Bioscience Method 2025, Vol.16 http://bioscipublisher.com/index.php/bm © 2025 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Bioscience Method 2025, Vol.16 http://bioscipublisher.com/index.php/bm © 2025 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. BioSci Publisher is an international Open Access publisher specializing in bioscience methods, including technology, lab tool, statistical software and relative fields registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher BioSci Publisher Editedby Editorial Team of Bioscience Methods Email: edit@bm.bioscipublisher.com Website: http://bioscipublisher.com/index.php/bm Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Bioscience Methods (ISSN 1925-1920) is an open access, peer reviewed journal published online by BioSci Publisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of bioscience, the range of topics including (but are not limited to) technology review, technique know-how, lab tool, statistical software and known technology modification. Case studies on technologies for gene discovery and function validation as well as genetic transformation. All the articles published in Bioscience Methods are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BioSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Bioscience Methods (online), 2025, Vol.16, No.3 ISSN 1925-1920 https://bioscipublisher.com/index.php/bm © 2025 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Genomic Strategies for Disease Resistance Breeding in Sugarcane: Identification of Resistance Genes, Transcriptomic Analysis, and Molecular Markers Dandan Huang, May H. Wang Bioscience Methods, 2025, Vol.16, No.3, 108-116 Continuing the Path of Green Income Growth to Realize the Dream of Industrial Revitalization WenjunCai Bioscience Methods, 2025, Vol.16, No.3, 117-136 Mitochondrial Genome Evolution of Abalone and Its Applications in Species Identification Chengmin Sun, Rudi Mai Bioscience Methods, 2025, Vol.16, No.3, 137-153 Optimization of Traditional Vinegar Brewing Processes Based on Natural Raw Materials and Analysis of Functional Components Xudong Chen, Zeqin Chen, Yelin Huang, Jinghong Wang, Lei Yong Bioscience Methods, 2025, Vol.16, No.3, 154-161 Identification of Disease Resistance Genes and CRISPR-Based Genome Editing in Channa spp. Fei Zhao, Jinni Wu Bioscience Methods, 2025, Vol.16, No.3, 162-172
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 108 Research Insights Open Access Genomic Strategies for Disease Resistance Breeding in Sugarcane: Identification of Resistance Genes, Transcriptomic Analysis, and Molecular Markers Dandan Huang1, May H. Wang1,2 1 Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China 2 Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding email: 174708555@qq.com Bioscience Methods, 2025, Vol.16, No.3 doi: 10.5376/bm.2025.16.0011 Received: 01 Mar., 2025 Accepted: 11 Apr., 2025 Published: 02 May, 2025 Copyright © 2025 Huang and Wang, 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: Huang D.D., and Wang H.M., 2025, Genomic Strategies for disease resistance breeding in sugarcane: identification of resistance genes, transcriptomic analysis, and molecular markerst, Bioscience Methods, 16(3): 108-116 (doi: 10.5376/bm.2025.16.0011) Abstract Sugar cane is an important sugar crop in the world. Its yield and quality are often affected by a variety of diseases, which seriously restricts industrial development. Traditional disease-resistant breeding methods have problems such as long cycles and low efficiency, which are difficult to meet the needs of modern agriculture for efficient and precise breeding. With the advancement of genomics technology, sugarcane disease-resistant breeding has entered a new stage. This study systematically reviews the genomic strategies of sugarcane disease-resistant breeding, covering genomic resource construction, disease-resistant gene mining and functional verification, transcriptome analysis, molecular marker development, and multiomic integration application. Particularly emphasized the potential of emerging technologies such as gene editing, pan-genome and artificial intelligence in improving the efficiency of disease-resistant breeding. By integrating multi-level omics data and advanced technologies, sugarcane disease-resistant breeding is expected to achieve the transformation from traditional experience to precise design, providing a solid theoretical foundation and technical support for cultivating new sugarcane varieties with high yield, high sugar and disease-resistant sugarcane. Keywords Sugarcane; Disease-resistant breeding; Genomics; Transcriptome analysis; Molecular marker 1 Introduction Sugarcane (Saccharumspp.) is an important sugar and bioenergy crop worldwide and is mainly grown in tropical and subtropical regions. However, various diseases seriously threaten their production, causing significant economic losses. To achieve sustainable cultivation and meet the growing demand for sugar and biofuels, it is especially important to cultivate disease-resistant sugar cane varieties. Sugarcane normally gets sick because of different germs like fungi, bacteria and viruses. The most common diseases are red rot disease, smut disease, white leaf disease and mosaic disease. Sugarcane plants do not mature well if they are infected by these diseases. As a result, farmers harvest a lot less sugarcane and its quality is also poor. This has proved to be a major problem for sugarcane fields across the globe, as it is now harder to grow enough healthy sugarcane (Pimenta et al., 2023). Because sugarcane has a complex polyploid genome, traditional disease-resistant breeding methods face many difficulties. This complexity increases the difficulty of genetic analysis and extends the breeding cycle (Wu et al., 2022). Furthermore, disease-resistant traits have quantitative genetic characteristics and are susceptible to environmental factors, making it difficult to obtain stable and lasting disease resistance by conventional methods (Lu et al., 2023; Lin et al., 2024). New gene technology is helping make sugarcane more disease-resistant. Scientists can now use DNA sequencing to find genes that fight diseases. This helps pick the best plants for breeding faster. Another method called GWAS looks at the whole genome to spot disease-resistant traits. By studying how genes work when plants get sick, we learn how sugarcane defends itself. Adding these gene tools to breeding programs speeds up creating stronger sugarcane types. This is good for farming long-term because healthier plants mean better harvests.
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 109 2 Sugarcane Genomic Resources and Identification of Disease Resistance Genes 2.1 Complexity of the sugarcane genome and recent assembly achievements Sugarcane harbors highly complex DNA that is difficult to handle. Scientists have identified some vital sets of genes that make the plant disease resistant. Experiments show that NBS-LRR genes are the key to ensuring sugarcane's immunity to infections. Wild sugarcane species, especially Saccharum spontaneum, contribute precious disease-resistance genes to the cultivated sugarcane. Researchers have also cloned catalase genes that make it possible for sugarcane to cope with stresses in the environment. These results reveal how sugarcane's complex genetic makeup enables it to survive. The findings indicate the value of wild sugarcane types for breeding hardier, disease-resistant crops (Jiang et al., 2023). 2.2 Identification and annotation of disease-related gene families Researchers have identified a number of disease-resistant genes in sugarcane using various genetic analysis methods (Parvaiz et al., 2021). One of the significant discoveries is resistance gene analogues (RGAs) - these genes have differential patterns of activity in disease-resistant sugarcane compared to susceptible ones, clearly demonstrating their protective role (Rody et al., 2019). Recent studies with improved genetic network analysis identified interrelated groups of genes involved in smut disease prevention as a group and in plant stress alleviation (Wu et al., 2022). These all give the insight into sugarcane's natural defense mechanisms. The research shows how certain genetic studies result in the discovery of sugarcane's innate protection networks, providing prospective knowledge for creating more resistant varieties of sugarcane. 2.3 Functional validation and expression analysis of resistance genes Functional verification and gene expression analysis are very critical to understanding the mechanism of action of disease-resistant genes. Studies have found that some genes (such as ScCAT1) are upregulated under pathogen stress, which can enhance disease resistance by regulating reactive oxygen levels (Wu et al., 2023). In addition, the expression of some specific disease-resistant genes (such as PR10 and HCT1) has been shown to be related to early infection processes and disease-resistant mechanisms (Hidayah et al., 2021). These findings emphasize the importance of functional verification in identifying key disease-resistant genes and also provide the possibility of its application in breeding. 3 Application of Transcriptome Analysis in Studying Disease Resistance Mechanisms 3.1 Transcriptomic changes in sugarcane under pathogen infection Transcriptome analysis plays an important role in revealing the response mechanism of sugarcane to pathogenic infection. For example, during Sporisorium scitamineum infection, studies have found a large number of differentially expressed genes (DEGs), showing a complex stress response mechanism in sugarcane (McNeil et al., 2018). Similarly, many DEGs associated with metabolic processes and phytohormone signaling were also detected after Xanthomonas albilineans infection, which are crucial for plant defense responses (Figure 1). These studies show that sugarcane has dynamic changes in its gene expression during its resistance to pathogen invasion. 3.2 Screening and functional classification of differentially expressed genes Scientists have been studying how sugarcane genes respond when the plant is sick. They have noticed that there are certain genes that get expressed when disease hits. These genes are associated with certain important defense responses in the plant. There are certain genes that act through stress response pathways. Some of these include the MAPK signaling pathway that functions as an alarm system, hormone signaling pathways, and pathways that assist the plant in fighting germs (Ntambo et al., 2019). Scientists found out that most of these active genes assist in making special chemicals that combat diseases. These are crucial for protecting the plant. In a surprising turn of events, even genes that regulate basic plant processes seem to play a role in defense. These are photosynthesis genes (the process by which plants generate food from sun energy) and amino acid biosynthesis genes (protein precursors) (Zhang et al., 2022). These findings confirm that sugarcane utilizes many different systems to protect itself against disease, along with its special defense genes. The plant's normal processes also help keep it in good health.
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 110 Figure 1 Transcriptome analysis of genes in the RNA-seq dataset of sugarcane (Adopted from Jiang et al., 2023) Image caption: Transcriptomic analysis in multiple RNA-seq datasets. (A) Differential expression analysis of S. spontaneumand S. officinarumalleles. (B) Differentially expressed NBS-LRR genes in multiple diseases. (Adopted from Jiang et al., 2023) 3.3 Construction and analysis of key disease resistance pathways Researchers are studying how the synergy of sugarcane genes operates when they resist disease. Through one method called WGCNA, sets of genes were discovered to collaborate in resisting smut disease (Wu et al., 2022). These sets of genes control critical processes in the plant like the synthesis of glutathione and flavonoids that function as a protective role. By comparing gene activity data to biological networks, scientists have gained more insight about disease-resistance genes called RGAs and how they work with other defense systems (Rody et al., 2021). The study is revealing sugarcane's natural defense while helping to decide on the best genes to employ in breeding healthier, disease-resistant sugarcane. The study provides vital information for breeding sugarcane that will be more resistant to disease but also maintain quality production. 3.2 Screening and functional classification of differentially expressed genes Scientists have been studying how sugarcane genes respond when the plant is sick. They have noticed that there are certain genes that get expressed when disease hits. These genes are associated with certain important defense responses in the plant. There are certain genes that act through stress response pathways. Some of these include the MAPK signaling pathway that functions as an alarm system, hormone signaling pathways, and pathways that assist the plant in fighting germs (Ntambo et al., 2019). Scientists found out that most of these active genes assist in making special chemicals that combat diseases. These are crucial for protecting the plant. In a surprising turn of events, even genes that regulate basic plant processes seem to play a role in defense. These are photosynthesis genes (the process by which plants generate food from sun energy) and amino acid biosynthesis genes (protein precursors) (Zhang et al., 2022). These findings confirm that sugarcane utilizes many different systems to protect itself against disease, along with its special defense genes. The plant's normal processes also help keep it in good health.
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 111 3.3 Construction and analysis of key disease resistance pathways Researchers are studying how the synergy of sugarcane genes operates when they resist disease. Through one method called WGCNA, sets of genes were discovered to collaborate in resisting smut disease (Wu et al., 2022). These sets of genes control critical processes in the plant like the synthesis of glutathione and flavonoids that function as a protective role. By comparing gene activity data to biological networks, scientists have gained more insight about disease-resistance genes called RGAs and how they work with other defense systems (Rody et al., 2021). The study is revealing sugarcane's natural defense while helping to decide on the best genes to employ in breeding healthier, disease-resistant sugarcane. The study provides vital information for breeding sugarcane that will be more resistant to disease but also maintain quality production. 4 Development of Molecular Markers and Their Application in Disease-Resistant Breeding 4.1 Development of SNP and SSR markers associated with disease resistance The development of molecular markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) has greatly promoted the development of disease-resistant breeding. In cassava, researchers have developed and verified some SNP markers associated with cassava mosaic disease resistance sites that have high prediction accuracy against traits (Ige et al., 2021). Similarly, SSR markers associated with resistance to multiple diseases were also found in other crops. For example, SSR markers in peanuts are associated with resistance to premature spot disease, SSR markers in rice are associated with resistance to brown planthoppers (Shabanimofrad et al., 2015), while SSR markers in cotton are associated with resistance to jassid (Venkatesulu et al., 2023). These markers are of great significance for identifying disease-resistant genotypes and promoting the application of marker-assisted selection (MAS) in breeding. 4.2 Association analysis between markers and disease resistance traits Researchers use correlation analysis to link DNA markers to disease resistance in plants. They discovered specific SSR markers linked to early spot disease resistance in peanuts, which helps breeders develop better varieties (Zongo et al., 2017). Research on rice showed the same SSR markers linked to resistance to brown planthoppers, explaining some of the defensive traits of the plants. Tobacco researchers also discovered SSR markers linked to resistance to potato Y virus, enabling breeders to select resistant plants using novel tools (Darvishzadeh et al., 2016). The marker research helps to confirm which genetic markers truly predict disease resistance and whether they work in real breeding programs so that crop improvement can become more precise and efficient. 4.3 Application of marker-assisted selection in disease-resistant breeding Marker-assisted selection (MAS) has become a core tool in disease-resistant breeding programs. In rice, SSR-labeled MAS was successfully selected to breed species that resist brown planthoppers (Shabanimofrad et al., 2015). In cassava, SNP markers are used to accelerate the introduction of resistance alleles such as mosaicism in breeding populations (Ige et al., 2021). In addition, SSR markers are also used for selective breeding in shrimp breeding to enhance their resistance to viral and bacterial pathogens (Yin et al., 2023). These applications show that MAS has significant results in improving the disease resistance of crops and breeding species and accelerating the breeding process. 5 Integration of Multi-Omics and Optimization of Disease-Resistant Breeding Strategies 5.1 Integrated analysis of genomic and transcriptomic data Scientists are linking genetic and gene expression data to better comprehend how sugarcane can resist disease. Scientists could find useful disease-resistance genes and how they work by studying the DNA of the plant as well as what genes are turned on when infected (Pimenta et al., 2023). For example, to evaluate mosaic virus resistance, they applied GWAS and RNA sequencing for gene network assembly, which showed that genes of photosynthesis and stress response are involved in the plant defense. Another smut disease research utilized WGCWA to uncover how groups of genes interact with each other during disease infection, stress-related genes being an important feature (Wu et al., 2022). These complementing methods offer a better picture of the natural resistance of sugarcane and allow scientists to ascertain the most valuable genes to utilize in breeding healthier, disease-free sugarcane varieties.
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 112 5.2 Application of proteomics and metabolomics in studying disease resistance mechanisms Proteomics and metabolomics provide a new perspective for studying the pathogenesis of sugarcane. Proteome studies have identified a variety of differentially expressed proteins (DEPs) that play an important role in disease resistance, including defense-related proteins that deal with pathogens such as Sporisorium scitamineum and Acidovorax avenae (Su et al., 2016). For example, there are significant expression differences in proteins related to metabolic processes, stress responses, and defense in disease-resistant and sensory sugarcane varieties, which may become potential disease-resistant biomarkers (Singh et al., 2019; Zhou et al., 2021). Although metabolomics is less studied, it has a complementary role in revealing the metabolic pathways activated during pathogen infestation, helping to further understand the biochemical basis of disease resistance. 5.3 Multi-omics data-driven strategies for disease-resistant breeding Integrating multiomic data such as genome, transcriptome, proteome and metabolomic is the key to formulating efficient disease-resistant breeding strategies. Through multidimensional data integration, researchers can identify a series of core disease-resistant genes, regulatory pathways and biomarkers, thereby providing strong support for breeding programs (Chen et al., 2024). For example, the integration of genomic and transcriptomic data plays an important role in identifying molecular markers associated with resistance to puff blight (Pokkah Boeng) and sugarcane yellow leaf virus (SCYLV), providing a key tool for marker-assisted selection (MAS) (Pimenta et al., 2021; Lin et al., 2024). In addition, a genomic prediction model combining machine learning and feature selection improves the accuracy of prediction of disease-resistant traits, providing a practical solution for the breeding of disease-resistant sugarcane varieties (Islam et al., 2021; Pimenta et al., 2023). These multiomic strategies not only help to have a deep understanding of the pathogenesis of sugarcane, but also accelerate the cultivation process of strongly resistant sugarcane varieties (Li, 2024b). 6 Prospects of Emerging Technologies in Sugarcane Disease-Resistant Breeding 6.1 Potential applications of gene editing technologies Gene editing technology, especially CRISPR/Cas9, is innovating the field of plant disease-resistant breeding. Compared with traditional gene editing tools such as megnucleases, zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 has the advantages of simple design, high success rate, wide application range and low cost, so it is more popular (Borrelli et al., 2018; Boubakri, 2023). This technology can accurately modify the plant genome, and cultivate disease-resistant crops by targeting and regulating susceptible genes. For example, CRISPR/Cas9 has been successfully applied to crops such as rice, tomato and wheat to enhance their resistance to virus, fungal and bacterial diseases (Park et al., 2024). In sugarcane breeding, the potential of CRISPR/Cas9 lies in its ability to create disease-resistant varieties that do not require genetically modified, which is of great significance for achieving sustainable agricultural development (Ahmad et al., 2020). However, gene editing technology also has many limitations (Figure 2). 6.2 Prospects of pan-genomics and single-cell omics in disease resistance research Researchers are applying new approaches called pangenomics and single-cell omics to investigate how plants defend against disease. The approaches enable the comparison of genetic variation among plant species and the identification of genes that enhance crop disease resistance. Researchers also integrate various approaches-screening genes, proteins, and metabolites in plants-to understand how crops react to environmental stressors (Razzaq et al., 2021). Utilization of these techniques in combination with the CRISPR gene-editing tool enables the study of particular genes and enhances crop resistance to pathogens. This strategy has the potential to develop novel and improved ways of safeguarding sugarcane from infection. The new technologies give researchers an insight into plant defense that was not possible with the previous techniques. 6.3 Application of artificial intelligence and big data in predicting disease resistance genes Artificial intelligence and big data are transforming learning on plant breeding, particularly the identification of disease-resistant genes. Such emerging technologies can analyze vast amounts of plant trait and genetic data and identify patterns that human methods previously overlooked. Smart computer algorithms search difficult data to make informed guesses about how genes interact with one another, thereby making it simpler for scientists to
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 113 identify new disease-fighting genes more quickly. When researchers combine AI with genetic data, breeding accelerates and yields more insights into how crops display disease resistance (Li, 2024a). The process has been especially helpful in breeding disease-resistant sugarcane. Figure 2 Limitations of the CRISPR/Cas9 system (Adopted from Ahmad et al., 2020) 7 Concluding Remarks Genome strategies have become an indispensable and important means in breeding of disease-resistant sugarcane varieties. The integration of genome selection and genome-wide association analysis (GWAS) greatly promotes the identification of disease-resistant genes and molecular markers, providing key support for the cultivation of disease-resistant varieties. For example, genomic selection has been shown to improve the accuracy of predictions for resistance traits such as brown rust and orange rust, where nonparametric models outperform parametric models, indicating an important role of non-additive genetic effects in disease resistance. In addition, the identification of single nucleotide polymorphism (SNP) sites associated with resistance such as sugarcane mosaic virus (SCMV) and red rot also provides practical pathways for marker assisted breeding. These progress highlights the important role of genomics in accelerating the breeding process and enhancing sugarcane disease resistance. Researchers are using a mix of various techniques to improve sugarcane breeding. By combining genetic studies, gene expression, and computerized machine learning, they're able to identify better how sugarcane defends itself against disease. For instance, research that examined which genes are expressed when the plant is under disease infection found important genes for photosynthesis and stress response that fight sugarcane mosaic virus. Computer programs are also helping to pinpoint precisely where in the sugarcane DNA the disease resistance is encoded so that it can be easily recognized and predicted such factors as brown rust resistance. If scientists collect all this diverse data, they can choose the most appropriate plants to breed much faster, leading to sugarcane varieties that stay healthier.
Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 114 Scientists who study disease-resistant sugarcane have to concentrate on several important things. First, they need to study more diseases. At the moment, scientists only study three important diseases: SCMV, red rot, and brown rust. By studying more diseases, we can learn more about how sugarcane fights infection. Scientists need to create improved computer programs to sort out which plants of sugarcane will be most resistant to disease. The latest attempts involving "attention mechanisms" appear to hold a great deal of promise. It also needs to combine various kinds of information-not only genetic information, but also growing conditions and characteristics of the plants. This will allow the growth of sugarcane that not only resists disease, but also exhibits healthy growth under a broad range of environmental conditions. Acknowledgments We are deeply grateful to Mr. Rudi Mai and Mr. Qixue Liang for their invaluable support in data compilation and verification, which significantly contributed to refining our manuscript. We also wish to express our sincere appreciation to the two anonymous reviewers for their thorough evaluation and constructive feedback, which greatly enhanced the quality of this work. Funding This study was supported by the Research and Training Fund of the Hainan Institute of Tropical Agricultural Resources (Project No. H2025-03). Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Ahmad S., Wei X., Sheng Z., Hu P., and Tang S., 2020, CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects, Briefings in Functional Genomics, 19(1): 26-39. https://doi.org/10.1093/bfgp/elz041 Borrelli V., Brambilla V., Rogowsky P., Marocco A., and Lanubile A., 2018, The enhancement of plant disease resistance using CRISPR/Cas9 technology, Frontiers in Plant Science, 9: 1245. https://doi.org/10.3389/fpls.2018.01245 Boubakri H., 2023, Recent progress in CRISPR/Cas9-based genome editing for enhancing plant disease resistance, Gene, 866: 147334. https://doi.org/10.1016/j.gene.2023.147334 Chen C., Bhuiyan S., Ross E., Powell O., Dinglasan E., Wei X., Atkin F., Deomano E., and Hayes B., 2024, Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches, Frontiers in Plant Science, 15: 1398903. https://doi.org/10.3389/fpls.2024.1398903 Darvishzadeh R., Heidari A., and Maleki H., 2016, Identification of SSR markers associated with resistance to potato virus Y in tobacco germplasm, Genetics in the Third Millennium, 14(2): 4262-4269. Hidayah N., McNeil M., Li J., Bhuiyan S., Galea V., and Aitken K., 2021, Resistance mechanisms and expression of disease resistance-related genes in sugarcane (Sacchrum officinarum) to Sporisorium scitamineuminfection, Functional Plant Biology, 48(12): 1302-1314. https://doi.org/10.1071/FP21122 Ige A., Olasanmi B., Mbanjo E., Kayondo I., Parkes E., Kulakow P., Egesi C., Bauchet G., Ng E., Lopez-Lavalle L., Ceballos H., and Rabbi I., 2021, Conversion and validation of uniplex SNP markers for selection of resistance to cassava mosaic disease in cassava breeding programs, Agronomy, 11(3): 420. https://doi.org/10.3390/AGRONOMY11030420 Islam M., McCord P., Olatoye M., Qin L., Sood S., Lipka A., and Todd J., 2021 Experimental evaluation of genomic selection prediction for rust resistance in sugarcane, The Plant Genome, 14(3): e20148. https://doi.org/10.1002/tpg2.20148 Jiang Z., Zhao M., Qin H., Li S., and Yang X., 2023, Genome-wide analysis of NBS-LRR genes revealed contribution of disease resistance fromSaccharum spontaneumto modern sugarcane cultivar, Frontiers in Plant Science, 14: 1091567. https://doi.org/10.3389/fpls.2023.1091567 Li J.Q., 2024a, Harnessing natural genetic diversity: the impact of wild rice alleles on cultivated varieties, Rice Genomics and Genetics, 15(3): 132-141. https://doi.org/10.5376/rgg.2024.15.0014 Li Y.Z., 2024b, Starch biosynthesis and engineering starch yield and properties in cassava, Molecular Plant Breeding, 15(2): 63-69. https://doi.org/10.5376/mpb.2024.15.0008 Lin H., Jiang Z., He T., Li G., Zhao M., Su L., Zhao J., Zou C., and Yang X., 2024, Mining of candidate genes and developing molecular markers associated with Pokkah Boeng resistance in sugarcane (Saccharumspp.), Plants, 13(24): 3497. https://doi.org/10.3390/plants13243497
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Bioscience Methods 2025, Vol.16, No.3, 117-136 http://bioscipublisher.com/index.php/bm 117 Review and Progress Open Access Continuing the Path of Green Income Growth to Realize the Dream of Industrial Revitalization WenjunCai 1,2 1 Zhejiang Pinshangdao Agricultural Development Co., LTD, Panan, 321000, Zhejiang, China 2 Zhejiang Agronomist College, Hangzhou, 310021, Zhejiang, China Corresponding email: 540906779@qq.com Bioscience Methods, 2025, Vol.16, No.3 doi: 10.5376/bm.2025.16.0012 Received: 13 Mar., 2025 Accepted: 22 Apr., 2025 Published: 14 May, 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 W.J., 2025, Continuing the path of green income growth to realize the dream of industrial revitalization, Bioscience Methods, 16(3): 117-136 (doi: 10.5376/bm.2025.16.0012) Abstract Pan'an faces the dual transformation challenges of ecological protection and increasing farmers' income. To this end, it actively practices the development concept of "Green water and green mountains are gold and silver mountains", implements innovative measures such as "Our Happiness Plan", and explores new paths to enrich the people through ecology. Taking Pan'an County, Zhejiang Province as an example, this study explores how the green development path of agriculture driven by biological resources and biotechnology can help rural industrial revitalization. It analyzes the rich natural biological resources and ecosystem service value of Pan'an, summarizes the innovation of agricultural production models led by "Our Happiness Plan", discusses the practical application of agricultural biotechnology such as biological breeding, biological control, and agricultural product processing in Pan'an's industrial revitalization, and sorts out the development path of the integration of the first, second, and third industries of green agriculture, including the agricultural production, processing, and marketing coordination mechanism, the value of ecological science popularization in the integration of agriculture and tourism, and the construction practice of the rural circular bio-economic system. On this basis, the current challenges in the field of agricultural biology are analyzed. The study believes that the development paradigm of "biology + ecology" integration not only reshapes the value of the agricultural industrial chain, achieves a win-win situation of ecological protection and economic development, but also provides a sustainable practice paradigm for rural revitalization in the new era. This study hopes to provide reference for biological-oriented agricultural green income increase and rural industrial revitalization. Keywords Pan'an; Rural revitalization; Green development; Ecological agriculture; Biotechnology; Ecosystem services 1 Introduction Located in the mountainous area of central Zhejiang, Pan'an County has a superior ecological environment, but agricultural development has long been restricted by the mountainous terrain. How to lead farmers to increase their income and become rich while protecting the green mountains and rivers is a prominent challenge facing local agriculture. In the past, extensive agriculture often sacrificed the environment in exchange for production growth, but this model is unsustainable, and ecologically fragile areas especially need to explore the path of green transformation. Pan'an has a forest coverage rate of up to 83.6%, and is known as the "green lung of central Zhejiang". The environment carries important functions such as water conservation and climate regulation. At the same time, Pan'an is also an old revolutionary base with a relatively weak economic foundation, limited per capita arable land, and traditional agricultural income is not enough to support the goal of common prosperity. This contradiction between "enriching the county with ecology" and "enriching the people and increasing their income" requires the transformation of the agricultural development model from extensive and high-consumption to green and efficient. In order to solve this problem, Pan'an has adhered to the development strategy of "enriching the people with ecology and strengthening the county with ecology" in recent years. Through institutional innovation and industrial innovation, it has strived to transform ecological advantages into economic advantages and embark on a green income increase path with mountain characteristics (Wei, 2023; Weng et al., 2024). In particular, the practical exploration represented by the "Our Happiness Plan" is committed to allowing more farmers to share the dividends brought by green mountains and clear waters, and to achieve the simultaneous advancement of ecological protection and farmers' income growth. This exploration is a microcosm of the transformation of agricultural ecological economy under the background of rural revitalization.
Bioscience Methods 2025, Vol.16, No.3, 117-136 http://bioscipublisher.com/index.php/bm 118 The development of modern agriculture increasingly relies on the integration of science and technology with ecological concepts. The progress of biotechnology has provided new impetus for the sustainable development of agriculture. For example, technologies such as genomic breeding, molecular marker selection, and CRISPR gene editing can cultivate new crop varieties that are resistant to pests and diseases and stress, while reducing the use of pesticides and fertilizers while increasing yields and nutritional quality. Studies have shown that the creation of insect-resistant and disease-resistant crops through biotechnology can significantly reduce the amount of pesticides used and soil damage, achieving a win-win situation of environmental friendliness and increased agricultural production. The application of biofermentation engineering, enzyme preparations, etc. in the processing and storage of agricultural products has increased the added value and processing efficiency of agricultural products (DeClerck et al., 2016; Rehman et al., 2022). At the same time, the importance of ecosystem services is becoming increasingly prominent in the sustainable development of agriculture. Healthy agricultural ecosystems can provide a variety of services including soil nutrient cycling, water conservation, pollination, and biological control. For example, soil microbial communities contribute to nutrient cycling and crop health; pollinating insects increase crop fruiting rates; and natural enemies can control pest populations. These services are essential to ensuring agricultural productivity and ecological environmental quality. Integrating the concept of ecosystem services into agricultural management can reduce dependence on chemical inputs and achieve synergy between agricultural production and ecological protection. Therefore, modern agriculture needs to give full play to the dual role of biotechnology and ecosystem services, improve resource utilization efficiency and system stability through scientific and technological innovation and ecological optimization, and thus provide support for the green development of agriculture. Green development has become the basic strategic orientation of my country's agricultural transformation in the new era. General Secretary Xi Jinping pointed out that "promoting the green development of agriculture is a profound revolution in the concept of agricultural development" and emphasized the dialectical unity of green waters and green mountains and gold and silver mountains. Since 2017, my country has launched the Green Development Action for Agriculture and issued a series of policies to encourage agricultural input reduction, resource recycling, and environmentally friendly technology promotion. These strategic measures have created favorable conditions for the biological upgrading of the agricultural industry. On the one hand, green development requires reducing the use of chemical fertilizers and pesticides, which objectively promotes the research and development and application of technologies such as biofertilizers and biopesticides. For example, by promoting biological control and integrated pest management (IPM) strategies, natural enemy insects, microbial preparations, etc. are used to replace some chemical pesticides, achieving the goal of reducing pesticides and increasing efficiency. As of recent years, the application area and market scale of biopesticides and biofertilizers in China have continued to expand, with an average annual growth rate of about 11% from 2018 to 2022, indicating that green plant protection is gradually being accepted by agricultural production (Wu et al., 2024). On the other hand, the green development strategy emphasizes the resource utilization of agricultural waste and the construction of a circular agricultural system, which provides an opportunity for the development of agricultural biomass energy and bioprocessing industries. For example, livestock and poultry manure can be used to produce organic fertilizer and biogas through biological fermentation, and straw can be converted into feed or base material through microbial treatment, which not only reduces pollution but also creates additional benefits. These practices reflect the combination of biotechnology and the concept of circular economy, and help to open up the transformation channel of the "two mountains" in agriculture. Under the guidance of policies, more and more agricultural enterprises and university research institutions are participating in agricultural green technology innovation, and the pace of agricultural biotechnology achievement transformation is accelerating. It can be said that the green development strategy has given traditional agriculture the wings of "biological upgrading" and accelerated the transformation of agricultural production methods to high efficiency, cleanliness and recycling. As a national pioneer county in agricultural green development, Pan'an has actively explored this aspect, such as being selected as the first batch of agricultural green development demonstration counties, creating a Chinese medicinal material specialty agricultural product advantage zone, and obtaining organic or geographical indication certification for many agricultural products. These all reflect the strong traction of the green strategy on the upgrading of the agricultural industry.
Bioscience Methods 2025, Vol.16, No.3, 117-136 http://bioscipublisher.com/index.php/bm 119 This study will evaluate Pan'an's biological resource advantages and regional ecosystem value, including natural resource endowment, ecosystem service functions and the agricultural value transformation of local characteristic species, analyze the agricultural biological model innovation contained in Pan'an's "Our Happiness Plan", such as ecological breeding and farming, agricultural product ecological certification, "company + cooperative + farmer" mechanism, etc., explore its role in increasing farmers' income and ecological protection, discuss the specific application practice of agricultural biotechnology in industrial revitalization, summarize the development path of green agricultural industry integration, including biological synergy of the first, second and third industries, ecological education function in agricultural and tourism integration, and the construction of a circular bio-economic system, analyze the challenges encountered by Pan'an in the process of promoting bio-oriented green industries, and put forward targeted development suggestions, and emphasize the value of bio-oriented green industrial chain reconstruction for achieving a virtuous cycle of ecological economy, point out the paradigm significance of Pan'an's experience for rural revitalization, and the sustainable development potential of the ecological-biological-economic integration model. This study sorts out and analyzes how the green agricultural income-increasing model driven by biological resources and biotechnology can help rural industrial revitalization, and provides experience reference based on the practice of Pan'an County, hoping to provide a reference for industrial revitalization ideas for regions with similar ecological and environmental conditions, that is, to embark on a sustainable development path of using biological resources and technology to achieve "green income increase". 2 Biological Resources and Ecosystem Value in the Region 2.1 Natural resources and biodiversity of Pan'an Pan'an is located in the remnant of the Kuancang Mountains. The Dapanshan National Nature Reserve is located within its territory and has a superior mountain and water ecosystem. The county is full of rolling mountains and dense vegetation, with a forest coverage rate of up to 83.6%. The air and water quality maintain the national Class I standard all year round. It is known as the "ancestor of mountains and the source of water". The good ecology has nurtured rich biodiversity and unique natural landscapes - cliff waterfalls, deep ravines and dense forests, and misty alpine environments, providing habitats for a variety of animals and plants. In the long process of evolution, Pan'an has formed a variety of types including subtropical evergreen broad-leaved forest ecosystems and mountain stream wetland ecosystems, which contain extremely high species diversity (Zhang et al., 2018; Liu et al., 2024). According to statistics, there are more than 1,800 vascular plants in the territory, including dozens of national key protected wild plants; wildlife resources are also quite rich, with a wide variety of birds, insects, amphibians and reptiles. Not only that, Pan'an is also known as the "Millennium Medicine Town" with rich Chinese medicinal materials resources. Today, there are more than 700 known Chinese medicinal materials. A considerable part of the local "Eight Flavors of Zhejiang" comes from Pan'an, which provides a good foundation for the development of the authentic medicinal materials industry. Pan'an is also a famous tea town and honey producing area. The Yushan Ancient Tea Farm has a long history of tea production and is known as the "living fossil" of Chinese tea culture. There are more than 15,000 ancient tea trees in the county with various varieties. More than 80% of the farmers in Huanglinkeng Village, Shanghu Town, the "No. 1 Bee Village in Central Zhejiang", raise Chinese bees, with more than 600 beehives and an annual honey production of more than 10,000 kilograms. This series of data and facts shows that Pan'an has unique biological resources and ecological diversity advantages, providing a rich material basis and gene pool for agricultural development. When implementing industrial revitalization, fully recognizing and utilizing these natural assets is a prerequisite for achieving sustainable income growth. 2.2 Ecosystem service functions The mountain, water, forest, farmland, lake and grass ecosystems of Pan'an not only nurture biodiversity, but also support regional agriculture and human well-being through diverse ecosystem services. The first is supply services. Forests and farmlands provide society with food crops, Chinese medicinal materials, tea, honey and other material products; abundant forests conserve water sources, and streams flow all year round, providing guarantees for agricultural irrigation and water supply for residents' lives. The second is regulation services. The high-coverage
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