Molecular Pathogens 2024, Vol.15 http://microbescipublisher.com/index.php/mp © 2024 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 2024, Vol.15 http://microbescipublisher.com/index.php/mp © 2024 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), 2024, Vol. 15 ISSN 1925-1998 http://microbescipublisher.com/index.php/mp © 2024 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 2024, Vol.15, No.5 【Research Perspective】 Breeding: New Methods and Application Prospects in Disease-Resistant Strawberry Breeding 219-226 Ben J.L. Zhong DOI: 10.5376/mp.2024.15.0021 【Research Insight】 Bacterial Diseases of Sugarcane: Insights into Pathogenicity and Control Measures 227-236 Kaiwen Liang DOI: 10.5376/mp.2024.15.0022 Harnessing Genetic Engineering for Durable Resistance Against Xanthomonas oryzae 237-245 Chengxi Wang, Jiawei Li DOI: 10.5376/mp.2024.15.0023 【Feature Review】 The Role of TAL Effectors in the Pathogenicity of Xanthomonas onLegumes 246-254 Xiaoxi Zhou, Tianxia Guo DOI: 10.5376/mp.2024.15.0024 Mechanisms of Stress Resistance and Sporulation in Bacillus subtilis 255-262 Xing Zhao, Minsheng Lin DOI: 10.5376/mp.2024.15.0025
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 219 Research Perspective Open Access Breeding: New Methods and Application Prospects in Disease-Resistant Strawberry Breeding Ben J.L. Zhong Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding email: jianli.zhong@hitar.org Molecular Pathogens, 2024, Vol.15, No.5 doi: 10.5376/mp.2024.15.0021 Received: 16 Jul., 2024 Accepted: 28 Aug., 2024 Published: 10 Sep., 2024 Copyright © 2024 Zhong, 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: Zhong B.J., 2024, Breeding: new methods and application prospects in disease-resistant strawberry breeding, Molecular Pathogens, 15(5): 219-226 (doi: 10.5376/mp.2024.15.0021) Abstract This study focuses on new methods and application prospects in disease-resistant strawberry breeding, exploring how modern breeding technologies can address the common disease challenges in strawberry cultivation. The research analyzes the limitations of traditional breeding methods and then delves into the application of emerging technologies, such as marker-assisted selection (MAS), gene editing (CRISPR-Cas9), and genomic selection (GS) in enhancing strawberry disease resistance. It also examines the potential of biotechnologies, such as gene mapping and RNA interference (RNAi), in controlling strawberry diseases and proposes the integration of traditional and modern breeding approaches to promote the sustainable development of the strawberry industry. Keywords Disease-resistant strawberry breeding; Marker-assisted selection; Gene editing; Genomic selection; RNA interference 1 Introduction Strawberries are a high-value crop globally, but their cultivation is significantly hampered by various diseases. Powdery mildew, caused by Podosphaera aphanis, is one of the most prevalent diseases affecting strawberries, leading to substantial economic losses (Menzel, 2021). Other notable diseases include anthracnose crown rot and grey mold, which also contribute to decreased yields and increased production costs (Bestfleisch et al., 2015; Xiao et al., 2020). Traditionally, chemical fungicides have been the primary method for controlling these diseases. However, there is a growing push from industry, environmental, and societal sectors to reduce the reliance on chemical controls due to their adverse effects and regulatory restrictions (O’Connor et al., 2022). Breeding for disease-resistant strawberry varieties presents a sustainable alternative to chemical fungicides. Disease-resistant cultivars can significantly reduce the need for chemical treatments, thereby lowering production costs and minimizing environmental impact. Moreover, disease resistance is often heritable, making it a viable long-term strategy for managing strawberry diseases (Davik and Honne, 2005). The integration of advanced breeding techniques, such as genome-wide association studies (GWAS) and high-throughput phenotyping (HTP), has shown promise in identifying and selecting disease-resistant traits more efficiently. These methods not only enhance the accuracy of selection but also accelerate the breeding process, making it possible to develop resistant varieties more quickly (Tapia et al., 2022). This study mainly discusses the latest methods and application prospects of disease resistant strawberry breeding, which will cover the challenges brought by various strawberry diseases, the importance of developing resistant varieties, and the innovative breeding techniques adopted to achieve this goal. The latest research and progress contribute to a comprehensive overview of the current status and future directions of disease resistant strawberry breeding, emphasizing the potential of these new methods to transform strawberry cultivation and make it more sustainable and economically feasible for growers. 2 Traditional Methods in Disease-Resistant Strawberry Breeding 2.1 Conventional Breeding Techniques Conventional breeding techniques have long been the cornerstone of developing disease-resistant strawberry cultivars. These methods primarily involve the selection, introduction, hybridization, and screening of plant
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 220 varieties to accumulate favorable genes that confer resistance to specific pathogens. The process typically starts with the identification of resistant cultivars, which are then crossed with local cultivars to introduce resistance genes into the breeding pool. Sources of resistance often include landraces, related species, mutations, and wild relatives (Khan et al., 2020). The breeding programs focus on two types of resistance: vertical resistance, controlled by major genes, and horizontal resistance, controlled by minor genes. Vertical resistance tends to be more specific and can be overcome by pathogen evolution, whereas horizontal resistance offers broader, albeit often weaker, protection (Jiménez et al., 2022). Despite the challenges, conventional breeding remains a cost-effective and environmentally friendly approach to managing plant diseases. 2.2 Limitations of Traditional Breeding in Addressing Disease Resistance While conventional breeding techniques have been instrumental in developing disease-resistant strawberry cultivars, they come with several limitations. One significant challenge is the rapid evolution of phytopathogens, which can quickly overcome the resistance bred into the plants. This dynamic nature of pathogen evolution makes it difficult to achieve long-lasting resistance (Fu, 2023). The genetic gains in breeding for resistance to certain diseases, such as Verticillium wilt and Phytophthora crown rot, have been negligible over the past decades. Studies have shown that a large proportion of the genetic resources preserved in public germplasm collections are moderately to highly susceptible to these diseases, indicating that traditional breeding methods have not been sufficiently effective (Feldmann et al., 2023). The heritability of resistance traits is often low to moderate, further complicating the breeding process (Pincot et al., 2020). 3 New Methods in Disease-Resistant Strawberry Breeding 3.1 Marker-assisted selection (MAS) Marker-assisted selection (MAS) is a method that utilizes molecular markers to assist in the selection of desirable traits, such as disease resistance, in plant breeding. This technique has been particularly effective in cases where disease resistance is controlled by one or a few genes with a large effect on the phenotype. MAS can significantly increase the efficiency of breeding programs by allowing for the precise targeting of these genes, thereby accelerating the development of disease-resistant varieties (He et al., 2014; Collins et al., 2018). For instance, genotyping-by-sequencing (GBS) has been developed as an advanced MAS tool, combining molecular marker discovery and genotyping to facilitate genome-wide association studies and genomic selection (Figure 1) (Merrick et al., 2021). In strawberries, MAS can be used to identify and select for genes associated with resistance to common diseases, thereby improving the overall resilience of the crop. 3.2 Genome editing (CRISPR-Cas9) Genome editing, particularly using the CRISPR-Cas9 system, has revolutionized the field of plant breeding by enabling precise and targeted modifications to the genome. This technology allows for the direct alteration of genes associated with disease resistance, thereby creating transgene-free, disease-resistant plant varieties (Chen, 2024). CRISPR-Cas9 has been successfully applied to develop disease-resistant crops by knocking out susceptibility genes or introducing resistance genes. The precision and efficiency of CRISPR-Cas9 make it a powerful tool for strawberry breeding, where it can be used to enhance resistance to pathogens that significantly impact yield and quality. The ability to make specific genetic changes without introducing foreign DNA is particularly advantageous for meeting regulatory requirements and consumer acceptance (Ahmad et al., 2020). 3.3 Genomic selection (GS) Genomic selection (GS) is an advanced breeding method that uses genome-wide markers to predict the breeding value of individuals, thereby facilitating the selection of superior genotypes. Unlike MAS, which focuses on a few specific markers, GS considers the entire genome, making it more effective for traits controlled by multiple genes with small effects (Merrick et al., 2022). GS has shown high predictive accuracy for quantitative disease
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 221 resistance, as demonstrated in various crops, including wheat and strawberries (Cockerton et al., 2021). By leveraging large datasets of genomic and phenotypic information, GS can accelerate the breeding cycle and increase genetic gains. In strawberries, GS can be used to improve complex traits such as disease resistance, yield, and fruit quality by selecting the best-performing individuals based on their genomic profiles (Crossa et al., 2017). This method holds great promise for developing robust, disease-resistant strawberry varieties that can thrive under diverse environmental conditions. Figure 1 Schematic diagram of plant breeding using molecular markers (Adopted from Jeon et al., 2023) 4 Applications of Biotechnology in Enhancing Disease Resistance 4.1 Gene mapping for disease resistance 4.1.1 Identification of disease resistance genes Gene mapping has become a pivotal tool in identifying disease resistance genes in strawberries. A study on octoploid strawberries identified a major locus, FaRPc2, on linkage group 7D, which is significantly associated with resistance to crown rot disease caused by Phytophthora cactorum. This locus contains multiple resistance alleles, making it a prime target for breeding programs aimed at enhancing disease resistance (Mangandi et al., 2017). Additionally, advances in plant genome sequencing have facilitated the discovery of novel resistance (R) genes, which can be leveraged to control diseases caused by various pathogens (Pandolfi et al., 2017). 4.1.2 Utilization of gene mapping in breeding The utilization of gene mapping in breeding programs allows for the precise selection of desirable traits. By employing quantitative trait locus (QTL) analyses in multiparental populations, breeders can increase the power of QTL detection and estimate allele effects across diverse genetic backgrounds. This approach has been successfully applied to improve resistance to diseases like crown rot in strawberries, thereby accelerating genetic gains and enhancing the efficiency of breeding programs (Yin and Qiu, 2019). Predictive breeding techniques, which combine phenotypic data with genomic information, have shown promise in developing cultivars with increased resistance to diseases such as verticillium wilt (Taliansky et al., 2019). 4.2 RNA interference (RNAi) in disease control 4.2.1 Mechanism and benefits of RNAi RNA interference (RNAi) is a gene regulatory mechanism that involves the silencing of specific genes through the action of small interfering RNAs (siRNAs) or microRNAs (miRNAs). This process can effectively down-regulate gene expression without affecting other genes, making it a precise tool for crop improvement. RNAi has been widely used to develop resistance against various pathogens, including viruses, bacteria, fungi, and nematodes, by targeting and silencing genes essential for pathogen survival or virulence (Kamthan et al., 2015). The benefits of
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 222 RNAi include its specificity, environmentally friendly nature, and potential to reduce the reliance on chemical pesticides (Halder et al., 2022; Koeppe et al., 2023). 4.2.2 Case studies of RNAi in strawberry In strawberries, RNAi has been employed to enhance disease resistance by creating RNAi intragenic silencing cassettes. These cassettes combine specific strawberry promoters with pathogen defense-related DNA sequences to silence corresponding endogenous genes during fruit ripening, thereby improving fruit quality and resistance to pathogens (Figure 2) (Súnico et al., 2021). Additionally, RNAi-based technologies have been explored for their potential to control plant viruses through the exogenous application of double-stranded RNAs (dsRNAs), which can induce systemic RNA silencing and provide a sustainable method for crop protection (Taliansky et al., 2019). These case studies highlight the versatility and effectiveness of RNAi in developing disease-resistant strawberry cultivars. Figure 2 Transient promoter probe analysis of the synthetic FvDOF2 and FvAAT2 DNA fragments, respectively, in F. × ananassa fruit (Adopted from Súnico et al., 2021) Image caption: Numbers 1 and 2 represent two different fruit samples. Histochemical GUS staining was performed after 5 days of fruit infiltration with agrobacterium carrying different query promoter constructs (pFvDOF2: GUS, pFvAAT2: GUS, and pCaMV35s: GUS) or the pKGWFS7.0 empty vector as a negative control (Ø). Query promoter constructs were injected in one half of the fruit, whereas the empty vector (Ø) was injected in the opposite half. For each construct, images represent tissues slices from two different fruit samples (Adopted from Súnico et al., 2021)
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 223 5 Prospects of Integrated Breeding Approaches 5.1 Combining conventional and modern breeding techniques Combining conventional breeding techniques with modern advancements offers a promising pathway to enhance disease resistance in strawberries. Traditional methods, while foundational, often fall short in efficiency and precision. Integrating high-throughput phenotyping (HTP) with genomic information, for instance, has shown significant improvements in selection accuracy for traits like powdery mildew resistance in strawberries. This approach leverages spectral analysis of canopy reflectance and genomic markers, resulting in up to a two-fold increase in predictive ability over models using markers alone (Tapia et al., 2022). The integration of speed breeding with AI and genomics-assisted breeding (GAB) can drastically reduce the breeding cycle time, making it possible to develop new cultivars more quickly and accurately (Bhat et al., 2023). 5.2 Use of multi-omics approaches for enhanced breeding efficiency The integration of multi-omics approaches—genomics, transcriptomics, proteomics, and metabolomics—has revolutionized plant breeding by providing a comprehensive understanding of the biological processes underlying desirable traits. This holistic view allows for the precise assembly of desired alleles using genome editing techniques, thereby enhancing breeding strategies for climate-resilient and nutrient-sufficient crops (Mahmood et al., 2022). The integration of omics databases is crucial for this process, as it enables the comprehensive analysis of complex traits and their interactions, ultimately improving the efficiency of crop breeding (Chao et al., 2023). By leveraging these advanced techniques, breeders can develop strawberry varieties with improved disease resistance and other beneficial traits more effectively (Langridge and Fleury, 2011). 5.3 The potential of big data and AI in strawberry breeding The advent of big data and artificial intelligence (AI) has opened new avenues for plant breeding. Machine learning (ML) algorithms, in particular, have shown great promise in analyzing vast amounts of complex data generated by high-throughput omics technologies. These tools can identify key genetic markers and predict breeding outcomes with high accuracy, thereby accelerating the development of new plant varieties (Najafabadi et al., 2023). AI techniques also enable the capture of non-linear and epistatic interactions in genome-wide association studies (GWAS) and genomic selection (GS), making these variations available for genomics-assisted breeding. The integration of big data and AI in strawberry breeding can thus significantly enhance the efficiency and precision of developing disease-resistant cultivars. 6 Challenges in Disease-Resistant Strawberry Breeding 6.1 Genetic complexity of disease resistance The genetic complexity of disease resistance in strawberries poses a significant challenge for breeders. The octoploid nature of the strawberry genome complicates the identification and introgression of resistance genes. Recent studies have highlighted the intricate genetic architecture of resistance traits, which often involve multiple loci and complex interactions between genes. For instance, the development of resistance to Phytophthora crown rot has been hindered by the quantitative nature of the resistance phenotypes and their moderate heritability (Mangandi et al., 2017; Jiménez et al., 2022). Additionally, the genetic background can significantly influence the expression and durability of resistance traits, as seen in the resistance to plant viruses (Gallois et al., 2018). 6.2 Environmental influences on disease resistance Environmental factors play a crucial role in the effectiveness of disease resistance in strawberries. The interaction between genotype and environment can lead to variability in resistance levels, making it challenging to develop universally resistant cultivars. For example, genotype-environment interactions were observed in the resistance to Colletotrichum gloeosporioides, with different transplant types showing varying levels of genetic control across locations (Osorio et al., 2014). Similarly, the spread of pests and pathogens due to climate change can alter the effectiveness of resistance traits, necessitating continuous adaptation in breeding programs (Súnico et al., 2021).
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 224 6.3 Evolution of pathogen resistance Pathogens are constantly evolving, which can lead to the breakdown of resistance in previously resistant strawberry cultivars. The evolution of resistance-breaking pathogen strains is a significant concern, as it can render existing resistance genes ineffective. This challenge is exemplified by the resistance to Verticillium wilt, where genetic gains in breeding for resistance have been negligible over the past 60 years, partly due to the evolution of the pathogen (Pincot et al., 2020; Feldmann et al., 2023). The genetic background of the host plant can also influence the evolution of resistance-breaking isolates, complicating the breeding process. 6.4 Challenges in breeding for broad-spectrum resistance Breeding for broad-spectrum resistance, which is effective against multiple pathogens, is particularly challenging. The complexity of host-pathogen interactions and the need to combine multiple resistance genes make this a difficult task. For instance, the development of resistance to Botrytis cinerea requires the identification of genotypes that combine resistance with desirable horticultural traits, a goal that has yet to be achieved (Bestfleisch et al., 2015). The identification and utilization of diverse resistance genes from underutilized gene bank resources can enhance the genetic variance and improve the accuracy of genomic selection for broad-spectrum resistance (Jiménez et al., 2022). 6.5 Regulatory and economic constraints Regulatory and economic constraints also pose significant challenges in disease-resistant strawberry breeding. The development and deployment of genetically modified or gene-edited crops face stringent regulatory hurdles, which can delay the introduction of new resistant cultivars. Moreover, the economic viability of breeding programs depends on the balance between the costs of developing resistant cultivars and the potential economic benefits. The use of advanced genomic and bioinformatics tools, such as synthetic biology-assisted intragenesis strategies, can accelerate genetic gains and reduce the reliance on pesticides, but these approaches require substantial investment and regulatory approval (Súnico et al., 2021). 7 Concluding Remarks Recent advancements in disease-resistant strawberry breeding have been significantly propelled by the advent of CRISPR/Cas9 genome-editing technology. This method has demonstrated remarkable precision and efficiency in creating targeted gene modifications, surpassing traditional breeding techniques in speed and accuracy. The application of CRISPR/Cas9 has enabled the development of transgene-free disease-resistant crops, which is crucial for addressing regulatory and public acceptance issues. Additionally, the integration of genomic selection and genome-wide association studies (GWAS) has provided deeper insights into the genetic basis of disease resistance, facilitating the identification of key resistance loci and enhancing the accuracy of breeding programs. These technological advancements have opened new avenues for the rapid development of disease-resistant strawberry cultivars, promising to mitigate the impact of pathogens and improve crop yields. Future research should focus on expanding the genetic diversity of breeding populations by incorporating underutilized gene bank resources, which can introduce rare and favorable alleles into modern cultivars. Efforts should be made to refine CRISPR/Cas9 techniques to minimize off-target effects and enhance editing specificity, possibly through the use of shorter single-guide RNAs and dual Cas9 nickases. It is also essential to develop robust delivery systems for CRISPR/Cas9 components that avoid the integration of foreign DNA, thereby addressing concerns related to genetically modified organisms (GMOs). Integrating genomic selection with traditional breeding methods can accelerate the development of disease-resistant cultivars by enabling early selection without extensive phenotyping. Collaborative efforts between researchers, breeders, and regulatory bodies will be crucial to streamline the adoption of these advanced breeding techniques and ensure their successful implementation in commercial strawberry production. The future of disease-resistant strawberry breeding looks promising, with CRISPR/Cas9 technology at the forefront of this transformation. The ability to make precise genetic modifications rapidly and efficiently offers unprecedented opportunities to develop cultivars that can withstand biotic and abiotic stresses. As the field of genome editing continues to evolve, it is anticipated that these technologies will play a pivotal role in sustainable agricultural practices, ensuring food security and environmental protection. By harnessing the full potential of
Molecular Pathogens 2024, Vol.15, No.5, 219-226 http://microbescipublisher.com/index.php/mp 225 CRISPR/Cas9 and integrating it with genomic selection and other advanced breeding strategies, the development of robust, disease-resistant strawberry cultivars will become more efficient and effective, paving the way for a resilient and productive future in strawberry cultivation. Acknowledgments I would like to thank the two peer reviewers for their feedback, and also like to thank Ms. Guo T. from the research team for her literature review. 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. 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Molecular Pathogens 2024, Vol.15, No.5, 227-236 http://microbescipublisher.com/index.php/mp 227 Research Insight Open Access Bacterial Diseases of Sugarcane: Insights into Pathogenicity and Control Measures Kaiwen Liang Hainan Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: kaiwen.liang@hitar.org Molecular Pathogens, 2024, Vol.15, No.5 doi: 10.5376/mp.2024.15.0022 Received: 30 Jul., 2024 Accepted: 09 Sep., 2024 Published: 23 Sep., 2024 Copyright © 2024 Liang, 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: Liang K.W., 2024, Bacterial diseases of sugarcane: insights into pathogenicity and control measures, Molecular Pathogens, 15(5): 227-236 (doi: 10.5376/mp.2024.15.0022) Abstract Sugarcane is a globally important economic crop, but bacterial diseases significantly impact its yield and quality. This study outlines the major types of bacterial diseases in sugarcane, including Ratoon Stunting Disease (RSD), Leaf Scald Disease, and Gumming Disease, and explores the pathogenic mechanisms of the bacteria, such as virulence factors, host-pathogen interactions, tissue colonization, and systemic infection mechanisms. Additionally, it discusses the influence of environmental factors on pathogenicity. To effectively address these diseases, current diagnostic techniques are proposed, including field-based visual diagnosis, molecular diagnostic tools, and serological and immunological methods. Control strategies, such as chemical control, biological control, and the breeding of disease-resistant varieties, are highlighted as key approaches. Notably, the use of beneficial microbes as biocontrol agents has seen new advancements. The concept of Integrated Disease Management (IDM), which combines biological, chemical, and cultural measures, is proposed to achieve sustainable management of sugarcane diseases. Keywords Sugarcane; Bacterial Diseases; Biological Control; Pathogenic Mechanisms; Integrated Disease Management 1 Introduction Sugarcane (Saccharum officinarumL.) is a vital crop predominantly cultivated in tropical and subtropical regions around the globe. Originally grown in South Eastern Asia and the Pacific for chewing, sugarcane has evolved into a crucial agricultural commodity with diverse applications, including the production of sugar, biofuels, and medicinal products (Bechem and Mbella, 2019). The economic significance of sugarcane cannot be overstated, as it serves as the primary source of sucrose and plays a pivotal role in the alcohol and biofuel industries (Hossain et al., 2020). The crop's extensive cultivation supports numerous economies, particularly in regions where it is a major agricultural product. Despite its economic importance, sugarcane production faces significant challenges due to various diseases, including those caused by bacteria. Bacterial diseases can severely impact sugarcane yield and quality, leading to substantial economic losses. For instance, diseases like red rot, caused by Colletotrichum falcatum, can result in yield losses ranging from 5% to 50%, with a corresponding reduction in sugar recovery to as low as 31% (Hossain et al., 2020). The prevalence of such diseases necessitates the implementation of effective management strategies to mitigate their impact and ensure the sustainability of sugarcane cultivation. This study provides an overview of bacterial diseases affecting sugarcane, with a focus on their pathogenicity and control measures. It also explores current and future disease detection and management strategies, aiming to propose effective methods to alleviate the spread of bacterial diseases in sugarcane plantations, improve the sustainability of sugarcane cultivation, and ensure the sustainable survival of the sugar industry in tropical and subtropical regions. 2 Major Bacterial Diseases Affecting Sugarcane 2.1 Ratoon stunting disease (RSD) Ratoon Stunting Disease (RSD) is a significant bacterial disease affecting sugarcane, caused by the bacterium Leifsonia xyli subsp. xyli (Lxx). This disease is notorious for its lack of visible symptoms, making it difficult to
Molecular Pathogens 2024, Vol.15, No.5, 227-236 http://microbescipublisher.com/index.php/mp 228 detect and manage effectively. RSD leads to substantial yield losses globally due to its highly contagious nature and the challenges associated with its detection and control (Cia et al., 2018; Zhu et al., 2021). Recent studies have provided insights into the molecular and physiological responses of sugarcane to Lxx infection. Transcriptomic analyses have revealed that sugarcane responds to Lxx infection by altering various metabolic pathways, including photosynthesis, phytohormone biosynthesis, and plant-pathogen interactions. Notably, Lxx infection significantly inhibits photosynthetic processes and down-regulates gibberellin response, contributing to the growth retardation observed in RSD-affected plants. Additionally, the identification of quantitative trait loci (QTL) associated with RSD resistance has opened new avenues for developing RSD-resistant sugarcane varieties through marker-assisted breeding (You et al., 2020). Efficient diagnostic methods are crucial for managing RSD. Techniques such as quantitative PCR on pooled leaf sheath biopsies and the development of mill-based diagnostics using crude cane juice have shown promise in detecting Lxx with high sensitivity, facilitating better disease surveillance and management (Young et al., 2016; Burman et al., 2023). 2.2 Leaf scald disease Leaf Scald Disease, caused by the bacterium Xanthomonas albilineans, is another major bacterial disease affecting sugarcane. This disease is characterized by the appearance of white to yellowish streaks on the leaves, which eventually lead to leaf necrosis and plant death. The pathogen infects the xylem vessels, disrupting water transport and causing wilting and scalding of the leaves (Quecine et al., 2016). The management of Leaf Scald Disease primarily involves the use of disease-free planting material, crop rotation, and the application of bactericides. Breeding for resistant varieties is also a key strategy in controlling this disease. However, the development of resistant varieties is challenging due to the complex nature of the disease and the genetic variability of the pathogen. 2.3 Gumming disease Gumming Disease, caused by the bacterium Xanthomonas vasculorum, is a significant threat to sugarcane production. This disease is characterized by the exudation of a gummy substance from the infected tissues, leading to the formation of lesions and cankers on the stalks and leaves. The pathogen infects the vascular system, causing wilting, stunted growth, and eventual plant death. Control measures for Gumming Disease include the use of disease-free planting material, sanitation practices to prevent the spread of the pathogen, and the application of bactericides (Chakraborty et al., 2023). Breeding for resistant varieties is also an important strategy, although it is complicated by the genetic diversity of the pathogen and the polyploid nature of sugarcane. 3 Mechanisms of Pathogenicity in Sugarcane Bacterial Diseases 3.1 Virulence factors in bacterial pathogens Virulence factors are critical components that enable bacterial pathogens to infect and cause disease in sugarcane. These factors include enzymes, toxins, and other molecules that facilitate the invasion and colonization of host tissues. For instance, Acidovorax avenae subsp. avenae, the causal agent of red stripe disease, exhibits various virulence factors such as proteases, amylases, and endoglucanases, which are essential for breaking down plant cell walls and facilitating infection (Bertani et al., 2023). Similarly, Sporisorium scitamineum, responsible for sugarcane smut, produces plant cell wall degrading enzymes (PCWDEs) like chitinase and laccase, which are crucial for tissue colonization and successful pathogen ingress (Nalayeni et al., 2021). The interplay among these virulence factors is complex and often involves multiple genes and pathways, highlighting the multifaceted nature of bacterial pathogenicity in sugarcane (Zhao et al., 2022). 3.2 Host-pathogen interactions The interaction between sugarcane and bacterial pathogens is a dynamic process involving both the pathogen's virulence mechanisms and the host's defense responses. Xanthomonas albilineans, which causes leaf scald, modulates the host's reactive oxygen species (ROS) homeostasis and salicylic acid (SA) pathway to establish
Molecular Pathogens 2024, Vol.15, No.5, 227-236 http://microbescipublisher.com/index.php/mp 229 infection. High pathogenicity strains of X. albilineans induce a significant increase in ROS production and a decrease in SA-mediated defense responses, thereby facilitating infection (Zhao et al., 2022). Sugarcane's response to Sporisorium scitamineuminvolves the upregulation of defense-related genes and hormone signaling pathways, which are crucial for mounting an effective defense against the pathogen (Agisha et al., 2022). These interactions underscore the importance of understanding both the pathogen's strategies and the host's defense mechanisms to develop effective control measures. 3.3 Mechanisms of tissue colonization and systemic infection Bacterial pathogens employ various strategies to colonize and spread within sugarcane tissues. For example, Sporisorium scitamineum uses stomata to penetrate host tissues and secretes hydrolytic enzymes to facilitate mycelial entry. Once inside, the pathogen can spread systemically, often aided by the production of quorum signals that enhance cell aggregation and infection efficiency (Zhang and Yang, 2024). Xanthomonas albilineans, on the other hand, produces a xanthan-like polymer that obstructs xylem vessels, leading to systemic infection and disease symptoms such as leaf yellowing and desiccation (Legaz et al., 2018). These mechanisms highlight the diverse strategies employed by bacterial pathogens to colonize and infect sugarcane, emphasizing the need for targeted control measures. 3.4 Environmental factors influencing pathogenicity Environmental factors play a significant role in influencing the pathogenicity of bacterial diseases in sugarcane (Figure 1). Factors such as temperature, humidity, and soil conditions can affect the expression of virulence genes and the overall fitness of the pathogen. For instance, the expression of pathogenicity-associated genes in Sporisorium scitamineumis influenced by environmental conditions, which can affect the timing and severity of disease outbreaks (Nalayeni et al., 2021). Additionally, the ability of bacterial pathogens to utilize various carbon and nitrogen sources, as well as their tolerance to pH and osmotic stress, can impact their survival and virulence in different environmental conditions (Singh et al., 2021). Understanding these environmental influences is crucial for predicting disease outbreaks and developing effective management strategies. Figure 1 Antifungal activity of strain B18 against Sporisorium scitamineum, Ceratocystis paradoxa, and Fusarium verticillioides sugarcane pathogens (Adopted from Singh et al., 2021) Image caption: The first row shows control plates, the second row shows growth inhibition of pathogens by strain B18 in dual culture plate assay, and the third row shows the agar well diffusion method. C (control) (Adopted from Singh et al., 2021)
Molecular Pathogens 2024, Vol.15, No.5, 227-236 http://microbescipublisher.com/index.php/mp 230 4 Diagnostic Techniques for Bacterial Diseases 4.1 Field-based visual diagnosis Field-based visual diagnosis involves the identification of disease symptoms directly in the field. This method is often the first step in diagnosing bacterial diseases in sugarcane. However, it has significant limitations, particularly for diseases like Ratoon Stunting Disease (RSD), which do not exhibit distinct external symptoms, making visual diagnosis challenging and often unreliable (Young et al., 2016; Chakraborty et al., 2023; Krishna et al., 2023). For instance, bacterial leaf wilt caused by Pantoea stewartii subsp. stewartii can be identified by symptoms such as leaf blade bleaching, blight, and necrotic lesions, but these symptoms can be confused with other stress factors (Cui et al., 2020). 4.2 Molecular diagnostic tools Molecular diagnostic tools have revolutionized the detection of bacterial pathogens in sugarcane. Techniques such as Polymerase Chain Reaction (PCR) and quantitative PCR (qPCR) are widely used due to their high sensitivity and specificity. For example, PCR-based methods have been developed for detecting pathogens responsible for diseases like RSD, leaf scald, and gumming disease (Srivastava et al., 2016; Viswanathan et al., 2018; Krishna et al., 2023). The use of isothermal amplification techniques, such as Loop-Mediated Isothermal Amplification (LAMP), has also been optimized for on-site diagnostics, allowing for rapid and accurate detection of pathogens like Leifsonia xyli subsp. xyli in crude cane juice at sugar mills (Burman et al., 2023). These molecular tools are essential for large-scale disease surveillance and management. 4.3 Serological and immunological methods Serological and immunological methods, including enzyme-linked immunosorbent assay (ELISA) and immunofluorescence, are used to detect bacterial pathogens based on antigen-antibody interactions. These methods are particularly useful for detecting pathogens in asymptomatic plants. Evaporative-binding enzyme immunoassay (EB-EIA) coupled with phase contrast microscopy (PCM) has been used to detect Leifsonia xyli subsp. xyli in sugarcane xylem sap (Liang, 2024). Although these methods can be highly specific, they often require sophisticated laboratory equipment and trained personnel, which can limit their use in field conditions. Nonetheless, they remain valuable tools for confirming diagnoses made by other methods (Viswanathan et al., 2018). 5 Control Measures for Bacterial Diseases 5.1 Chemical control strategies 5.1.1 Use of antibiotics and chemicals Chemical control strategies for bacterial diseases in sugarcane often involve the use of antibiotics and chemical treatments. These methods aim to reduce the bacterial load and prevent the spread of pathogens. For instance, certain chemicals have been used to manage diseases like red rot caused by Colletotrichum falcatum(Hossain et al., 2020). However, the effectiveness of these treatments can vary, and their application must be carefully managed to avoid resistance development and environmental harm. 5.1.2 Challenges of chemical control in sugarcane The use of chemical control in sugarcane faces several challenges. One major issue is the potential for environmental pollution and disruption of soil microbial flora due to excessive and long-term application of chemical fertilizers and pesticides (Singh et al., 2021). Additionally, the high cost and labor-intensive nature of chemical treatments can be prohibitive for many farmers. There is also the risk of developing resistant strains of pathogens, which can render chemical treatments ineffective over time (Chakraborty et al., 2023). 5.2 Biological control approaches 5.2.1 Beneficial microbes as biocontrol agents Biological control approaches utilize beneficial microbes to combat bacterial diseases in sugarcane. Endophytic bacteria, such as those from the genus Bacillus, have shown promise in controlling pests and diseases by colonizing plant tissues and producing antimicrobial compounds (Rocha et al., 2021). Similarly, rhizosphere
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