Research Report
Rice Varietal Resistance to Insect Pests: Genetic Mechanisms and Breeding Approaches 


Molecular Entomology, 2024, Vol. 15, No. 1
Received: 26 Dec., 2023 Accepted: 06 Feb., 2024 Published: 26 Feb., 2024
This study aims to explore the genetic mechanisms and breeding strategies employed to enhance rice varietal resistance to insect pests. The primary goal is to provide a comprehensive understanding of the current advancements in genetic traits, resistance mechanisms, and breeding techniques that contribute to the development of insect-resistant rice varieties. Significant progress has been made in identifying and mapping resistance genes and quantitative trait loci (QTLs) associated with insect resistance in rice. For instance, the identification of novel resistance genes such as Bph from wild rice species and BPH from cultivated varieties has provided new avenues for breeding. Advanced molecular approaches, including marker-assisted selection and RNA interference technology, have been successfully integrated with conventional breeding methods to enhance resistance. The development of multi-resistance rice varieties through transgene stacking systems has also shown promising results in conferring resistance to multiple pests and diseases. Additionally, the suppression of serotonin biosynthesis has been identified as a novel mechanism to enhance resistance against planthoppers and stem borers. The integration of conventional and molecular breeding techniques has significantly improved the development of insect-resistant rice varieties. These advancements have important implications for sustainable rice cultivation and effective pest management. The continuous identification and characterization of resistance genes, along with the application of advanced genomic tools, will further enhance the durability and effectiveness of insect-resistant rice varieties.
Rice (Oryza sativa) is a staple food for more than half of the world's population, making its production critical for global food security. However, rice cultivation faces significant challenges from various insect pests, which can cause substantial yield losses and economic damage. Among these pests, the brown planthopper (BPH), white-backed planthopper (WBPH), and striped stem borer (SSB) are particularly notorious for their destructive impact on rice crops (Zhou et al., 2021). The continuous evolution of pest biotypes and their ability to overcome existing resistant rice varieties necessitate ongoing research and development of new resistant strains (Haliru et al., 2020).
The global challenge posed by rice pests is immense, with outbreaks leading to severe reductions in rice yield and quality. Traditional pest control methods, such as chemical pesticides, are not only costly but also pose environmental and health risks. Therefore, developing rice varieties with inherent resistance to insect pests is considered the most sustainable and eco-friendly approach to pest management (Li et al., 2020). Resistance breeding not only reduces the reliance on chemical controls but also contributes to long-term pest management strategies by incorporating durable resistance genes into rice cultivars (Dash, 2020).
This study aims to provide a comprehensive overview of the genetic mechanisms and breeding approaches used to develop rice varieties resistant to insect pests. Identify and characterize resistance genes is summarize the current understanding of the genetic basis of resistance to major rice pests, including the identification and functional analysis of resistance genes. Explore breeding strategies is discussing conventional and molecular breeding techniques used to incorporate resistance genes into rice varieties, including transgene stacking and marker-assisted selection. Evaluate the effectiveness of resistant varieties is assessing the performance of newly developed resistant rice lines in terms of pest resistance and agronomic traits. By synthesizing findings from recent research, this study aims to highlight the progress made in breeding insect-resistant rice and identify future directions for enhancing resistance through genetic and breeding innovations.
1 Genetic Foundations of Resistance in Rice
1.1 Resistance to various insect pests in rice
Genetic traits that confer resistance to various insect pests in rice are diverse and have been identified through extensive research. For instance, the novel resistance gene Bph, derived from the wild rice species Oryza rufipogon Griff., has been shown to provide high resistance to both brown planthopper (BPH) and white-backed planthopper (WBPH) (Figure 1) (Yang et al., 2020). Similarly, the gene Bph (Radchenko et al., 2022), identified through genome-wide association studies, confers resistance to multiple BPH biotypes and is associated with high nucleotide diversity, indicating its evolutionary significance (Zhou et al., 2021). Additionally, the deficiency of the mitochondrial outer membrane protein 64 (OM64) gene in rice has been linked to increased resistance to both piercing-sucking insects like BPH and chewing insects such as the striped stem borer (SSB) (Guo et al., 2020).
Figure 1 Figure 1 Evaluation of resistance of 1,520 accessions of Oryza sativa to three brown planthopper (BPH) biotypes (Adopted from Zhou et al., 2021) Image caption: (A)Typical images showing the appearance of adult BPH female after feeding on various rice accessions for 48 h. The values below the images indicate weight gain rate (WG) of each insect. (B) Representative photographs of rice plants with variable resistance levels in the bulk seedling test. The values below the images show the associated plant resistance score, which can be negatively related to the WG values in (A). Note that the accessions in (A) are not identical to those shown in (B). (C) Distribution of WG for BPH biotype I on all 1,520 accessions. (D, E) Distribution of WG for BPH biotypes II and III, respectively. (F) Percentage of the 1,520 rice accessions with resistant (R; WG < 0.3), moderately resistant (MR; 0.3 < WG < 0.6), moderately susceptible (MS; 0.6 < WG < 0.9), and susceptible (S; WG > 0.9). (G) Boxplots of WG for the three BPH biotypes in 1,520 rice accessions. Significant differences between biotypes are indicated by different lowercase letters (P < 0.05, least significant difference test) (Adopted from Zhou et al., 2021) |
The findings of Zhou et al., (2021) indicate significant variations in plant responses and pest infestation levels. The visual data demonstrate differences in plant health and growth under varying conditions, as well as the distribution of certain traits or measurements among different groups. Statistical analyses highlight distinct patterns and significant differences among the biotypes studied, reflecting variations in resistance and susceptibility. This comprehensive visual representation underscores the complexity of plant-pest interactions and the importance of understanding biotype-specific responses for effective management strategies.
1.2 Molecular genetics
The molecular genetics underlying resistance in rice involves various genes and their interactions with pest populations. For example, many insect resistance genes have been identified, and 14 such genes have been cloned via a map-based cloning approach. These genes activate defense pathways, including the expression of defense-related genes such as mitogen-activated protein kinase, plant hormone, and transcription factors (Du et al., 2020). The Bph14 and OsLecRK1 genes, when stacked together, have been shown to provide resistance to BPH, demonstrating the potential of combining multiple resistance genes for enhanced protection. Furthermore, the molecular mechanisms of BPH resistance involve the deposition of callose and cell wall thickening, which inhibit BPH feeding and damage.
1.3 Breeding Strategies
Breeding strategies for incorporating resistance traits into rice varieties have evolved significantly, encompassing both traditional and modern techniques. Traditional breeding approaches have successfully incorporated resistance to insect pests through the selection and crossing of resistant varieties. However, the continuous evolution of virulent pest biotypes necessitates the use of advanced molecular approaches. Marker-assisted selection (MAS) and transgene stacking systems have been employed to combine multiple resistance genes from diverse sources into a single genetic background, resulting in rice varieties with durable resistance (Li et al., 2020). Additionally, the identification of quantitative trait loci (QTLs) such as BPH41 and BPH42 has facilitated the development of BPH-resistant rice varieties through fine mapping and the use of recombinant lines (Tan et al., 2021).
In summary, the genetic foundations of resistance in rice involve a complex interplay of genetic traits, molecular mechanisms, and innovative breeding strategies. The integration of traditional and modern approaches has led to the development of rice varieties with enhanced resistance to various insect pests, contributing to sustainable rice production and pest management.
2 Breeding Approaches for Enhancing Resistance
2.1 Conventional breeding
Conventional breeding methods have been instrumental in developing rice varieties resistant to insect pests. These methods typically involve selecting and crossbreeding plants that exhibit desirable traits, such as resistance to specific pests. For instance, traditional breeding has successfully incorporated resistance to leaf folder and other leaf-feeding insects, which are significant due to their ability to defoliate rice plants and reduce yield (Dash, 2020). However, the effectiveness of conventional breeding is often limited by the genetic diversity of the cultivated rice gene pool and the continuous evolution of virulent insect biotypes (Dash, 2020). Despite these challenges, conventional breeding remains a cornerstone of integrated pest management strategies, providing an ecologically viable approach to pest control (Dash, 2020).
2.2 Marker-assisted selection
Marker-assisted selection (MAS) has revolutionized the breeding of insect-resistant rice varieties by enabling the precise identification and incorporation of resistance genes. This technology uses molecular markers linked to resistance traits to facilitate the selection process, thereby increasing the efficiency and accuracy of breeding programs. For example, MAS has been used to introgress resistance genes against gall midge, planthoppers, and leafhoppers into elite rice varieties (Bentur et al., 2021). The combined approach of marker-assisted forward and backcross breeding has also been employed to improve the Indian rice variety Naveen, resulting in lines with enhanced resistance to multiple biotic stresses, including blast, bacterial blight, and gall midge (Ramayya et al.,2021). These advancements highlight the potential of MAS to develop rice varieties with durable and multiple pest resistance (Bentur et al., 2021).
2.3 Genetic engineering
Genetic engineering has opened new avenues for developing rice varieties with enhanced resistance to specific insect pests. Advances in this field include the use of RNA interference (RNAi) and CRISPR-based genome editing techniques. RNAi-based gene silencing has shown promise in conferring resistance to pests such as the brown planthopper and yellow stem borer (Figure 2) (Bentur et al., 2021). Additionally, CRISPR technology is being explored to target insect susceptibility genes in rice, offering a novel approach to pest control. Transformation of rice plants with insecticidal genes has also been a proven technology, although no insect-resistant transgenic rice cultivars are currently commercially available. The identification and cloning of resistance genes from wild rice species, such as the novel Bph38 gene from Oryza rufipogon, further exemplify the potential of genetic engineering in enhancing pest resistance (Yang et al., 2020). These advances underscore the importance of genetic engineering in developing next-generation insect-resistant rice varieties (Yang et al., 2020).
Figure 2 Schematic representation of host-induced gene silencing in insects through siRNA approach (Adopted from Bentur et al., 2020) Image caption: (1) Integration of insect gene-targeted siRNA cassette (transgene) into rice genome; (2) fate of transgene in rice cells; (3) expression of transgene in rice cell generates the mRNA; (4) formations of dsRNA through self-complementation of transgene’s sense and antisense strands in rice cell; (5) host Dicer-mediated specific cleavage of dsRNA leads to production of siRNAs in rice cell; (6) host-generated siRNAs processed by host Argonaute protein (the main component of RNA-induced silencing complex or RISC); (7) host-generated siRNAs are nonfunctional in rice cells due to absence of targeted gene; (8 and 9) host-synthesized dsRNAs/siRNAs transfer from rice plant to insect through feeding on rice tissues; (10) fate of transferred dsRNA/siRNAs in insect cells; (11) generation of siRNAs from dsRNA through insect Dicer-mediated cleavage; (12) the siRNAs are processed by insect Argonaute proteins/RISC complex; (13a) formation of activated RISC along with target-specific guide RNA; (13b and 13c) the passenger RNA is separated from guide RNA and degraded; (14) transcription of insect DNA resulted in the expression of targeted functional mRNA (transcript); (15) guide strand of siRNA helps in identification and binding of activated RISC to the targeted mRNA; (16) silencing of targeted gene expression by RISC-mediated cleavage of corresponding mRNA (Adopted from Bentur et al., 2020) |
The findings of Bentur et al., (2020) shows the induction of host gene silencing in insects by siRNA approach. The process starts with the integration of transgenic fragments (siRNA cassettes) specifically targeting insect genes into the rice genome, demonstrating the application of gene editing technology between plants and insects, and the use of siRNA function to regulate gene expression, which is of research value, and which can alter plant insect resistance or nutritional value as a means of biocontrol. However, there are potential risks associated with this technology, such as genetic drift or affecting non-target species.This mechanism demonstrates the potential of using transgenic plants to induce gene silencing in pests, providing a biotechnological approach for pest control.
By integrating conventional breeding, marker-assisted selection, and genetic engineering, researchers can develop rice varieties with robust and durable resistance to insect pests, thereby contributing to sustainable pest management and improved crop yields.
3 Case Studies
3.1 Successful Modifications
Several case studies have demonstrated the successful genetic modification of rice to enhance resistance to specific insect pests. One notable example is the development of "multi-resistance rice" (MRR) through a transgene stacking system. This approach involved the assembly of multiple resistance genes, including those for glyphosate tolerance, lepidopteran pest resistance, brown planthopper resistance, bacterial blight resistance, and rice blast resistance. The modified rice variety, derived from the widely used japonica rice cultivar Zhonghua 11, exhibited significantly improved resistance to these pests and diseases, resulting in higher yields under natural field conditions (Li et al., 2020). Another successful case involves the identification and cloning of the Bph37 gene, which confers resistance to brown planthopper (BPH). This gene was identified through genome-wide association studies on a global rice germplasm collection. The Bph37 gene, along with other resistance loci, showed high nucleotide diversity and ancient balancing selection, indicating its long-term effectiveness in providing resistance against various BPH biotypes (Zhou et al., 2021).
A third example is the discovery of the Bph38 gene from the wild rice species Oryza rufipogon Griff. This gene confers high resistance to both brown planthopper and white-backed planthopper. Near-isogenic lines carrying Bph38 were developed, showing strong resistance and desirable agronomic traits, making this gene a valuable resource for breeding insect-resistant rice varieties (Yang et al., 2020).
3.2 Impact Assessments
Field performance assessments of genetically modified rice varieties have shown promising results. The multi-resistance rice (MRR) developed through transgene stacking demonstrated significantly higher yields compared to the recipient cultivar Zhonghua 11 under natural pest and disease conditions. This indicates the practical benefits of genetic modifications in enhancing rice resistance and productivity (Li et al., 2020). In another study, the Qingliu rice variety, known for its resistance to leaffolders, was found to be moderately resistant to brown planthopper as well (Figure 3). Transcriptomic analyses revealed that Qingliu activates different defense mechanisms in response to different types of herbivores, highlighting its dual resistance capabilities. This variety's performance in the field suggests that it can provide broad-spectrum resistance, which is valuable for integrated pest management (Li et al., 2021).
Figure 3 Determination of key defensive mechanisms taking place in Qingliu leaves under leaffolder herbivory (Adopted from Li et al., 2021) Image caption: a GO enrichment of upregulated genes identified in Qingliu leaves in response to leaffolder herbivory. Enriched GO terms from biological process (BP), cellular component (CC) and molecular function (MF) GO categories are shown with bar length depicting enrichment significance and color intensity of bars depicting gene number. Coexpression network using b Os07g0542400, Os07g0537500, Os07g0537600, Os08g0203100 c Os02g0165100, Os05g0127300 coexpressed protein kinase genes induced by leaffolder feeding. Based on KEGG pathway annotation, genes associated with JA biosynthesis and the phenylpropanoid pathway are indicated by dotted line black and orange ellipses, respectively. Blue rimmed nodes = protein kinase genes, arrowhead nodes=genes encoding peroxidase, phenylalanine ammonia-lyase or 4-coumarate:coenzyme A ligase, hexagonal nodes = JA biosynthesis genes, square nodes = transcription factor genes, triangular nodes = germin-like protein genes. DEGs mapped to the coexpression networks are shown in red nodes for upregulation and green nodes for downregulation (Adapted from Li et al., 2021) |
The findings of Li et al., (2021) indicate a complex and multifaceted response of plants to pathogen or pest attacks. The visual data illustrate various biological processes and molecular mechanisms that are activated during such interactions. The involvement of different genes and pathways, including those related to stress response, signaling, metabolic functions, and defensive mechanisms, is evident. The graphical representation underscores the intricate network of reactions within the plant cells, highlighting the critical roles of specific cellular components and regulatory pathways. This comprehensive depiction emphasizes the importance of understanding the dynamic and interconnected nature of plant defense systems to develop effective strategies for crop protection and improvement.
The Bph38 gene from Oryza rufipogon Griff. was also assessed for its impact on agronomic traits and pest resistance. Near-isogenic lines carrying this gene showed strong resistance to both brown planthopper and white-backed planthopper, with agronomic traits similar to the recurrent parents. This indicates that the gene can be effectively introgressed into elite rice varieties without compromising yield or other desirable traits (Yang et al., 2020).
3.3 Pilot Projects
Pilot projects have been conducted to test the scalability and practicality of deploying genetically modified rice in different agricultural settings. One such project involved the large-scale production and release of BPH-resistant rice varieties in various rice-growing regions. These varieties, developed through conventional breeding and molecular approaches, have shown durable resistance to multiple BPH biotypes, demonstrating their scalability and effectiveness in real-world conditions (Haliru et al., 2020). Another pilot project focused on the use of CRISPR/Cas9 genome modification technology to understand and enhance insecticide resistance in rice. This project highlighted the potential of genome editing tools to develop rice varieties with improved resistance to insect pests, providing a scalable and practical approach for future breeding programs (Douris et al., 2020). A third pilot project examined the genetic diversity and resistance of farmer's varieties (FVs) of rice in Odisha, India, against brown planthopper biotype-4. The study identified several resistant FVs and suggested that these could be used to develop robust resistant rice varieties through genomic approaches. This project demonstrated the feasibility of using local germplasm resources to enhance pest resistance in rice (Anant et al., 2021).
By integrating these successful modifications, impact assessments, and pilot projects, the systematic study highlights the potential of genetic mechanisms and breeding approaches in developing rice varieties with enhanced resistance to insect pests. These efforts contribute to sustainable rice production and improved food security.
4 Challenges and Limitations in Current Research
4.1 Technical challenges
Current genetic research and breeding for insect resistance in rice face several technical challenges. One significant limitation is the complexity of the genetic mechanisms underlying resistance. The identification and cloning of resistance genes, such as the 14 genes identified through map-based cloning, require extensive resources and time (Du et al., 2020). Additionally, the continuous evolution of insect pests and the emergence of new biotypes necessitate ongoing research to identify new resistance genes and understand their mechanisms (Yang et al., 2020). The lack of efficient insect rearing and varietal screening protocols further complicates the breeding process (Dash, 2020). Moreover, the genetic homogeneity of crops can accelerate the adaptive microevolution of pests, making it challenging to maintain durable resistance (Radchenko et al., 2022).
4.2 Economic viability
The economic viability of developing and deploying resistant rice varieties is a critical consideration. While the incorporation of host-plant resistance is a cost-effective alternative to chemical control, the initial investment in research and development can be substantial (Mishra et al., 2022). The use of advanced molecular approaches, such as genotyping by sequencing and high-throughput phenotyping, can expedite the breeding process but also increase costs (Smith, 2020). Additionally, the economic returns on investment can vary depending on the region and the prevalence of specific pests. For instance, the deployment of resistant varieties in regions heavily affected by brown planthopper (BPH) can lead to significant economic benefits by reducing yield losses and the need for insecticides. However, the economic impact of resistant varieties must be evaluated in the context of integrated pest management (IPM) strategies to ensure long-term sustainability and profitability (Horgan and Peñalver-Cruz, 2022).
4.3 Environmental impact
The environmental impact of genetically modified (GM) and conventionally bred resistant rice varieties is a crucial aspect of sustainability. Conventional breeding approaches have been central to integrated pest management, offering an ecologically viable solution to biotic constraints (Dash, 2020). However, the excessive use of chemical-based pesticides in conjunction with resistant varieties can lead to soil fertility reduction and the development of pesticide-resistant insect populations (Kapoor et al., 2020). The use of molecular tools, such as RNAi-based gene silencing and CRISPR-based genome editing, offers potential for more targeted and environmentally friendly pest control methods. Nevertheless, the long-term ecological effects of these technologies need to be thoroughly assessed. The combination of genomics and genetic engineering can improve natural plant resistance, but it is essential to consider the potential risks and benefits to ensure sustainable agricultural practices (Bentur et al., 2021).
While significant progress has been made in understanding and developing insect-resistant rice varieties, several technical, economic, and environmental challenges remain. Addressing these challenges requires a multidisciplinary approach, integrating advanced molecular techniques with traditional breeding methods and considering the broader economic and ecological impacts.
5 Future Perspectives
5.1 Research gaps
Despite significant advancements in understanding the genetic mechanisms of insect resistance in rice, several research gaps remain. One critical area needing further exploration is the identification and functional characterization of additional resistance genes. While many genes have been identified, the complexity of insect-rice interactions suggests that numerous other genes and pathways are yet to be discovered (Du et al., 2020). Additionally, there is a need for more comprehensive studies on the stability and durability of resistance genes under field conditions, as environmental factors can significantly influence gene expression and effectiveness (Radchenko et al., 2022). Another gap is the limited understanding of the molecular mechanisms underlying resistance to less-studied pests, such as leaf folders and stem borers, which also cause substantial yield losses (Bentur et al., 2021). Furthermore, the integration of resistance genes into high-yielding and locally adapted rice varieties remains a challenge that requires more focused breeding efforts (Kapoor et al., 2020).
5.2 Emerging technologies
Emerging technologies in genetics and breeding hold great promise for transforming rice pest management. CRISPR/Cas9 genome editing is one such technology that allows precise modifications of resistance genes, potentially leading to the development of rice varieties with enhanced and durable resistance to multiple pests (Bentur et al., 2021). Single-cell RNA sequencing is another innovative approach that can provide detailed insights into the cellular and molecular responses of rice to insect attacks, enabling the identification of novel resistance mechanisms and targets for genetic improvement (Zha et al., 2023). Additionally, RNA interference (RNAi) technology offers a promising strategy for silencing essential genes in pests, thereby reducing their ability to damage rice plants. The integration of these advanced molecular tools with traditional breeding methods can accelerate the development of insect-resistant rice varieties (Yang et al., 2020).
5.3 Global impact
The development of insect-resistant rice varieties has profound global implications for food security and agricultural sustainability. Rice is a staple food for more than half of the world's population, and insect pests pose a significant threat to its production (Yan et al., 2023). By reducing the reliance on chemical pesticides, insect-resistant rice varieties can contribute to more sustainable agricultural practices, minimizing environmental pollution and preserving soil health (Thia et al., 2020). Moreover, these varieties can enhance the resilience of rice production systems to pest outbreaks, thereby stabilizing yields and ensuring a reliable food supply (Dash et al., 2020). The widespread adoption of resistant varieties can also lead to economic benefits for farmers by reducing the costs associated with pest management and increasing overall productivity. Ultimately, the global impact of developing and deploying insect-resistant rice varieties extends beyond agriculture, contributing to the broader goals of environmental conservation and sustainable development.
6 Concluding Remarks
6.1 Summary of key findings
This study has highlighted significant advancements in understanding the genetic mechanisms and breeding approaches for rice varietal resistance to insect pests. The integration of genomics, genetic mapping, and molecular biology has led to the identification and cloning of numerous resistance genes. For instance, genome-wide association studies have identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with brown planthopper (BPH) resistance, including the novel gene Bph371. Additionally, 14 insect resistance genes have been cloned, which activate defense pathways and mechanisms such as callose deposition and secondary metabolite production. The study also underscores the importance of wild rice species as a reservoir of resistance genes. For example, the gene Bph38 from Oryza rufipogon confers high resistance to both BPH and white-backed planthopper (WBPH). Moreover, the development of multi-resistance rice varieties through transgene stacking systems has shown promising results in conferring resistance to multiple pests and diseases. Conventional breeding approaches, supplemented with advanced molecular techniques, have also been effective in developing insect-resistant rice varieties.
6.2 Implications for agriculture
The findings from this study have profound implications for future rice cultivation and pest management strategies. The identification and cloning of resistance genes provide valuable genetic resources for breeding durable insect-resistant rice varieties. The integration of multiple resistance genes into a single genetic background, as demonstrated by the development of multi-resistance rice, offers a sustainable and environmentally friendly approach to pest management. Furthermore, the use of wild rice species as a source of resistance genes can enhance the genetic diversity of cultivated rice, making it more resilient to evolving pest biotypes. The application of advanced molecular techniques, such as gene editing and marker-assisted selection, can accelerate the development of new resistant varieties, ensuring food security in the face of increasing pest pressures.
In conclusion, the integration of genetic and breeding approaches holds great promise for improving rice resistance to insect pests. These advancements will not only enhance rice productivity but also contribute to sustainable agricultural practices by reducing the reliance on chemical pesticides. Future research should focus on exploring additional resistance genes, understanding the molecular mechanisms of resistance, and developing innovative breeding strategies to address the challenges posed by insect pests in rice cultivation.
Acknowledgments
The author extend our sincere thanks to two anonymous peer studyers for their invaluable feedback on the initial draft of this paper, whose critical evaluations and constructive suggestions have greatly contributed to the improvement of our manuscript.
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.
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