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Molecular Pathogens 2025, Vol.16, No.2 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 Editedby 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. 2 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 Advances in Rice Breeding for Resistance to Fungal and Bacterial Diseases Xinguang Cai Molecular Pathogens, 2025, Vol. 16, No. 2, 45-52 Signaling Pathways in Potato’s Response to Phytopathogens Yinghua Chen Molecular Pathogens, 2025, Vol. 16, No. 2, 53-60 Genetic Resistance to Pathogens in Rapeseed: A Comprehensive Review Kaiwen Liang Molecular Pathogens, 2025, Vol. 16, No. 2, 61-68 Meta-Analysis of Resistance Genes in Maize Against Fungal Diseases Baixin Song, Jiayi Wu Molecular Pathogens, 2025, Vol. 16, No. 2, 69-76 Grapevine Defense Mechanisms Against Pathogens: Molecular Insights and Breeding Strategies Hui Xiang Molecular Pathogens, 2025, Vol. 16, No. 2, 77-86
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 45 Feature Review Open Access Advances in Rice Breeding for Resistance to Fungal and Bacterial Diseases Xinguang Cai Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China Corresponding email: xinguang.cai@cuixi.org Molecular Pathogens, 2025, Vol.16, No.2 doi: 10.5376/mp.2025.16.0006 Received: 10 Jan., 2025 Accepted: 20 Feb., 2025 Published: 18 Mar., 2025 Copyright © 2025 Cai, 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: Cai X.G., 2025, Advances in rice breeding for resistance to fungal and bacterial diseases, Molecular Pathogens, 16(2): 45-52 (doi: 10.5376/mp.2025.16.0006) Abstract This study systematically reviews recent advances in breeding strategies aimed at enhancing rice resistance to major fungal pathogens, such as Magnaporthe oryzae (rice blast) and Rhizoctonia solani (sheath blight), as well as bacterial pathogens, including Xanthomonas oryzae pv. oryzae (bacterial leaf blight). The role of resistance (R) genes, quantitative trait loci (QTLs), and their integration into elite cultivars through marker-assisted selection (MAS), genomic selection, and gene pyramiding is discussed. Research indicates that cutting-edge molecular techniques, such as CRISPR genome editing, hold significant potential for developing broad-spectrum disease-resistant rice varieties. Environmental and agronomic management practices have been shown to significantly influence disease incidence and resistance expression, with field trials and successful breeding programs further validating the effectiveness and feasibility of these strategies. This study underscores the importance of integrating traditional breeding approaches with modern biotechnological tools to achieve durable resistance, ensuring sustainable rice production and effective disease management. Keywords Rice disease resistance; Rice blast; Bacterial leaf blight; Resistance genes; Genome editing 1 Introduction Rice blast and white leaf blight are one of the most serious rice diseases in the world. Rice blast is a fungal disease that can occur at almost any growth stage of rice. Once the environment is suitable, it may leave the entire rice field pellet free (Zarbafi and Ham, 2019; Sahu et al., 2022). Bacterial diseases of rice, such as bacterial blight and bacterial strabular plaque, are caused by white leaf blight bacteria and will also greatly reduce rice yields (Jiang et al., 2020; Ji et al., 2022). These bacteria change very quickly and can often break through existing disease-resistant genes, which is very troublesome to prevent and treat. In order to ensure stable rice yield and food security, cultivating disease-resistant varieties is a key method. Past research has shown that combining disease-resistant genes can effectively control these diseases (Liu et al., 2021). However, new bacterial variants continue to appear, so we have to continue to work hard to cultivate rice varieties that can resist various diseases for a long time. Now, biotechnology like molecular breeding and CRISPR/Cas9 has brought many new opportunities to rice disease-resistant breeding and has made green and sustainable planting more promising (Kumar et al., 2018). This study introduces new advances in rice antifungal and antibacterial breeding. The main contents include the discovery and utilization of disease-resistant genes, the application of molecular breeding technology, and the difficulties encountered in improving lasting resistance. I hope these contents can provide reference for future rice breeding and contribute to global food security. 2 Fungal Diseases Affecting Rice and Current Resistance Strategies 2.1 Rice blast (Magnaporthe oryzae) and resistance breeding approaches Rice blast is caused by a fungus and is one of the most serious diseases of rice in the world. This disease is difficult to prevent because it will quickly lose resistance to rice, causing unstable rice yields in many places. To deal with this problem, researchers have used many molecular breeding methods, such as QTL localization, marker-assisted selection, resistance gene combination, and gene transformation. These methods can introduce
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 46 disease-resistant genes into species that are prone to infection and improve the persistence of disease-resistant ability (Ashkani et al., 2015; Sahu et al., 2022). 146 disease-resistant genes for rice blast have been found, of which 37 have been studied in detail. These studies lay the foundation for us to develop disease-resistant varieties using marker breeding and gene editing techniques. There are also some genetically modified methods, such as adding the chitinase 1 gene of corn to rice, which also shows certain disease resistance (Anwaar et al., 2024). 2.2 Sheath blight (Rhizoctonia solani): challenges and resistant varieties Trefoil blight is caused by a pathogen called Rhizoma delta and is also harmful to rice. However, no genes that are completely resistant to diseases have been found, which makes breeding difficult. Environmental factors can also easily aggravate the condition, such as when the temperature is high and the humidity is high, the disease will be even more serious. Nowadays, breeding work mainly relies on finding varieties with "partial resistance", but this resistance will also be affected by the environment. The good news is that with the development of molecular genetics, researchers have found a lot of QTLs related to anti-treatment blight. These findings allow us to slowly breed rice with stronger disease resistance using marker-assisted selection methods (Zarbafi and Ham, 2019). However, these resistances are not stable enough and further research and improvement are needed. 2.3 Brown spot (Bipolaris oryzae) and genetic sources of resistance Brown spot disease is also a fungal disease, which has become more common in recent years due to rising temperatures. The bacteria of this disease grow especially fast at high temperatures, so warming makes it easier to explode. Compared with other rice diseases, no complete disease-resistant gene has been found in brown spot disease. Therefore, everyone can only rely on some resistance strategies. Through research, scientists have discovered some QTLs related to anti-brown spot disease, which is very important for breeding efforts (Mizobuchi et al., 2016). Only by constantly screening resistant materials and adding molecular breeding methods can this disease be better controlled and provide guarantees for the continuous production of rice. 3 Bacterial Diseases and Breeding for Resistance 3.1 Bacterial leaf blight (Xanthomonas oryzae pv. oryzae) 3.1.1 Major resistance genes (Xa genes) and their role Rice white leaf blight (BLB for short) is a very serious problem in rice cultivation and is caused by the white leaf blight bacteria (Xoo). It is currently found that whether rice can resist this disease is mainly related to a disease-resistant gene called “Xa gene”. These genes are very important for cultivating disease-resistant rice varieties. So far, scientists have found 44 Xa genes, 15 of which have been successfully cloned and studied (Joshi et al., 2020; Yang et al., 2022). These genes can recognize the substances released by the bacteria and then activate the rice’s own defense response, so they play a key role in preventing diseases. 3.1.2 Development of Xa-gene-pyramided varieties The researchers found that putting several different Xa genes into the same rice variety can make the disease resistant stronger. This practice is called “gene stacking” or “gene pyramid”. For example, some modified varieties such as Pusa Basmati-1 and Samba Mahsuri have introduced gene combinations such as xa5, Xa4, xa13 and Xa21, and the ability to resist BLB has been significantly improved. In this process, scientists used marker-assisted selection techniques, which can more conveniently integrate multiple disease-resistant genes into one variety (Huang et al., 2023; Yang, 2024). This also makes breeding faster and more accurate. 3.1.3 Field trials and resistance stability Doing field experiments is a very important step. It can help us understand whether these varieties with multiple Xa genes can really resist diseases in different places and climates. These tests allow us to determine whether these disease-resistant varieties are effective for different types of Xoo strains. If the disease resistance can play a stable role in the long term, it means that this variety is successful and is more suitable for promotion and cultivation. Therefore, field tests are essential to verify the resistance effect.
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 47 3.2 Bacterial leaf streak (Xanthomonas oryzae pv. oryzicola) 3.2.1 Genetic loci associated with resistance Bacterial stripe disease (BLS for short) is caused by the leukoplakia (Xoc) and is another common disease in rice (Figure 1). Current research has found several gene loci related to disease resistance. These sites are important for breeding efforts because they can help rice fight bacteria. These genes and substances released by bacteria will react, just like the Xa gene used in white leaf blight, which can enable rice to activate its own defense mechanism and thus play a role in anti-disease (Jiang et al., 2020). 3.2.2 Breeding challenges and advances Although we have achieved some results in researching anti-BLS, there are still many difficulties in the breeding process. One of the biggest challenges is that the bacteria change too quickly, and the pathogenesis of rice is quite complicated. Fortunately, molecular breeding technology has developed rapidly in recent years, and technologies such as genome-wide association analysis have helped us find some new disease-resistant genes. These methods also allow us to breed BLS-resistant rice varieties faster. This is very critical to controlling the disease. Figure 1 Symptoms of (a) bacterial light caused by Xanthomonas oryzae pv. oryzae and (b) bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola(Adopted from Jiang et al., 2020) 3.3 Other emerging bacterial diseases and their impact In addition to white leaf blight and stripe spot disease, some new bacterial diseases have also appeared on rice in recent years. These diseases also pose new threats to yield. To solve these problems, we have to continue to do research and continue to carry out breeding. Finding new disease-resistant genes and using them in breeding is the key to controlling these new diseases. Now, people are also using modern methods such as genetic engineering and marker-assisted selection. These new technologies can improve the efficiency of disease-resistant breeding and can also help us better deal with these new bacterial diseases (Chukwu et al., 2019; Liu et al., 2021; Matsumoto et al., 2021). 4 Molecular and Genomic Approaches in Disease-Resistant Rice Breeding 4.1 Application of CRISPR and genome editing in resistance enhancement TThe emergence of CRISPR and other gene editing technologies has given new ways to resist disease breeding in rice. In particular, CRISPR/Cas9 technology can directly change some genes that make rice prone to disease, which is the so-called "susceptible gene" (S gene), thereby enhancing the disease resistance of rice. For example, after the S genes such as Pi21, Bsr-d1 and Xa5 are changed, rice has become more resistant to pathogens such as rice blast bacteria and white leaf blight bacteria, and the normal growth of rice is not affected (Mishra et al., 2021; Tao et al., 2021). This technology can also modify multiple genes at once, helping to breed rice varieties that are resistant to multiple diseases. 4.2 Identification and mapping of quantitative trait loci (QTLs) To figure out how rice has the disease resistance, it is very important to find QTL related to disease resistance.
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 48 Recently, many studies have used SNP genetic maps to find QTLs related to some rice diseases, such as bacterial ear blight, leaf strip disease and brown strip disease. Some studies have also found important regions related to resistance to ramen disease on chromosomes 2, 4, 5, 7 and 9 through high-precision methods (Neelam et al., 2021). Later, the researchers further integrated these QTLs using meta-analysis methods, thus finding multiple candidate genes related to disease resistance (Kumar and Nadarajah, 2020). 4.3 Transcriptomic and proteomic insights into disease resistance In addition to QTL, we are now using transcriptomics and proteomics to study how rice fights diseases. These methods can help verify whether candidate genes in QTL work, and can also tell us which genes in rice are changing before and after bacterial infection (Fang et al., 2023). Through this analysis, researchers have a clearer understanding of how rice fights bacteria and can also find key disease-resistant genes and signaling pathways that can be used in breeding (Liu et al., 2021; Akohoue and Miedaner, 2022). Combining these molecular data with genomic information will help to more accurately carry out disease-resistant breeding. 5 Integration of Biotechnological Tools in Traditional Breeding Programs 5.1 Marker-assisted selection (MAS) for accelerated breeding Marker-assisted selection (MAS) is now a very commonly used tool in rice disease-resistant breeding. It can help us accurately add disease-resistant genes to varieties that are prone to disease, much faster than traditional methods. For example, MAS has been used to place several disease-resistant genes in a rice variety together, which can make rice more resistant to white leaf blight and blast (Ashkani et al., 2015; Chukwu et al., 2019; Sahu et al., 2022). The Tellahamsa variety bred with MAS can resist both diseases at the same time, which shows that this method is very useful (Jamaloddin et al., 2020). 5.2 Genomic selection and its role in developing resistant lines Genome selection is also a new breeding method. It uses genome-wide data to predict which varieties may be more resistant to disease, and then select them to perform well. This method can screen multiple disease-resistant genes at once, helping to cultivate rice varieties that can fight multiple diseases at the same time. Using genome selection with traditional breeding methods can also make breeding faster (Kumar et al., 2018; Tao et al., 2021). Moreover, by integrating multiple disease-resistant genes, resistance can also be longer-lasting and not easily broken by bacteria. 5.3 Use of molecular markers in breeding programs across regions In many regions, breeding projects have begun to use molecular marking technology to breed suitable local disease-resistant varieties. These markers can help us find disease-resistant genes in different genetic materials, and then transfer these genes to excellent varieties to enhance resistance. For example, some studies have used molecular markers to find new disease-resistant genes from wild rice and have been successfully introduced into cultivated rice (Ke et al., 2017). This provides new genetic resources for breeding and also allows rice varieties to be more adapted to local disease conditions. 6 Environmental and Agronomic Factors Influencing Disease Resistance 6.1 Influence of climatic conditions on disease incidence and resistance The weather has a great impact on the disease condition and resistance of rice. For example, rising temperatures can make some diseases more likely to break out. Like brown spots and bacterial seedling decay, it is more likely to occur at high temperatures around 30 °C because bacteria grow fast at this temperature (Mizobuchi et al., 2016). Therefore, to deal with these situations, we must breed rice varieties that can withstand high temperature diseases. Light also has an impact. When there are more cloudy days and less sun, rice will have a decrease in disease resistance, especially its resistance to rice blast disease becomes weak. This shows that light has a regulatory effect on the rice immune system and must also be taken into account during breeding (Liu et al., 2019). 6.2 Impact of soil health and microbiome on rice disease suppression Whether the soil is healthy and whether there are beneficial microorganisms in it will have a great impact on
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 49 whether rice is prone to illness. Good bacteria in the soil can help plants enhance their immunity, thereby reducing the chances of occurrence such as rice blast and bacterial blight. The current breeding work can also be done in combination with this aspect. For example, using marker-assisted selection techniques can select varieties that are more suitable for utilizing beneficial soil microorganisms, thereby enhancing disease resistance (Ludwików et al., 2015; Zhang et al., 2022). 6.3 Role of agronomic practices in enhancing resistance Daily planting management will also affect rice disease resistance. Methods such as crop rotation and adding organic fertilizer can improve soil conditions, make rice healthier, and the risk of getting sick is lower. Some disease-resistant genes can also be used through breeding. For example, the Xa4 gene can not only enhance cell walls and improve resistance, but also not affect yield (Hu et al., 2017). In addition, genetic engineering can help. For example, using bacteria-inducible promoters (such as those that control WRKY45) to regulate the expression of disease-resistant genes has been shown in some breeding experiments (Goto et al., 2016). 7 Case Studies of Successful Rice Breeding Programs 7.1 Development of IR64 and its blast resistance improvement IR64 is a high-yield rice variety, and its cultivation is an important breakthrough in rice breeding. This variety not only has high yields, but also has improved its resistance to rice blast disease later. The researchers used molecular methods such as marker-assisted selection and gene stacking to quickly introduce multiple disease-resistant genes into IR64. This allows it to resist a variety of bacteria and has a long-lasting resistance effect (Ashkani et al., 2015; Tao et al., 2021; Anwaar et al., 2024). Through these technologies, we can breed more disease-resistant and stable rice varieties, which is very helpful to food security. 7.2 Breeding programs in southeast asia targeting bacterial leaf blight In Southeast Asia, white leaf blight (BLB) is one of the main diseases affecting rice harvest. In order to deal with it, local breeding projects focus on developing varieties that can resist diseases for a long time, using both traditional breeding methods and molecular technology. In these projects, researchers found several useful disease-resistant genes (R genes) and used them in breeding, which increased the broad-spectrum resistance of rice to BLB (Chukwu et al., 2019; Jiang et al., 2020). The addition of marker-assisted selection and genetic engineering has accelerated the introduction of disease-resistant genes and also reduced the impact of this disease on yield. 7.3 Lessons from large-scale field trials and farmer adoption Large-area field experiments and actual use by farmers are important steps in testing rice breeding results. Experiments can tell us how newly bred varieties perform under different climates and planting conditions. In the land rice breeding project in Brazil, researchers screened out some varieties that were highly resistant to multiple diseases through repeated trials. After the promotion of these varieties, farmers are very enthusiastic about planting because of stable yields and fewer diseases, and the benefits are also improved. A specific example is the Tellahamsa breed. It has high yield and strong adaptability, but it is prone to infection with BB and Blast. Later, the researchers used marker-assisted backcross breeding (MABB) technology to introduce two BB disease-resistant genes (Xa21 and xa13) and two blast disease-resistant genes (Pi54 and Pi1) into Tellahamsa, and bred two new lines: TH-625-159 and TH-625-491 (Jamaloddin et al., 2020; Alves et al., 2021). These two new lines performed well after trials in different regions. They not only had strong disease resistance, but also retained the good yield and quality of the original varieties (Figure 2). This example shows that advanced breeding methods combined with field trials are key to achieving sustainable disease management. 8 Challenges and Future Directions in Rice Disease Resistance Breeding 8.1 Overcoming pathogen evolution and resistance breakdown A major problem with rice disease-resistant breeding is that the bacteria change too quickly. Sometimes, an originally resistant variety will lose its effect in no time. For example, after some new rice blast bacteria appear, the old varieties will no longer work (Singh et al., 2018). To deal with this situation, the researchers thought of
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 50 many solutions. A commonly used method is "gene stacking", which means combining multiple disease-resistant genes, so that rice can be more difficult to break by bacteria. However, if the bacteria continue to adapt to the new environment, it may still break through these defense lines, so this method is not 100% insurance. Figure 2 a: BB screening of ICF3 (TH-625-159 and TH-625-491) lines at ARI, Hyderabad, During Kharif, 2015-2016. Screening of selected ICF3 (TH-625-159 and TH-625-491) lines having Xa21+xa13+Pi54+Pi1 genes against local BB isolate (DX-020). ICF3 progenies were highly resistant against BB isolate (DX-020). TH: Tellahamsa- Recurrent parent (Susceptible); ISM: Improved Samba Mahsuri (Resistant); 159 and 491: ICF3progenies (TH-625-159 and TH-625-491). b: Blast screening of ICF3 (TH-625-159 and TH-625-491) lines at IIRR, Hyderabad, During Kharif, 2015-2016. Screening of selected ICF3 (TH-625-159 & TH-625-491) lines having Xa21+xa13+Pi54+Pi1 genes against local blast isolate (NLR-1). ICF3 lines were highly resistant against blast isolate (NLR-1). TH: Tellahamsa- Recurrent parent (Susceptible); NLR145- (Resistant check); HR12- (Susceptible check); 159 and 491: ICF3 lines (TH-625-159 and TH-625-491) (Adopted from Jamaloddin et al., 2020) 8.2 Enhancing genetic diversity in breeding populations To make rice more resistant to disease, the genetic diversity of breeding populations must be large enough. Different gene combinations can provide more resistance to disease. Nowadays, many people use molecular techniques, such as marker-assisted selection and genome editing, to introduce various disease-resistant genes into rice (Liu et al., 2021; Tao et al., 2021). Technologies like CRISPR/Cas9 can specifically change genes that are prone to illness. This not only enhances resistance, but also does not affect rice yield and quality (Ma, 2024). Finding more broad-spectrum resistance genes and using them in breeding will provide more options for future work. 8.3 Collaborative international efforts in rice disease resistance research Rice disease is a global problem, and international cooperation is crucial to better solve it. Countries share disease-resistant genes, technologies and research results, which can enable new varieties to be developed faster. Now many countries have cooperated together to find many useful disease-resistant genes and loci (Anwaar et al., 2024). These results are very important for breeding programs around the world. Moreover, through international cooperation, newly bred varieties can also be tested in different regions to see how they perform in different climates and planting conditions. This cooperation will not only accelerate the promotion of disease-resistant varieties, but also contribute to global food security.
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 51 Acknowledgments Thanks Dr. J. Zhong from the Institute of Life Science of Jiyang College of Zhejiang A&F University for his 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 Akohoue F., and Miedaner T., 2022, Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize, Frontiers in Plant Science, 13: 1050891. https://doi.org/10.3389/fpls.2022.1050891 Alves N.B., Castro D.G., Félix M.R., Tomé L.M., Neto A.R., and Botelho F.B.S., 2021, Performance of upland rice strains in reaction to fungal diseases, Scientia Agraria Paranaensis, 2021: 24-31. https://doi.org/10.18188/SAP.V20I1.25542 Anwaar S., Jabeen N., Ahmad K.S., Shafique S., Irum S., Ismail H., Khan S.U., Tahir A., Mehmood N., and Gleason M., 2024, Cloning of maize chitinase 1 gene and its expression in genetically transformed rice to confer resistance against rice blast caused by Pyricularia oryzae, Plos One, 19(1): e0291939. https://doi.org/10.1371/journal.pone.0291939 Ashkani S., Rafii M.Y., Shabanimofrad M., Miah G., Sahebi M., Azizi P., Tanweer F., Akhtar M., and Nasehi A., 2015, Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop, Frontiers in Plant Science, 6: 886. https://doi.org/10.3389/fpls.2015.00886 Chukwu S., Rafii M., Ramlee S., Ismail S., Hasan M., Oladosu Y., Magaji U., Akos I., and Olalekan K., 2019, Bacterial leaf blight resistance in rice: a review of conventional breeding to molecular approach, Molecular Biology Reports, 46: 1519-1532. https://doi.org/10.1007/s11033-019-04584-2 Fang Y., Ding D., Gu Y., Jia Q., Zheng Q., Qian Q., Wang Y., Rao Y., and Mao Y., 2023, Identification of QTLs conferring resistance to bacterial diseases in rice, Plants, 12(15): 2853. https://doi.org/10.3390/plants12152853 Goto S., Sasakura-Shimoda F., Yamazaki M., Hayashi N., Suetsugu M., Ochiai H., and Takatsuji H., 2016, Development of disease-resistant rice by pathogen-responsive expression of WRKY45, Plant Biotechnology Journal, 14(4): 1127-1138. https://doi.org/10.1111/pbi.12481 Hu K.M., Cao J.B., Zhang J., Xia F., Ke Y.G., Zhang H.T., Xie W.Y., Liu H.B., Cui Y., Cao Y.L., Sun X.L., Xiao J.H., Li X., Zhang Q.L., and Wang S.P., 2017, Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement, Nature Plants, 3(3): 1-9. https://doi.org/10.1038/nplants.2017.9 Huang F., He N., Yu M., Li D., and Yang D., 2023, Identification and fine-mapping of a new bacterial blight resistance gene Xa43(t) in Zhangpu wild rice (Oryza rufipogon), Plant Biology, 25(3): 433-439. https://doi.org/10.1111/plb.13502 Jamaloddin M., Rani C.V., Swathi G., Anuradha C., Vanisri S., Rajan C.P.D., Raju K., Bhuvaneshwari V., Jagadeeswar R., Laha G., Prasad M., Satyanarayana P., Cheralu C., Rajani G., Ramprasad E., Sravanthi P., Kumar A., Kumari A., Yamini K., Mahesh D., Rao S., Sundaram R., and Madhav M., 2020, Marker assisted gene pyramiding (MAGP) for bacterial blight and blast resistance into mega rice variety “Tellahamsa”, PLoS ONE, 15(6): e0234088. https://doi.org/10.1371/journal.pone.0234088 Ji Z., Sun H., Wei Y., Li M., Wang H., Xu J., Lei C., Wang C., and Zhao K., 2022, Ectopic expression of executor gene Xa23 enhances resistance to both bacterial and fungal diseases in rice, International Journal of Molecular Sciences, 23(12): 6545. https://doi.org/10.3390/ijms23126545 Jiang N., Yan J., Liang Y., Shi Y., He Z., Wu Y., Zeng Q., Liu X., and Peng J., 2020, Resistance genes and their interactions with bacterial blight/leaf streak pathogens (Xanthomonas oryzae) in rice (Oryza sativa L.)-an updated review, Rice, 13(1): 3. https://doi.org/10.1186/s12284-019-0358-y Joshi J.B., Arul L., Ramalingam J., and Uthandi S., 2020, Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management, Journal of Biosciences, 45(1): 112. https://doi.org/10.1007/s12038-020-00085-8 Ke Y., Deng H., and Wang S., 2017, Advances in understanding broad‐spectrum resistance to pathogens in rice, The Plant Journal, 90: 738-748. https://doi.org/10.1111/tpj.13438 Kumar I.S., and Nadarajah K., 2020, A meta-analysis of quantitative trait loci associated with multiple disease resistance in rice (Oryza sativa L.), Plants, 9(11): 1491. https://doi.org/10.3390/plants9111491
Molecular Pathogens, 2025, Vol.16, No.2, 45-52 http://microbescipublisher.com/index.php/mp 52 Kumar K., Kokiladevi E., Arul L., Varanavasiappan S., and Sudhakar D., 2018, Engineering disease resistance in rice, Biotechnologies of Crop Improvement, 2: 183-206. https://doi.org/10.1007/978-3-319-90650-8_8 Liu M., Zhang S., Hu J., Sun W., Padilla J., He Y., Li Y., Yin Z., Liu X., Wang W., Shen D., Li D., Zhang H., Zheng X., Cui Z., Wang G., Wang P., Zhou B., and Zhang Z., 2019, Phosphorylation-guarded light-harvesting complex II contributes to broad-spectrum blast resistance in rice, Proceedings of the National Academy of Sciences, 116: 17572-17577. https://doi.org/10.1073/pnas.1905123116 Liu Z.Q., Zhu Y.J., Shi H.B., Qiu J.H., Ding X.H., and Kou Y.J., 2021, Recent progress in rice broad-spectrum disease resistance, International Journal of Molecular Sciences, 22(21): 11658. https://doi.org/10.3390/ijms222111658 Ludwików A., Cieśla A., Arora P., Das G., Rao G.J.N., and Das R., 2015, Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar, Frontiers in Plant Science, 6: 698. https://doi.org/10.3389/fpls.2015.00698 Ma H.L., 2024, Advanced genetic tools for rice breeding: CRISPR/Cas9 and its role in yield trait improvement, Molecular Plant Breeding, 15(4): 178-186. https://doi.org/10.5376/mpb.2024.15.0018 Matsumoto H., Fan X., Wang Y., Kusstatscher P., Duan J., Wu S., Chen S., Qiao K., Wang Y., B., Zhu G., Hashidoko Y., Berg G., Cernava T., and Wang M., 2021, Bacterial seed endophyte shapes disease resistance in rice, Nature Plants, 7: 60-72. https://doi.org/10.1038/s41477-020-00826-5 Mishra R., Zheng W., Joshi R., and Zhao K., 2021, Genome editing strategies towards enhancement of rice disease resistance, Rice Science, 28: 133-145. https://doi.org/10.1016/J.RSCI.2021.01.003 Mizobuchi R., Fukuoka S., Tsushima S., Yano M., and Sato H., 2016, QTLs for resistance to major rice diseases exacerbated by global warming: brown spot bacterial seedling rot and bacterial grain rot, Rice, 9: 1-12. https://doi.org/10.1186/s12284-016-0095-4 Neelam K., Kumar K., Kaur A., Kishore A., Kaur P., Babbar A., Kaur G., Kamboj I., Lore J., Vikal Y., Mangat G., Kaur R., Khanna R., and Singh K., 2021, High-resolution mapping of the quantitative trait locus (QTLs) conferring resistance to false smut disease in rice, Journal of Applied Genetics, 2022: 1-11. https://doi.org/10.1007/s13353-021-00659-8 Sahu P.K., Sao R., Choudhary D., Thada A., Kumar V., Mondal S., Das B., Jankuloski L., and Sharma D., 2022, Advancement in the breeding biotechnological and genomic tools towards development of durable genetic resistance against the rice blast disease, Plants, 11(18): 2386. https://doi.org/10.3390/plants11182386 Singh P.K., Nag A., Arya P., Kapoor R., Singh A., Jaswal R., and Sharma T.R., 2018, Prospects of understanding the molecular biology of disease resistance in rice, International Journal of Molecular Sciences, 19(4): 1141. https://doi.org/10.3390/ijms19041141 Tao H., Shi X., He F., Wang D., Xiao N., Fang H., Wang R., Zhang F., Wang M., Li A., Liu X., Wang G., and Ning Y., 2021, Engineering broad-spectrum disease-resistant rice by editing multiple susceptibility genes, Journal of Integrative Plant Biology, 63(9): 1639-1648. https://doi.org/10.1111/jipb.13145 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 Y., Zhou Y., Sun J., Liang W., Chen X., Wang X., Zhou J., Yu C., Wang J., Wu S., Yao X., Zhou Y., Zhu J., Yan C., Zheng B., and Chen J., 2022, Research progress on cloning and function of xa genes against rice bacterial blight, Frontiers in Plant Science, 13: 847199. https://doi.org/10.3389/fpls.2022.847199 Zarbafi S., and Ham J., 2019, An overview of rice QTLs associated with disease resistance to three major rice diseases: blast sheath blight and bacterial panicle blight, Agronomy, 9(4): 177. https://doi.org/10.3390/AGRONOMY9040177 Zhang A.N., Liu Y., Wang F.M., Kong D.Y., Bi J.G., Zhang F.Y., Luo X.X., Wang J.H., Liu G.L., Luo L.J., and Yu X.Q., 2022, Molecular breeding of water-saving and drought-resistant rice for blast and bacterial blight resistance, Plants, 11(19): 2641. https://doi.org/10.3390/plants11192641
Molecular Pathogens, 2025, Vol.16, No.2, 53-60 http://microbescipublisher.com/index.php/mp 53 Review and Progress Open Access Signaling Pathways in Potato’s Response to Phytopathogens Yinghua Chen Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding email: yinghua.chen@jicat.org Molecular Pathogens, 2025, Vol.16, No.2 doi: 10.5376/mp.2025.16.0007 Received: 22 Feb., 2025 Accepted: 23 Mar., 2025 Published: 31 Mar., 2025 Copyright © 2025 Chen, 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: Chen Y.H., 2025, Signaling pathways in potato’s response to phytopathogens, Molecular Pathogens, 16(2): 53-60 (doi: 10.5376/mp.2025.16.0007) Abstract This study reviews the signaling pathways of potatoes to cope with plant pathogens, and focuses on the role of key signaling molecules such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) in regulating plant defense responses. By analyzing the interactions of signaling pathways and their regulatory role in resistance gene expression, the core role of the StMKK5-StSIPK module in enhancing resistance and the key function of reactive oxygen species (ROS) in signaling transmission is demonstrated. The research explores the application prospects of CRISPR/Cas9 technology in genome editing and the disease prevention effect of exogenous signaling molecules (such as SA) in actual agriculture, providing important theoretical basis and practical guidance for future potato disease-resistant breeding and agricultural applications. Keywords Signaling pathways; Salicylic acid; Disease resistance; Phytophthora infestans; Molecular breeding 1 Introduction Potatoes are a very important crop in the world. It can not only be used as a staple food, but also contains rich nutrition. Globally, it is the fourth largest food crop after rice, wheat and corn. It is critical to both food security and agricultural development (Wang et al., 2023). However, potato cultivation is often affected by various diseases. These diseases will not only reduce yield, but also affect quality. Late blight caused by Phytophthora infestans and bacterial blight caused by Ralstonia solanacearumare common and serious diseases that may cause great economic losses (Yang et al., 2020). To enhance potato’s disease resistance, we need to figure out how plants defend against pathogens through signaling pathways in the body. Ethylene, salicylic acid and jasmonic acid are several important signaling molecules that help plants fight bacteria (Yang et al., 2023). These signals will influence each other, forming a complex network that activates the plant’s defense mechanism (Zheng et al., 2020; Yang et al., 2024). For example, the StMKK5-StSIPK module in potatoes can activate salicylic acid and ethylene pathways, making it more resistant to late-birth pathogens. In addition, the MAPK signaling pathway is also important, which regulates immune responses and enhances resilience to adverse environments (Zaynab et al., 2021). This study mainly discusses several signaling pathways involved in potatoes when fighting bacteria, such as ethylene, salicylic acid, jasmonic acid and MAPK. We combine transcriptome and multiomic data from recent years to further understand their role in disease resistance. These studies help us to have a clearer understanding of how these signals work and can also provide some ideas for improving potatoes’ disease resistance. 2 Phytopathogens and Their Interaction with Potatoes 2.1 Common potato phytopathogens (e.g., Phytophthora infestans) Potatoes are often affected by a pathogen called Phytophthora infestans, which can cause a serious disease called late blight. This disease will cause a large reduction in potato yields and has become a major problem in potato cultivation around the world (Yu et al., 2024). Besides it, there are also common pathogens that are also troublesome, such as Ralstonia solanacearum, which causes bacterial blight, and Potato virus Y, which causes necrotic ring spots. These pathogens also affect yield and quality (Cao et al., 2020).
Molecular Pathogens, 2025, Vol.16, No.2, 53-60 http://microbescipublisher.com/index.php/mp 54 2.2 Mechanisms of pathogen infection Pathogens like Phytophthora infestans have a set of “routines” to deal with potatoes. It interferes with the potato's own immune system, especially defense-related signaling pathways, such as salicylic acid (SA) and jasmonic acid (JA)-related pathways (Saubeau et al., 2016). It can make these pathways “fail”, which makes it more susceptible to infection. The study found that a transcription factor called StbZIP61 can regulate the synthesis of SA, which is important for resistance to P. infestans. In addition, StMKK5-StSIPK module can activate SA and ethylene signaling pathways, thereby improving the disease resistance of plants (Yang et al., 2023). 2.3 Effects of pathogens on potato growth and yield Pathogens like Phytophthora infestans have a very big impact on potatoes. Infected plants usually don’t grow well and photosynthesis can also be affected. Leaves and tubers are often destroyed, which eventually leads to a significant decline in yield (Zheng et al., 2020). Worse, these pathogens are highly adaptable and spread quickly, making them difficult to control (Zhang et al., 2020). Multiple defense signaling pathways in plants, such as SA, JA and ethylene-related pathways, will participate in the defense response together. But these pathogens can also find ways to bypass these defenses, so it is challenging to prevent and treat (Zhou et al., 2018). 3 Overview of Potato Signaling Pathways 3.1 Classification of signaling pathways: hormonal signals, defense signals, and systemic acquired resistance (SAR) In order to deal with bacteria, potatoes will initiate many signaling pathways. It can be roughly divided into three categories: hormone signals, defense signals, and system acquisition resistance, also called SAR. Hormone signals are mainly three plant hormones: salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), each of which has different functions. Salicylic acid is mainly used to deal with trophic pathogens and is a key ingredient in establishing SAR. SAR is a long-term defense method that can work against a variety of bacteria (Shine et al., 2019; Zeier, 2021). Jasmonic acid and ethylene are more commonly used to defend against saprophytic bacteria and plant-eating insects. These two hormones often work together and can enhance the plant’s defense response (Yang et al., 2020; Yan et al., 2022). 3.2 Key signaling molecules: salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) These three hormones-SA, JA, and ET-are the “commanders” of the entire defense pathway. Studies have found that when plants are attacked by pathogens, SA increases rapidly, and then activates some disease-resistant genes (called PR genes) to increase resistance (Saubeau et al., 2016). JA is responsible for regulating a portion of the genes related to defense. ET mainly helps fight disease by regulating various defense enzymes and transcription factors. These three hormones are not each doing their own, but are connected to each other. Sometimes, JA and ET inhibit the signaling effect of SA, allowing plants to choose different coping methods based on different bacteria (Wang, 2024). 3.3 Cross-regulation among signaling pathways The “match” between these signaling pathways is an important part of plant defense. SA, JA, and ET not only work alone, they also influence each other. For example, sometimes SA and JA/ET “dry” against each other, but in some cases they will also cooperate to activate certain defense proteins, such as calmodulin kinase (CDPK) and RPM1-interacting protein 4 (Yang et al., 2023). This mutual cooperation can help plants find a balance between “growth” and “disease prevention”. In general, these signaling pathways in potatoes form a very flexible system that can adjust the response according to different situations, thereby more effectively fighting various bacteria. 4 Potato Signaling Pathways in Response to Phytopathogens 4.1 The salicylic acid pathway and its role in defense The salicylic acid pathway is an important method used by potatoes to deal with bacteria. It can initiate many defense reactions, such as expressing pathologically related proteins (PR proteins) and enhancing plant systemic gain resistance (SAR). After potatoes are infected with Phytophthora infestans, expression of SA-related genes such as EDS1, WRKY1, PR-1 and PR-2 is significantly increased (Saubeau et al., 2016). Studies have found that
Molecular Pathogens, 2025, Vol.16, No.2, 53-60 http://microbescipublisher.com/index.php/mp 55 the StMKK5-StSIPK module can activate the SA pathway, which is very important for potatoes to resist this bacteria. StMKK5 is a kinase that works with StSIPK and can trigger programmed cell death (also called HR) by initiating SA signals, thereby preventing bacteria from spreading. When StMKK5 or its downstream gene SIPK is “silenced”, the HR response triggered by INF1 becomes weaker. This suggests that this module is important for SA-mediated immune responses. If there is a problem with StMKK5, such as a mutation, the HR reaction will also disappear, indicating that its kinase activity is critical. Even if StMKK5 is overexpressed, the lesions area does not change much compared with the control group, indicating that the SA signal is also regulated by other signals (Figure 1) (Yang et al., 2023). In addition, other pathways such as SA and ethylene also interact to make defense more complicated (Fantino et al., 2017). Figure 1 Overexpression of potato StMKK5 triggers a SIPK-dependent plant cell death in Nicotiana benthamiana (Adopted from Yang et al., 2023) 4.2 Synergistic action of the jasmonic acid-ethylene pathway The two signal pathways, jasmonic acid and ethylene, often cooperate to help potatoes defend against bacteria, especially when fighting Phytophthora infestans. Research has found that spraying ethylene in disease-resistant potatoes can stimulate a defensive response, which shows that ethylene not only works on its own, but is also related to other hormones such as JA. The relationship between these two hormones is complex. Sometimes they cooperate to enhance resistance, but sometimes they may also inhibit each other, such as when controlling certain defense genes or protein kinases (Yan et al., 2022). 4.3 Role of reactive oxygen species (ROS) in signaling pathways Reactive oxygen species (ROS) is also a very critical ingredient in potato disease prevention. It can quickly activate defenses, such as triggering hypersensitivity reactions or hardening the cell walls. In potatoes, reactive oxygen species like H₂O₂ are produced quickly. A protein called StRac1 regulates the level of H₂O₂, thereby enhancing resistance (Zhang et al., 2020). ROS can also work with signal molecules like SA to produce stronger defense effects. This also shows that ROS plays an important role in the immune signal of plants (Zheng et al., 2020). 4.4 Functions of signaling proteins (e.g., MAPKs, NLR proteins) Some proteins are also important in potato disease prevention, such as MAPK (migen-activated protein kinase) and NLR (proteins with nucleotide binding and leucine repeat structures). For example, the MAPK module StMKK5-StSIPK can activate the SA and ethylene pathways to make potatoes more resistant to disease (Chen et al., 2021). Another protein, StMPK7, is downstream of StMKK1, which also enhances resistance through SA signaling (Liu, 2024). These proteins can integrate signals from different pathways to regulate defense responses, thereby dealing with pathogens more effectively.
Molecular Pathogens, 2025, Vol.16, No.2, 53-60 http://microbescipublisher.com/index.php/mp 56 5 Interaction Between Signaling Pathways and Resistance Genes 5.1 Activation and regulation of resistance genes To start the disease-resistant gene in potatoes, some signaling pathways need to be used to “help”. For example, the MAPK cascaded pathway (modules like StMKK5-StSIPK) can activate two important signal pathways, salicylic acid (SA) and ethylene (ET). This is critical to increasing potato resistance to Phytophthora infestans. This module mainly triggers cell death by phosphorylating StSIPK, that is, “turning on the switch”, which is actually a way of defense. This process can also activate a series of genes related to SA and ET (Yang et al., 2023). In addition, ethylene can also stimulate the immune response of potatoes. Studies have found that under ethylene treatment, the expression of some specific transcription factors and kinases will change. This shows that in the defense reaction, hormones will also affect each other, forming a relatively complex network. 5.2 Effector-triggered immunity (ETI) involving Rgenes Effector-triggered immunity, referred to as ETI, is an important mechanism for plant disease prevention and usually depends on the R gene. In potatoes, StMPK7 in the MAPK signaling pathway is a downstream member of StMKK1, which plays a big role in combating late blight. StMPK7 can be activated after being phosphorylated, and then it can enhance resistance through SA signal. This also shows that R genes play a central role in ETI (Chen et al., 2021). There is also a protein called StRac1 that is also very important. It can regulate the production of reactive oxygen species (H₂O₂), which is one of the common defense methods in ETI reactions. 5.3 Case study: The Rpi gene family in late blight resistance Rpi is a highly studied potato disease-resistant gene, specifically used to fight late blight caused by Phytophthora infestans. These genes work with a variety of signaling pathways, including hormone pathways such as SA, JA, and ET. These pathways cooperate with each other to help activate defense responses faster and more efficiently. In some disease-resistant varieties, the SA pathway is particularly active, with significantly increased expression of defense genes such as EDS1 and PR-1, which is very critical for late blight disease (Zhang et al., 2020). These studies also show that the coordination between the Rpi gene and different signaling pathways is very complex. This cross-regulation mechanism allows plants to make corresponding adjustments according to different bacteria and improve overall resistance. 6 Case Study: Signaling Regulation in Potato Late Blight 6.1 Phytophthora infestans infection process and induced signaling responses Phytophthora infestans is the pathogen that causes late blight. It attacks some important signaling pathways in the potato body, causing infection. It suppresses the salicylic acid (SA) pathway through an effector called Pi06432, which is important to the plant's immune system. Pi06432 targets a protein called StUDP, which has a ubiquitin-like domain in potatoes. Pathogens use this to reduce the activity of the proteasome, which will also make a transcription factor called SARD1 unstable, and ultimately reduce SA synthesis, and the plant s defense will become weaker (Wang et al., 2023). However, during the infection, the abscisic acid (ABA) signal is also activated. There is a non-coding RNA called StlncRNA13558, which can promote the production of reactive oxygen species (ROS) and affect the SA pathway, thereby improving disease resistance. Experiments have found that if the RNA is overexpressed, the expression of the StPRL gene will also be significantly improved; and if StPRL is inhibited, the resistance will become worse. In addition, the expression of StlncRNA13558 and StPRL can also be increased after ABA application, making the plant more resistant. This shows that this RNA can trigger local immunity by allowing ROS to accumulate, and also plays an important role in signaling and cell death (Figure 2) (Shang et al., 2024). 6.2 Roles of salicylic acid and jasmonic acid pathways in late blight resistance The two pathways, salicylic acid (SA) and jasmonic acid (JA), are both critical in fighting late blight. The StMKK5-StSIPK module in potatoes can activate the SA and ethylene (ET) pathways, which can strengthen defenses and initiate programmed cell death to prevent bacteria from spreading. There is also a transcription factor called StbZIP61, which regulates SA synthesis by binding to StNPR3L. It only works in the presence of SA,
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