in order to truly enable resistance breeding to go far and stand firm. Acknowledgments The authors would like to thank all teachers and colleagues who provided guidance and assistance during this research, and for the peer review's revision suggestions. Conflict of Interest Disclosure The authors confirm that the study was conducted without any commercial or financial relationships and could be interpreted as a potential conflict of interest. References Adilbayeva K., Kenzhebekova R., Mendybayeva A., Kapytina A., and Gritsenko D., 2025, Induced RNA interference and its impact on potato virus amplification in plants, Bulletin of the l.n, Gumilyov Eurasian National University, Bioscience Series, 150(1): 22-38. https://doi.org/10.32523/2616-7034-2025-150-1-22-38 Akai K., Asano K., Suzuki C., Shimosaka E., Tamiya S., Suzuki T., Takeuchi T., and Ohki T., 2023, De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene (Rychc) derived from Solanum chacoense, Breeding Science, 73: 168-179. https://doi.org/10.1270/jsbbs.22078 Asano K., and Endelman J., 2023, Development of KASP markers for the potato virus Y resistance gene Rychc using whole-genome resequencing data, bioRxiv, 73(2): 168-179. https://doi.org/10.1101/2023.12.20.572658 Bhoi T., Samal I., Majhi P., Komal J., Mahanta D., Pradhan A., Saini V., Raj N., Ahmad M., Behera P., and Ashwini M., 2022, Insight into aphid mediated potato virus Y transmission: a molecular to bioinformatics prospective, Frontiers in Microbiology, 13: 1001454. https://doi.org/10.3389/fmicb.2022.1001454 Biryukova V., Shmiglya I., Zharova V., Beketova M., Rogozina E., Mityushkin A., and Meleshin A., 2019, Molecular markers of genes for extreme resistance to potato virus Y in Solanum tuberosum L., Cultivars and Hybrids, Russian Agricultural Sciences, 45: 517-523. https://doi.org/10.3103/s106836741906003x
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Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 266 Case Study Open Access Rhizosphere Microbiome-Assisted Breeding: Integrating Microbial Induction and Host Variety Improvement for Enhanced Disease Resistance Jin Wang 1, Chunyang Zhan 2 1 Tropical Microbial Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Hainan Institute of Biotechnology Haikou, 570206, Hainan, China Corresponding author: chunyang.zhan@hitar.org Molecular Pathogens, 2025, Vol.16, No.6 doi: 10.5376/mp.2025.16.0027 Received: 27 Sep., 2025 Accepted: 11 Nov., 2025 Published: 20 Nov., 2025 Copyright © 2025 Wang and Zhan, 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: Wang J., and Zhan C.Y., 2025, Rhizosphere microbiome-assisted breeding: integrating microbial induction and host variety improvement for enhanced disease resistance, Molecular Pathogens, 16(6): 266-275 (doi: 10.5376/mp.2025.16.0027) Abstract The Rhizosphere microbiota plays a core role in plant health, especially in regulating crops' resistance to soil-borne pathogenic substances, which is of great significance. Facing the practical demands of sustainable agricultural development, intermicrobiota assisted breeding, as an emerging strategy, has demonstrated great potential in enhancing the disease resistance of crops by integrating the induction of beneficial microorganisms with the genetic improvement of host varieties. This study systematically reviewed the composition characteristics and ecological functions of the rhizosphere microbial community, expounded the molecular mechanism of induced systemic resistance (ISR), and the influence of plant genetic background on microbial recruitment. It further explored the integrated breeding strategy of "core microorganisms + resistant varieties" And through actual cases such as tomato-Pseudomonas fluorescens and wheat-Bacillus subtilis, the application effect of microbiota intervention in disease-resistant breeding was demonstrated. This research provides a theoretical basis and technical support for the development of a low-dependence pesticide and green, efficient disease-resistant breeding system. Keywords Rhizosphere microbiota; Disease-resistant breeding; Inductive system resistance; Microbiota-plant interaction; Multiomics integration 1 Introduction Plant diseases are not a new problem, but in the current context where global agricultural pressure continues to intensify, the threat they pose to crop yields and food security is particularly intractable. All kinds of prevention and control measures are no longer blank, including chemical pesticides, disease-resistant varieties and crop rotation systems. Almost every one of them has been widely adopted in agricultural practice. But problems arise after long-term use - although pesticides can take effect quickly, they also bring environmental pollution and health risks, and force pathogens to evolve resistance rapidly. As for resistant varieties, they seem safe, but the pathogens develop quickly, and the disease-resistant ones grown often have a short "shelf life". Biological pesticides sound environmentally friendly, but in practical application, they are limited by their stability and range of action. However, nowadays, the focus of research seems to be quietly shifting to the "circle of friends" of plants - rhizosphere microorganisms. The microbial community surrounding the plant root system may seem insignificant, but it plays an increasingly important role in the health and disease resistance of plants. Studies have found that plants do not passively accept these microorganisms but actively "pick people" through root secretions. That is to say, they will attract those microorganisms that can help them resist diseases (Yang et al., 2023). These recruited "Allies" can not only directly suppress pathogens but also enable plants to activate their own defense mechanisms. What's more interesting is that some beneficial bacteria can be passed down from generation to generation, from the mother to the offspring, just like giving plants a natural "disease resistance vaccine" (Araujo et al., 2024). Of course, all of this is not static. The structure of the rhizosphere microbiome constantly changes with the environment and the plant's own conditions. Especially when facing pathogenic bacteria attacks, plants sometimes "reorganize their lineup", allowing more inhibitory bacteria to enter the rhizosphere. This "combat mechanism" of plant-microorganism interaction will ultimately determine whether diseases break out and whether plants can survive (Berendsen et al., 2018).
Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 267 This study will integrate the current knowledge of rhizosphere microbiome-assisted breeding, with a focus on the combination of microbial induction and host variety improvement to enhance crop disease resistance. It will review the limitations of traditional crop disease management methods and emphasize the necessity of microbiome-based methods. Clarify the mechanism by which the interaction between rhizosphere microorganisms and plant hosts endows them with disease resistance; Propose a breeding framework that combines microbiome manipulation with host genetic improvement. By bridging plant genetics and microbiome science, this study aims to advance sustainable crop protection strategies and contribute to building resilient agricultural systems. 2 Composition and Functions of Rhizosphere Microbial Communities 2.1 Major microbial groups in the rhizosphere ecosystem The "liveliness" at Genji far exceeded imagination. Here, there are not only bacteria and fungi, but also actinomycetes, archaea, protozoa, and even viruses - although the latter types are often overlooked, they are indeed present. Ultimately, however, the most frequently concerned ones are still bacteria and fungi. Bacteria such as Proteobacteria, actinomycetes and Bacteroides are often detected in the rhizosphere (Ling et al., 2022; Maphosa et al., 2025). Fungi are not simple either. Whether it is mycorrhizal fungi that can help plants absorb phosphorus or saprophytic fungi that live by decomposing organic matter, they are all involved in nutrient cycling and plant interactions (Chauhan et al., 2023). Actinomycetes are also worth mentioning. These microorganisms, which look like "bacterial fungi", can not only produce antibiotics but also improve plant health. Ultimately, whether there are many of these microorganisms and which species prevail largely depends on the plant's own genotype, the composition of root secretions, and the overall condition of the soil and environment (Ren et al., 2025). 2.2 Mutualistic relationships between microbial communities and plant roots Plants themselves also "nurture bacteria". The large amount of substances secreted by the root system - sugars, amino acids, organic acids, secondary metabolites - is like a carefully prepared "menu", attracting various beneficial microorganisms to approach and eventually participating in the construction of the rhitrosphere community. This is not a one-way giving. The microorganisms attracted have shown their respective abilities in helping plants absorb nutrients, stimulating growth and preventing pathogenic bacteria from invading. Probiotic bacteria like PGPR and mycorrhizal fungi, when cooperating with plants, not only have high efficiency but also enhance stress resistance. However, this relationship is not static. Environmental factors, the developmental stage of the plant itself, and even genetic background can all cause fluctuations in this "cooperation". 2.3 Functional roles of beneficial microorganisms in plant disease defense When it comes to disease resistance, plants are not fighting alone. Their "microbial friends" have taken on quite a few tasks in this area - and in many ways. Some directly act, such as some Pseudomonas, Bacillus or actinomycetes, which suppress the growth of pathogenic bacteria by producing antibacterial substances (Lazcano et al., 2021). Some are more like behind-the-scenes commanders, mobilizing the plant's own defense system by inducing systemic resistance (ISR), enabling the plant to respond more quickly when facing different pathogens. Some microorganisms take the lead in occupying resources or space and compete with pathogenic bacteria for territory. Once they win, it becomes very difficult for the pathogenic bacteria to take root. What is more complex is the microbial network in the rhizosphere that checks and balances each other yet collaborates. Its stability and recovery ability themselves can help plants resist diseases. These methods are not mutually exclusive; instead, they often occur simultaneously, forming an "invisible" protective barrier and providing the possibility of reducing reliance on pesticides. 3 Microbe-Induced Systemic Resistance Mechanisms in Plants 3.1 Molecular basis of ISR (induced systemic resistance) and SAR (systemic acquired resistance) Plants do not only become "tough" when they encounter diseases. Sometimes, even when there is no illness or disaster, some "good bacteria" can also activate its immune state in advance. Rhizosphere bacteria like PGPR and certain fungi often play the role of such a "quiet reminder", inducing the ISR response. And immune mechanisms like SAR are usually activated only after pathogen invasion. Ultimately, both can eventually prepare plants in
Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 268 advance for "battle", but the processes are somewhat different (Yu et al., 2022). For instance, SAR requires the accumulation of salicylic acid (SA) and also the activation of disease-related (PR) genes. ISR, on the other hand, relies more on the jasmonic acid (JA) and ethylene (ET) signaling pathways and can often be activated without the SA and PR genes. Of course, there are exceptions. Sometimes the two pathways may "visit each other", and ISR may also be related to SA. Rashid and Chung (2017) mentioned that both immune mechanisms actually enable plants to enter a standby state in advance, allowing them to respond more quickly when they are actually attacked. 3.2 Activation of defense signaling pathways (e.g., JA/ET, SA) triggered by beneficial microbes Not all microorganisms can activate plant immunity, and not all activations follow a single pathway. JA/ET is the most common pathway in the ISR reaction, through which many beneficial microorganisms express defense genes such as PDF1.2 and induce the synthesis of some enzymes or defense substances (Wang et al., 2025). On the SAR side, it is more accustomed to following the SA line. After PR-like genes like PR1, PR2, and PR5 are activated, their resistance is significantly enhanced. However, there are also some microorganisms that "act on two boats" and can simultaneously trigger SA and JA/ET. For instance, Bacillus cereus AR156 has been proven to bring about a stronger disease resistance effect (Yang et al., 2023). There is also NPR1, which acts like a coordinator. No matter which path you take, many signals still have to be aggregated here in the end to be effectively executed (Martin-Rivilla et al., 2020). 3.3 Epigenetic regulation in plant immunity mediated by interactions with Rhizosphere microbiota Whether a plant has a good memory or not sometimes depends on whether its epigenetic system is effective. Recent studies have found that factors such as small RNA and chromatin modification are not absent when plants interact with beneficial microorganisms. Small Rnas can precisely regulate which immune genes should be activated and which should be temporarily dormant. This "sense of proportion" is actually one of the key steps to activate ISR (Romera et al., 2019). More interestingly, some defense states activated by microorganisms can not only last for a relatively long time but may also be passed on to the next generation, which opens up new doors for resistance breeding using the microbiome (Darshita et al., 2025). It can be said that this is not a simple immune response, but rather more like a subtle "immune training". 4 Influence of Host Plant Genetic Background on Microbial Recruitment 4.1 Genotype-specific preferences for particular rhizosphere microorganisms Different plant varieties do not treat microorganisms equally. Even if they are planted in the same field, different genotypes can lead to significant differences in the structure of their rhizosphere microbial communities. For crops such as wheat, barley, carrots, cotton and chrysanthemums, studies have shown that their respective cultivated varieties or ecological types often form bacterial or fungal communities with "variety labels". Not all microorganisms are welcome. Drought-tolerant wheat prefers a wide variety of fungi with complex functions and is significantly more "selective" than drought-tolerant varieties (Yue et al., 2024). In the recruitment of Pseudomonas, varieties of barley and carrots also show considerable individuality, especially modern cultivated species, which seem to be more adept at attracting bacteria that match the secretions of their root systems. However, not all community differences can be explained by genetic distance. For example, the composition of fungal groups is not directly influenced by host genetics as bacteria do (Rotoni et al., 2022). 4.2 Mechanisms of microbe recruitment mediated by plant-derived metabolites The key to whether microorganisms will recruit and who they will recruit lies in what plants secrete. The roots of plants release a large amount of substances, such as sugar, amino acids, organic acids, and various secondary metabolites. Behind these combinations, it is actually genes at work (Anderson et al., 2024). The quantity and types of metabolites vary greatly among different varieties. Specific metabolites such as coumarin (Arabidopsis thaliana) or hexose (barley) are "invitations" to some microorganisms and may be "prohibitions" to others (Pacheco-Moreno et al., 2024). Root morphology is not insignificant either. It determines whether microorganisms can "take root" smoothly. Of course, things are not set in stone. If plants encounter stresses such as diseases or drought, the chemicals secreted by their roots will also change, which invisibly regulates their microbial circle of friends (Sharma et al., 2023).
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