1 Introduction

Rice blast is the world's most serious rice disease affecting the safe production of rice, caused by the infestation of the rice blast fungus. This disease significantly impacts rice yield and quality, posing a major threat to food security, especially in regions heavily dependent on rice as a staple food (Helliwell et al., 2013; Liu et al., 2013; Chen et al., 2018). The interaction between rice and M. oryzae has been extensively studied, revealing complex mechanisms of plant immunity and pathogen virulence (Ribot et al., 2008; Liu et al., 2013; Yan et al., 2022). Effective blast resistance is crucial for sustainable rice production, as it helps mitigate the economic losses caused by this pathogen and ensures stable rice supply (Ray et al., 2016; Mgonja et al., 2017).

Asian cultivated rice (Oryza sativa L.) features phenotypically divergent ecotypes, upland rice and paddy rice , adapted to distinct hydrological cultivation systems. Upland rice was domesticated as a unique ecotype with high drought-aerobic adaptation under long-term natural and artificial selection in aerobic and dry soil conditions (Lyu et al., 2014; Xu et al., 2020). Traditional paddy or lowland rice is grown in paddy fields with its basal section covered by water; its production depends on a large volume of freshwater, and climate change, freshwater shortage and drought have enormously affected food security (Tuhina-Khatun et al., 2015).

Paddy rice and upland rice are two important categories of rice that are cultivated in various regions. Paddy rice is known for its high yield potential and adaptability to different environmental conditions, making it a popular choice among farmers (Mgonja et al., 2017). Upland rice, on the other hand, is typically grown in non-irrigated, rain-fed conditions and is valued for its resilience to drought and other abiotic stresses (Jagadeesh et al., 2020). Both types of rice have unique genetic backgrounds and agronomic traits, which can be leveraged to enhance blast resistance through breeding programs (Chen et al., 2011).

The upland rice has a significant contribution to total rice production and also plays an important role in crop rotation in the South to northern areas of the country (Fongfon et al., 2021).

The aim of this review is to explore the genetic diversity of blast resistance in paddy rice and upland rice. By understanding the genetic basis of resistance in these rice types, we aim to identify key resistance genes and quantitative trait loci (QTLs) that can be utilized in breeding programs to develop rice varieties with enhanced resistance to M. oryzae. We also seek to contribute to the broader understanding of plant-pathogen interactions and the molecular mechanisms underlying blast resistance in rice. Ultimately, the synthetic knowledge from this review will support the development of more resilient rice cultivars, ensuring food security and sustainable agricultural practices.

2 Understanding Rice Blast Disease

2.1 Causal agent: Magnaporthe oryzae

Rice blast is the world's most serious rice disease affecting the safe production of rice, caused by the infestation of the rice blast fungus. This pathogen has emerged as a model organism for studying plant-pathogen interactions due to its complex infection mechanisms and significant impact on rice yield (Liu et al., 2013). M. oryzae infects rice plants by forming specialized structures called appressoria, which facilitate the penetration of the host plant's surface (Martin-Urdiroz et al., 2016). The fungus then proliferates within the plant tissue, deploying effector proteins that suppress plant immunity and promote fungal growth (Figure 1) (Oliveira-Garcia et al., 2023).

Figure 1 Secretion and translocation of Magnaporthe oryzae effectors into rice cells (Adopted from Oliveira-Garcia et al., 2023) Image caption: The figure collectively demonstrates the complex process by which Magnaporthe oryzae effectors are secreted and translocated into rice cells. The schematic in panel A provides a theoretical model of this process, while panels B and C offer experimental evidence, particularly focusing on the role of clathrin-mediated vesicle trafficking and the impact of Brefeldin A on effector localization. This research is crucial for understanding the molecular mechanisms of host-pathogen interactions and could inform strategies to enhance resistance to rice blast disease (Adopted from Oliveira-Garcia et al., 2023)

2.2 Symptoms and impact on rice yield

The symptoms of rice blast disease include the appearance of lesions on various parts of the rice plant, such as leaves, stems, and panicles. These lesions can be elliptical or diamond-shaped with a grayish center and dark brown margins (Liang et al., 2018). In severe cases, the disease can lead to the complete destruction of the rice crop, significantly reducing yield. The impact of rice blast on yield is profound, as it can cause up to 50% yield loss in susceptible rice varieties under favorable conditions for the pathogen (Chen et al., 2018). The disease not only affects the quantity of the rice produced but also its quality, leading to economic losses for farmers and affecting food security (Liu et al., 2013; Martin-Urdiroz et al., 2016).

2.3 Historical perspective on blast disease management

The prevention and control methods of rice blast include the treatment and selection of seeds, the scientific control of cultivation density, the strengthening of water and fertilizer management in the field, the elimination of bacterial sources, the cutting off of transmission routes, the use of chemical agents to prevent and control, etc., but some chemical agents will produce fungicide resistance to pathogens. Therefore, the development of blast-resistant rice varieties has been a cornerstone of disease management. This approach involves the identification and incorporation of resistance genes (R genes) into rice cultivars. Advances in molecular genetics and genomics have facilitated the discovery of numerous resistance genes and quantitative trait loci (QTLs) associated with blast resistance. Genome-wide association studies (GWAS) have identified several loci that contribute to resistance, providing valuable insights for breeding programs. Despite these efforts, the genetic diversity and adaptability of M. oryzae continue to pose significant challenges, necessitating ongoing research and the development of integrated disease management strategies (Figure 2) (Kang et al., 2016; Sheoran et al., 2021; Yan et al., 2022). Understanding the biology and impact of M. oryzae, along with historical and contemporary management practices, is crucial for developing effective strategies to combat rice blast disease and ensure global food security.

Figure 2 Transcriptional profile analysis of a time-course of plant infection by the rice blast fungus M. oryzae (Adopted from Yan et al., 2022) Image caption: The figure overall shows how the rice blast fungus progresses in rice tissue over time, visualizing the infection process, the impact on plant tissue, and quantifying the extent of fungal spread or damage under different conditions. The data seem to indicate that certain treatments or genetic factors could mitigate or exacerbate the effects of the fungus, providing insights into possible control strategies (Adopted from Yan et al., 2022)

3 Genetic Basis of Blast Resistance

3.1 Resistance (R) genes identified in upland and paddy rice

Resistance (R) genes play a crucial role in providing rice plants with the ability to resist blast disease caused by the fungus M. oryzae. Over the years, numerous R genes have been identified and characterized. Since the first genetic study for rice blast in 1922, 118 genes have been mapped and 28 genes have been cloned (Ashkani et al., 2016). The Pi2 cluster on chromosome 6 has been reported for the four successfully cloned genes (Pi2, Pi9, Pi-gm and Piz-t) (Meng et al., 2020). Among the 27 mapped genes on chromosome 11, six genes (Pik, Pik-h, Pik-m, Pik-p, Pi1 and Pi-ke) were located in Pik cluster (Meng et al., 2021). For instance, a comprehensive review identified numerous blast resistance genes, which have been mapped on the rice genome, providing valuable insights into their distribution and potential for breeding programs (Ballini et al., 2008; Ashkani et al., 2016). Specific R genes such as Pi1, Pi2, Pi9, Pi54, Pigm, and Piz-t have been cloned and utilized in molecular breeding to develop resistant rice varieties (Ning et al., 2020). Additionally, the Pita2 gene, which encodes a novel R protein distinct from Pita, has been shown to confer broad-spectrum resistance, making it a valuable target for breeding programs (Meng et al., 2020). The identification of elite R-gene combinations, such as Pita+Pi3/5/i and Pita+Pia, has also been instrumental in improving blast resistance in Geng rice varieties (Gao et al., 2023).

3.2 Quantitative trait Loci (QTLs) for blast resistance

Quantitative Trait Loci (QTLs) are genomic regions that contribute to the variation in complex traits such as disease resistance. In rice, approximately 350 QTLs associated with blast resistance have been identified and mapped, providing a comprehensive resource for understanding the genetic basis of partial resistance (Ballini et al., 2008). For example, a study on the japonica rice cultivar Moroberekan identified ten chromosomal segments associated with partial resistance to blast, illustrating the complex genetic architecture underlying durable resistance. Another study on upland rice identified a major QTL for leaf blast resistance on chromosome 11, which was further fine-mapped to a 108.9-kb genomic region, highlighting the potential for marker-assisted selection in breeding programs (Tan et al., 2022). Most of the cloned R-QTL were associated with leaf rice blast resistance at the seedling stage, whereas only a few genes such as Pb1, Pi25, Pi64 and Pi68 were resistant to spike rice blast. While the majority of R-QTL provided race-specific resistance, a few R-QTL including Pi2, Pi54, Pi9, Pigm, Pizt and Pi54 provided broad-spectrum resistance (Shanika et al., 2024). Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability.

3.3 Molecular mechanisms of blast resistance

In the long-term evolution of rice, two natural immune systems develop when rice is infested with rice blast fungus (Ting et al., 2021). These include pathogenic factor-related molecular pattern-triggered immunity (Pattern-triggered Immunity, PTI) and resistance protein (R protein)-mediated effector protein-triggered immunity (Effector-triggered Immunity, ETI). Both immune systems are capable of inducing rice to develop rice blast disease resistance. Previous studies have shown that the first layer of immunity, PTI, is a relatively weak immune response that inhibits or prevents pathogen infestation by triggering a defense response after sensing rice blast pathogens through extracellular, transmembrane, or pattern-recognition receptors. PTI is mediated by secondary metabolite production, cell-wall thickening, and programmed cell death, by signaling of mitogen-activated protein kinases, by WRKY transcription factors, and by transcriptional recoding mediated by WRKY. Mediated transcriptional recoding, and reactive oxygen species (ROS) generation as pathways of defense against rice blast (Li et al., 2017). The second layer of immunity, ETI, is activated by highly polymorphic intracellular R proteins recognizing avirulence effectors (Avr), which has a higher level of resistance compared to PTI, and generally elicits a hypersensitivity reaction at the site of infection during the defense process, which is effective in controlling rice blast disease. It is a highly specialized disease resistance mechanism for breeding in the host (Ning et al., 2020；Oliveira-Garcia et al., 2023).

The molecular mechanisms underlying blast resistance in rice involve a complex interplay of genetic and biochemical pathways. The Pi-d2 was reported to encode a B-lectin receptor kinase (Kouzai et al. 2013), while the recessive gene pi21 encodes a proline-rich protein (Fang et al. 2019), Bsr-d1 encodes a C₂H₂-type transcription factor protein (Li et al. 2017), and Bsr-k1 encodes a tetratricopeptide repeats-containing protein (Zhou et al. 2018). One key mechanism is the interaction between R genes and their corresponding avirulence (Avr) genes in the pathogen, which triggers a defense response in the plant. For instance, the Pita2 gene has been shown to recognize specific AvrPita isolates, leading to a robust resistance response (Meng et al., 2020). Additionally, non-race-specific resistance, which is often more durable, has been linked to natural alleles of transcription factors such as bsr-d1, a single nucleotide change in the promoter of the bsr-d1 gene, resulting in reduced expression of the gene through the binding of the repressive MYB transcription factor and consequently, enhanced disease resistance by inhibiting H₂O₂ degradation (Li et al., 2017). The identification of differentially expressed genes (DEGs) in response to blast infection further elucidates the molecular pathways involved in resistance. For example, transcriptome analysis in upland rice revealed DEGs that are functionally annotated to catalytic responses against disease stimuli, providing insights into the cellular mechanisms of resistance (Tan et al., 2022). The genetic basis of blast resistance in rice is multifaceted, involving a combination of R genes, QTLs, and intricate molecular mechanisms. These insights are crucial for developing durable and broad-spectrum resistant rice varieties through advanced breeding strategies.

4 Genetic Diversity in Upland Rice

4.1 Adaptation and cultivation conditions of upland rice

Upland rice is primarily cultivated in rainfed areas with limited water availability, making it crucial for these varieties to possess traits that enable them to thrive under drought conditions. Upland rice has evolved distinct morphological and physiological adaptations to cope with water scarcity, such as deeper root systems and efficient water use mechanisms (Xia et al., 2019). The study represents the first genomic investigation in a large sample of upland rice, providing valuable gene list for understanding upland rice adaptation, especially drought-related adaptation, and its subsequent utilization in modern agriculture (Lyu et al., 2014) (Figure 3). These adaptations are a result of bi-directional selection processes that have shaped the genetic makeup of upland rice, allowing it to maintain productivity even under drought stress (Wang et al., 2023). The cultivation of upland rice is predominantly practiced by smallholder farmers in regions like Latin America and Africa, where the risk of dry spells is high (Lanna et al., 2021).

Figure 3 Phylogenetic tree of rice accessions (Adopted from Lyu et al., 2014) Image caption: Green, black and orange branches refer to upland, irrigated and wild accessions respectively. Analysis showed that differentiation between Indica and Japonica has existed within the wild population, since there are strains of wild rice close to both Indica and Japonica respectively, supporting the double domestication model. The tree shows multiple origins for upland rice, though the upland japonicas may bear a single origin. Bootstrap values are indicated in some of the major internal nodes. Some of the leaf nodes are labeled with the sample number of the rice accessions. ‘ru’ refers to ‘rufipogon’, and ‘ni’ refers to ‘nivara’ (Adopted from Lyu et al., 2014)

4.2 Identified blast resistance genes in upland rice

Elite upland rice cultivars have the advantages of less water requirement along with high yield but are usually susceptible to various diseases. Blast disease, caused by the fungus M. oryzae, is also a significant threat to upland rice production. To date, only a few genes conferring non-race-specific resistance have been isolated in rice, act as recessive alleles. For instance, Pi21 encodes a proline-rich protein containing a metal-binding domain and a loss-of-function allele (pi21) confers non-race specific, durable resistance (Fukuoka et al., 2009). Bsr-d1, from Digu (upland rice), encodes a C₂H₂-type TF, which is directly regulated by a MYB family TF. These two TFs regulate expression of H₂O₂-degradation enzymes to accomplish resistance to M. oryzae, constituting a novel mechanism employed by rice blast resistance (Figure 4) (Li et al, 2017). Recently, the fine-mapping of a novel QTL for blast resistance in upland rice variety UR0803, enhanced the genetic understanding of the mechanism of blast resistance in upland rice (Tan et al., 2022).

Figure 4 A Model for bsr-d1-Mediated Disease Resistance In Digu (bsr-d1), MYBS1 binds to the Bsr-d1 promoter with high affinity, suppressing Bsr-d1 expression; low BSR-D1 levels in turn downregulate expression of downstream genes including two peroxidases, resulting in accumulation of H2O2 and enhanced resistance to M. oryzae. In susceptible rice varieties (Bsr-d1), like LTH, Bsr-d1 is highly expressed, activating specific H2O2 degradation activities, leading to susceptibility (Adopted from Li et al, 2017)

4.3 Diversity analysis using molecular markers

Molecular markers have been instrumental in analyzing the genetic diversity of rice. GWAS and QTL mapping have identified several genes and genomic regions associated with drought resistance and other adaptive traits. Compared with conventional gene targeting methods, GWAS of rice can accomplish the detection of high-density SNPs in parental, genetic or natural diversity populations at one time, which greatly improves the research efficiency. For example, a study using whole genome variation data revealed differentiated genes that account for the phenotypic and physiological differences between upland and irrigated rice (Lyu et al., 2014). Additionally, specific regions on chromosome 7 have been linked to traits such as tiller and panicle numbers, root growth angle, and drought response, which are critical for upland adaptation (Uddin and Fukuta, 2020). The use of molecular markers not only aids in understanding the genetic basis of these traits but also facilitates marker-assisted selection (MAS) in breeding programs aimed at developing stress-resistant upland rice varieties (Bernier et al., 2008).

5 Comparative Analysis of Blast Resistance

5.1 Methodologies for comparative genetic studies

Comparative genetic studies on blast resistance in rice employ a variety of methodologies to identify and map resistance genes and QTLs. One common approach is the use of QTL mapping, which involves crossing resistant and susceptible rice varieties and analyzing the resulting populations. For instance, an F₂ mapping population was developed from a cross between a resistant upland rice genotype UR0803 and a paddy rice susceptible cultivar Lijiang Xintuan Heigu (LTH), leading to the identification of a major QTL for leaf blast resistance on chromosome 11. Another method is bulked segregant analysis (BSA) combined with high-throughput sequencing, which helps in pinpointing candidate regions associated with disease resistance traits (Tan et al., 2022).

Genome-wide meta-analyses also play a crucial role in understanding blast resistance. These analyses compile data from multiple studies to map resistance genes and QTLs across the rice genome, providing a comprehensive overview of known resistance loci (Ballini et al., 2008). Additionally, gene-specific markers are used to dissect genetic diversity at significant blast resistance loci, as demonstrated in studies involving Indian rice landraces (Yadav et al., 2019).

Advanced backcross populations and recurrent selection are other methodologies used to enhance blast resistance. For example, recurrent selection in the CNA-IRAT 5 upland rice population has been shown to improve partial blast resistance over multiple generations (Veillet et al., 1996). Transgenic approaches, such as the introduction of chitinase and beta-1,3-glucanase genes into Dian-type hybrid rice, have also been employed to enhance resistance (Xu et al., 2003).

5.2 Key findings from comparative studies

Comparative studies have yielded several key findings regarding blast resistance in rice. The identification of a major QTL on chromosome 11 in upland rice highlights the potential for fine-mapping and functional annotation of candidate genes involved in resistance (Tan et al., 2022). Meta-analyses have mapped 85 blast resistance genes and approximately 350 QTLs, providing valuable insights into the genetic basis of both partial and complete resistance (Ballini et al., 2008).

Studies on Indian rice landraces have revealed significant genetic diversity at blast resistance loci, with landraces harboring between five to nineteen resistance genes. This diversity is crucial for breeding programs aimed at developing resistant varieties (Yadav et al., 2019). In the CNA-IRAT 5 population, recurrent selection has been shown to efficiently improve partial blast resistance, with hybrid breeding appearing slightly more advantageous than pure line breeding (Veillet et al., 1996).

Additionally, fine-mapping of QTLs, such as Pikahei-1(t) from upland rice Kahei, has identified candidate resistance genes that can be targeted in breeding programs (Xu et al., 2008).

5.3 Implications for breeding programs

The findings from comparative genetic studies have significant implications for rice breeding programs. The identification and fine-mapping of major QTLs and resistance genes provide valuable genetic resources that can be introgressed into elite cultivars to enhance blast resistance. For instance, the QTL identified on chromosome 11 in upland rice can be used to develop new resistant varieties through marker-assisted selection (Tan et al., 2022).

The genetic diversity observed in Indian rice landraces suggests that these landraces can serve as a reservoir of resistance genes for breeding programs. By incorporating diverse resistance genes, breeders can develop varieties with broad-spectrum and durable resistance to blast (Yadav et al., 2019). The success of recurrent selection in improving partial blast resistance in the CNA-IRAT 5 population indicates that this approach can be applied to other rice populations to enhance resistance (Veillet et al., 1996).

Transgenic approaches offer another avenue for improving blast resistance. The successful introduction of chitinase and beta-1,3-glucanase genes into Dian-type hybrid rice demonstrates the potential of genetic engineering in developing resistant varieties (Xu et al., 2003). Fine-mapping of QTLs, such as Pikahei-1(t), provides specific targets for breeding programs, enabling the development of varieties with strong field resistance (Xu et al., 2008).

6 Breeding Strategies for Enhanced Blast Resistance

6.1 Marker-assisted selection (MAS) in breeding

MAS has become a pivotal tool in rice breeding programs aimed at enhancing blast resistance. MAS involves the use of molecular markers that are closely linked to resistance genes, allowing for the precise selection of desirable traits. For instance, the use of RFLP markers for genes such as Pi1, Piz-5, and Pita has been instrumental in developing blast-resistant rice varieties (Hittalmani et al., 2000). Similarly, the integration of genes Pi-d(t)1, Pi-b, and Pi-ta2 through MAS has demonstrated significant improvements in blast resistance in hybrid rice lines. The application of MAS not only accelerates the breeding process but also ensures the incorporation of multiple resistance genes, thereby enhancing the overall resistance profile of the rice cultivars (Narayanan et al., 2004; Dahu et al., 2015).

6.2 Pyramiding resistance genes

Gene pyramiding is a strategy that involves stacking multiple resistance genes into a single rice variety to achieve broad-spectrum and durable resistance against blast disease. Some studies have shown that the resistance rate of spike canker with three resistance genes increased by 54.3% compared with one gene, but more studies have concluded that there is no significant negative correlation between the number of resistance genes carried and resistance to rice blast, and that the polymerization of resistance genes is not a simple superposition of resistance spectra, and that the polymerization of genes with good resistance and complementary spectrums of resistance should be selected, which not only broadens the spectrum of resistance, but also improves the resistance to some physiological microspecies. The studies showed that the correlation between the number of resistance genes carried and the resistance to spikelet plague was not significant. For the improvement of resistance to spikelet plague, in addition to the simple polymerization of resistance genes, the strengths and weaknesses of resistance genes and the interactions between genes in different genetic backgrounds should be taken into full consideration. (Wu et al., 2023). This approach has been successfully implemented using MAS to combine genes such as Pi2, Pi9, and others, resulting in rice lines with enhanced resistance to multiple biotic stresses (Ludwików et al., 2015). For example, the pyramiding of Pi9 and Xa23 genes in the GZ63S line has led to significant improvements in resistance to both blast and bacterial blight (Ni et al., 2015). Additionally, the combination of Piz5 and Pi54 genes in the PRR78 line has shown promising results in developing blast-resistant Basmati rice (Singh et al., 2013). The effectiveness of gene pyramiding is further supported by the successful integration of up to five blast-resistance genes in japonica rice varieties, providing a robust defense against diverse strains of the pathogen (Zampieri et al., 2023).

6.3. Integration of modern biotechnologies (CRISPR, Genomics)

The advent of modern biotechnologies such as CRISPR and advanced genomic tools has revolutionized the field of rice breeding. CRISPR/Cas9 technology allows for precise genome editing, enabling the targeted modification of blast resistance genes to enhance their effectiveness. This technology has the potential to introduce novel resistance genes or enhance existing ones, thereby providing a powerful tool for developing blast-resistant rice varieties (Miah et al., 2013). Genomic selection, which involves the use of genome-wide markers to predict the performance of breeding lines, has also been employed to accelerate the development of resistant varieties. The integration of these biotechnologies with traditional breeding methods and MAS can significantly enhance the efficiency and precision of breeding programs aimed at combating blast disease (Das et al., 2017; Fukuoka, 2018). However, the cycle of selecting disease-resistant varieties through traditional breeding methods is very long and labor-intensive for phenotypic characterization. In general, it takes at least 6 years to improve disease resistance in an old variety, and the identification of rice blast resistance is time-consuming and labor-intensive, and lacks a certain degree of accuracy through direct phenotyping. Mining disease resistance genes and utilizing them through molecular marker-assisted selection is an effective way to rapidly improve varietal disease resistance and extend the life of old varieties (Sang et al., 2022)

7 Challenges and Future Directions

7.1 Technical and logistical challenges

The exploration of genetic diversity for blast resistance in Dian-type hybrid and upland rice faces several technical and logistical challenges. One significant challenge is the complexity of the rice genome and the polygenic nature of blast resistance, which involves multiple genes and quantitative trait loci (QTLs) (Ballini et al., 2008; Tan et al., 2022). The identification and mapping of these genes require advanced molecular techniques and high-throughput sequencing, which can be resource-intensive and time-consuming (Ashkani et al., 2015; Ning et al., 2020). Additionally, the integration of resistance genes into elite cultivars through breeding programs is complicated by the need to maintain other desirable agronomic traits, such as yield and quality (Xu et al., 2008). The variability in pathogen populations and the emergence of new virulent strains further complicate the breeding process, necessitating continuous monitoring and updating of resistance genes (Nizolli et al., 2017; Herawati et al., 2022).

7.2 Research gaps and unresolved questions

Despite significant progress, several research gaps and unresolved questions remain in the study of blast resistance in rice. One major gap is the limited understanding of the molecular mechanisms underlying partial and complete resistance to blast disease (Ballini et al., 2008). While numerous resistance genes and QTLs have been identified, their functional roles and interactions are not fully elucidated (Ning et al., 2020; Tan et al., 2022). Another unresolved question is the durability of resistance conferred by these genes. Many resistance genes provide only short-term protection, and the mechanisms that contribute to long-lasting resistance are not well understood (Ashkani et al., 2015; Nizolli et al., 2021). Additionally, there is a need for more comprehensive studies on the host-pathogen interactions and the environmental factors that influence the expression of resistance genes (Xu et al., 2008; Yadav et al., 2019). In future breeding, it is necessary to continuously select and breed new materials to realize high yield and disease resistance, gene editing breeding practice shows that although new variants can be rapidly created in different rice variety backgrounds, the application of some yield-related genes is not ideal, and some genes even show yield reduction effects, so high quality and high yield is an important breeding goal, and diversified control of rice blast fungus is the direction of future development, and the cultivation of New disease-resistant varieties, searching for low-toxicity and low-residue fungicide, and reducing the use of chemical and biological pesticides are inevitable trends. In the future, with the continuous development of molecular biology, genomics and biotechnology, rice molecular marker-assisted selection breeding technology will be more mature and perfect.

7.3 Prospects for future research and breeding efforts

Future research and breeding efforts should focus on several key areas to enhance blast resistance in Dian-type hybrid and upland rice. One promising direction is the use of advanced genomic tools, such as genome-wide association studies (GWAS) and CRISPR/Cas9 gene editing, to identify and manipulate resistance genes with greater precision (Ning et al., 2020; Srichant et al., 2019). The development of high-throughput phenotyping platforms can also accelerate the screening of large breeding populations for blast resistance (Xu et al., 2008; Tan et al., 2022). Another important area is the pyramiding of multiple resistance genes to create cultivars with broad-spectrum and durable resistance (Ashkani et al., 2015; Srichant et al., 2019). Collaborative efforts between researchers, breeders, and farmers are essential to ensure the successful implementation of these strategies and to address the evolving challenges posed by blast disease (Xu et al., 2008; Herawati et al., 2022). Finally, the integration of traditional breeding methods with modern biotechnological approaches can provide a holistic framework for developing resilient rice varieties that can withstand the pressures of both biotic and abiotic stresses (Yadav et al., 2019; Ning et al., 2020).

The importance of genetic diversity in blast resistance cannot be overstated. Diverse genetic backgrounds provide a broader spectrum of resistance, reducing the likelihood of widespread disease outbreaks. This study underscores the need to preserve and utilize the genetic diversity present in traditional landraces and wild rice species, which harbor unique resistance genes that can be crucial for future breeding efforts. The integration of advanced genomic tools and traditional breeding techniques will be essential in harnessing this diversity to develop rice varieties that can withstand the evolving challenges posed by blast disease and other biotic stresses. Ultimately, maintaining and enhancing genetic diversity in rice will be key to ensuring sustainable rice production and global food security.

Funding

This work was supported by the grants from the Central Leading Local Science and Technology Development Project (grant no. 202207AA110010) and the Key and Major Science and Technology Projects of Yunnan (grant nos. 202202AE09002102, 202402AE090026-04).

Acknowledgments

We extend our sincere thanks to two anonymous peer reviewers 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.

References

Ashkani S., Rafii M., Shabanimofrad M., Miah G., Sahebi M., Azizi P., Tanweer F., Akhtar M., and Nasehi A., 2015, Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop, Frontiers in Plant Science, 6: 886.

https://doi.org/10.3389/fpls.2015.00886

Bernier J., Atlin G., Serraj R., Kumar A., and Spaner D., 2008, Breeding upland rice for drought resistance, Journal of the Science of Food and Agriculture, 88: 927-939.

https://doi.org/10.1002/JSFA.3153

Chen J., Shi Y., Liu W., Chai R., Fu Y., Zhuang J., and Wu J., 2011, A pid3 allele from rice cultivar gumei2 confers resistance to Magnaporthe oryzae, Journal of genetics and genomics, 38(5): 209-216.

Chen X., Chen H., Yuan J., Köllner T., Chen Y., Guo Y., Zhuang X., Chen X., Zhang Y., Fu J., Nebenführ A., Guo Z., and Chen F., 2018, The rice terpene synthase gene OsTPS19 functions as an (S)-limonene synthase in planta, and its overexpression leads to enhanced resistance to the blast fungus Magnaporthe oryzae, Plant Biotechnology Journal, 16: 1778-1787.

https://doi.org/10.1111/pbi.12914

Das G., Patra J., and Baek K., 2017, Insight into MAS: a molecular tool for development of stress resistant and quality of rice through gene stacking, Frontiers in Plant Science, 8: 985.

https://doi.org/10.3389/fpls.2017.00985

Fongfon S., Pusadee T., Promuthai C., Rerkasem B., and Jamjod S., 2021, Diversity of purple rice (Oryza sativa L.) landraces in northern thailand, Agronomy, 10: 2029-2029.

Fukuoka S., 2018, Marker-assisted gene pyramiding for durable resistance to blast, Rice Genomics,Genetics and Breeding, 20: 393-415.

https://doi.org/10.1007/978-981-10-7461-5_20

Gao P., Li M.Y., Wang X.Q., Xu Z.W., Wu K.T., Sun Q.Y., Du H.B., Younas M., Zhang Y., Feng Z.M., Hu K.M., Chen Z.X., and Zuo S.M., 2023, Identification of elite R-gene combinations against blast disease in geng rice varieties, International Journal of Molecular Sciences, 24(4): 3984.

https://doi.org/10.3390/ijms24043984

Helliwell E., Wang Q., and Yang Y., 2013, Transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens Magnaporthe oryzae and Rhizoctonia solani, Plant Biotechnology Journal, 11(1): 33-42.

https://doi.org/10.1111/pbi.12004

Herawati R., Herlinda S., Ganefianti D., Bustamam H., and S., 2022, Improving broad spectrum blast resistance by introduction of the pita2 gene: encoding the NB-ARC domain of blast-resistant proteins into upland rice breeding programs, Agronomy, 12(10): 2373.

https://doi.org/10.3390/agronomy12102373

Hittalmani S., Parco A., Mew T., Zeigler R., and Huang N., 2000, Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice, Theoretical and Applied Genetics, 100: 1121-1128.

https://doi.org/10.1007/s001220051395

Jagadeesh D., Kumar M., Amruthavalli C., and Devaki N., 2020, Genetic diversity of Magnaporthe oryzae, the blast pathogen of rice in different districts of Karnataka, India determined by simple sequence repeat (SSR) markers, Indian Phytopathology, 73: 713-723.

https://doi.org/10.1007/s42360-020-00257-4

Kang H.X., Wang Y., Peng S.S., Zhang Y.L., Xiao Y.H., Wang D., Qu S.H., Li Z.Q., Yan S.Y., Wang Z.L., Liu W.D., Ning Y.S., Korniliev P., Leung H., Mezey J., McCouch S., and Wang G.L., 2016, Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae. Molecular Plant Pathology, 17(6): 959-972.

https://doi.org/10.1111/mpp.12340

Lanna A., Coelho G., Moreira A., Terra T., Brondani C., Saraiva G., Lemos F., Guimarães P., Júnior O., and Vianello R., 2021, Upland rice: phenotypic diversity for drought tolerance, Scientia Agricola, 78(5): e20190338.

https://doi.org/10.1590/1678-992x-2019-0338

Li W.T., Zhu Z.W., Chern M., Yin J.J., Yang C., Ran L., Cheng M.P., He M., Wang K., Wang J., Zhou X.G., Zhu X.B., Chen Z.X., Wang J.C., Zhao W., Ma B.T., Qin P., Chen W.L., Wang Y.P., Liu J.L., Wang W.M., Wu X.J., Li P., Wang J.R., Zhu L.H,, Li S.G., and Chen X.W., 2017, A natural allele of a transcription factor in rice confers broad-spectrum blast resistance, Cell, 170: 114-126.

https://doi.org/10.1016/j.cell.2017.06.008

Liang Y., Zhao J., Wang C., Jing Y., Chengyun L., and Baldwin T., 2018, Infection with blast fungus (Magnaporthe orzyae) leads to increased expression of an arabinogalactan-protein epitope in both susceptible and resistant rice cultivars, Physiological and Molecular Plant Pathology, 102: 136-143.

https://doi.org/10.1016/J.PMPP.2018.01.002

Liu W.D., Liu J.L., Ning Y.S., Ding B., Wang X.L., Wang Z.L., and Wang G.L., 2013, Recent progress in understanding PAMP-and effector-triggered immunity against the rice blast fungus Magnaporthe oryzae, Molecular Plant, 6(3): 605-620.

https://doi.org/10.1093/mp/sst015

Ludwików A., Cieśla A., Arora P., Das G., Rao G., and Das R., 2015, Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar, Frontiers in Plant Science, 6: 698.

https://doi.org/10.3389/fpls.2015.00698

Lyu J., Li B.Y., He W.M., Zhang S.L., Gou Z.H., Zhang J., Meng L.Y., Li X., Tao D.Y., Huang W.Q., Hu F.Y., and Wang W., 2014, A genomic perspective on the important genetic mechanisms of upland adaptation of rice, BMC Plant Biology, 14: 160.

https://doi.org/10.1186/1471-2229-14-160

Mao T., Zhu M., Ahmad S., Ye G., Sheng Z., Hu Si., and Shao G., 2021, Superior japonica rice variety YJ144 with improved rice blast resistance, yield, and quality achieved using molecular design and multiple breeding strategies, Molecular Breeding, 10: 65-65.

Martin-Urdiroz M., Osés-Ruiz M., Ryder L., and Talbot N., 2016, Investigating the biology of plant infection by the rice blast fungus Magnaporthe oryzae, Fungal Genetics and Biology, 90: 61-68.

https://doi.org/10.1016/j.fgb.2015.12.009

Meng X.L., Xiao G., Telebanco-Yanoria M., Siazon P., Padilla J., Opulencia R., Bigirimana J., Habarugira G., Wu J., Li M.J., Wang B.H., Lu G.D., and Zhou B., 2020, The broad-spectrum rice blast resistance (R) gene pita2 encodes a novel R protein unique from Pita, Rice, 13: 19.

https://doi.org/10.1186/s12284-020-00377-5

Mgonja E., Park C., Kang H., Balimponya E., Opiyo S., Bellizzi M., Mutiga S., Rotich F., Ganeshan V., Mabagala R., Sneller C., Correll J., Zhou B., Talbot N., Mitchell T., and Wang G., 2017, Genotyping-by-sequencing-based genetic analysis of African rice cultivars and association mapping of blast resistance genes against Magnaporthe oryzae populations in Africa, Phytopathology, 107(9): 1039-1046.

https://doi.org/10.1094/PHYTO-12-16-0421-R

Miah G., Rafii M., Ismail M., Puteh A., Rahim H., Islam K., and Latif M., 2013, A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance, International Journal of Molecular Sciences, 14: 22499-22528.

https://doi.org/10.3390/ijms141122499

Narayanan N., Baisakh N., Oliva N., VeraCruz C., Gnanamanickam S., Datta K., and Datta S., 2004, Molecular breeding: marker-assisted selection combined with biolistic transformation for blast and bacterial blight resistance in Indica rice (cv. CO39), Molecular Breeding, 14: 61-71.

https://doi.org/10.1023/B:MOLB.0000037995.63856.2d

Ni D.H., Song F.S., Ni J.L., Zhang A.F., Wang C.L., Zhao K.J., Yang Y.C., Wei P.C., Yang J.B., and Li L., 2015, Marker-assisted selection of two-line hybrid rice for disease resistance to rice blast and bacterial blight, Field Crops Research, 184: 1-8.

https://doi.org/10.1016/J.FCR.2015.07.018

Xiao N., Wu Y.Y., and Li A.H., 2020, Strategy for use of rice blast resistance genes in rice molecular breeding, Rice Science, 27(4): 263-277.

https://doi.org/10.1016/j.rsci.2020.05.003

Nizolli V., Pegoraro C., and Oliveira A., 2021, Rice blast: strategies and challenges for improving genetic resistance, Crop Breeding and Applied Biotechnology, 21(S): e387721S9.

https://doi.org/10.1590/1984-70332021v21sa22

Oliveira-Garcia E., Yan X., Osés-Ruiz M., de Paula S., and Talbot N., 2023, Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae, The New Phytologist, 241(3): 1007-1020.

https://doi.org/10.1111/nph.19446

Ray S., Singh P., Gupta D., Mahato A., Sarkar C., Rathour R., Singh N., and Sharma T., 2016, Analysis of Magnaporthe oryzae genome reveals a fungal effector, which is able to induce resistance response in transgenic rice line containing resistance gene, Pi54, Frontiers in Plant Science, 7: 1140.

https://doi.org/10.3389/fpls.2016.01140

Ribot C., Hirsch J., Balzergue S., Tharreau D., Nottéghem J., Lebrun M., and Morel J., 2008, Susceptibility of rice to the blast fungus, Magnaporthe grisea, Journal of Plant Physiology, 165(1): 114-124.

https://doi.org/10.1016/J.JPLPH.2007.06.013

Sang S.F., Wang J.Y., Zhou J., Cao M.Y., Wang Y.N., Zhang J.Q., and Zhang W.L., 2022, Development of Pi-k^h marker for rice blast resistance gene and its application in disease resistance breeding, Molecular Plant Breeding, 20(5): 1588-1596.

https://doi.org/10.13271/j.mpb.020.001588

Shanika G., Janani W., Menaka F., Sachith A., Indika W., and Chandima A., 2024, Functional genomic regions associated with blast disease resistance in rice predicted syntenic orthologs and potential resistance gene candidates from diverse cereal genomes, Physiological and Molecular Plant Pathology, 133: 102344.

https://doi.org/10.1016/j.pmpp.2024.102344

Sheoran N., Ganesan P., Mughal N., Yadav I., and Kumar A., 2021, Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity, Fungal Biology, 125(9): 733-747.

https://doi.org/10.1016/J.FUNBIO.2021.04.007

Srichant N., Chankaew S., Monkham T., Thammabenjapone P., and Sanitchon J., 2019, Development of sakon nakhon ice ariety for blast resistance through marker assisted backcross breeding, Agronomy, 9(2): 67.

https://doi.org/10.3390/AGRONOMY9020067

Tan Q.Q., He H.Y., Chen W., Huang L., Zhao D.L., Chen X.J., Li J.Y., and Yang X.H., 2022, Integrated genetic analysis of leaf blast resistance in upland rice: QTL mapping, bulked segregant analysis and transcriptome sequencing, AoB Plants, 14(6): plac047.

https://doi.org/10.1093/aobpla/plac047

Tuhina-Khatun M., Hanafi M.M., Rafii Y.M., Wong M.Y., Salleh F.M., and Ferdous J., 2015, Genetic variation, heritability, and diversity analysis of upland rice (Oryza sativa L.) genotypes based on quantitative traits, BioMed Research International, 27: 290861.

https://doi.org/10.1155/2015/290861

Uddin M., and Fukuta Y., 2020, A region on chromosome 7 related to differentiation of rice (Oryza sativa L.) between lowland and upland ecotypes, Frontiers in Plant Science, 11: 1135.

https://doi.org/10.3389/fpls.2020.01135

Veillet S., Filippi M., and Gallais, A., 1996, Combined genetic analysis of partial blast resistance in an upland rice population and recurrent selection for line and hybrid values, Theoretical and Applied Genetics, 92: 644-653.

https://doi.org/10.1007/BF00226084

Wang Y.L., Jiang C.H., Zhang X.T., Yan H.M., Yin Z.G., Sun X.M., Gao F.H., Zhao Y., Liu W., Han S.C., Zhang J.J., Zhang Y.G., Zhang Z.Y., Zhang H.L., Li J.J., Xie X.Z., Zhao Q.Z., Wang X.N., Ye G.Y., Li J.Z., Ming R., and Li Z.C., 2023, Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding, Plant Biotechnology Journal, 22(3): 662-677.

https://doi.org/10.1111/pbi.14215

Wu Z., Li H., Chen C., Liu G., Luo Q., Qin S., and Zhu Q., 2023, Analysis of rice blast resistance genes and spike-neck blight resistance in conventional indica rice varieties, Journal of South China Agricultural University, 5: 718-724.

Xia H., Luo Z., Xiong J., Ma X.S., Lou Q.J., Wei H.B., Qiu J., Yang H., Liu G.L., Fan L.J., Chen L., and Luo L.J., 2019, Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice in drought resistance and productivity, Molecular Plant, 12(2): 170-184.

https://doi.org/10.1016/j.molp.2018.12.011

Xu M.H., Tang Z.S., Tan Y.L., Tian Y.C., Li C.Y., Zhang S.H., Chen Z.H., and Tian W.Z., 2003, A study on introduction of chitinase gene and beta-1,3-glucanase gene into restorer line of Dian-type hybrid rice (Oryza sativa L.) and enhanced resistance to blast (Magnaporthe grisea), Acta Genetica Sinica, 30(4): 330-334.

https://doi.org/10.1023/A:1022289509702

Xu X., Chen H., Fujimura T., and Kawasaki S., 2008, Fine mapping of a strong QTL of field resistance against rice blast, pikahei-1(t), from upland rice kahei, utilizing a novel resistance evaluation system in the greenhouse, Theoretical and Applied Genetics, 117: 997-1008.

https://doi.org/10.1007/s00122-008-0839-7

Yadav M., Aravindan S., Ngangkham U., Raghu S., Prabhukarthikeyan S., Keerthana U., Marndi B., Adak T., Munda S., Deshmukh R., Pramesh D., Samantaray S., and Rath P., 2019, Blast resistance in Indian rice landraces: genetic dissection by gene specific markers, PLoS ONE, 14(3): e0213566.

https://doi.org/10.1371/journal.pone.0211061

Yan X., Tang B., Ryder L., MacLean D., Were V., Eseola A., Cruz-Mireles N., Foster A., Osés-Ruiz M., and Talbot N., 2022, The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors, The Plant Cell, 35: 1360-1385.

https://doi.org/10.1093/plcell/koad036

Zampieri E., Volante A., Marè C., Orasen G., Desiderio F., Biselli C., Canella M., Carmagnola L., Milazzo J., Adreit H., Tharreau D., Poncelet N., Vaccino P., and Valè G., 2023, Marker-assisted pyramiding of blast-resistance genes in a japonica elite rice cultivar through forward and background selection, Plants, 12(4): 757.

https://doi.org/10.3390/plants12040757

Zhu Y.Y., Chen H.R., Fan J.H., Wang Y.Y., Li Y., Chen J.B., Fan J.X., Yang S.S., Hu L.P., Leung H., Mew T.W., Teng P.S., Wang Z.H., and Mundt C.C., 2000, Genetic diversity and disease control in rice, Nature, 406: 718-722.