The potential of genome editing to create novel alleles of resistance genes in rice.

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

Gene based markers improve precision of genome-wide association studies and accuracy of genomic predictions in rice breeding.

It is hypothesized that the genome-wide genic markers may increase the prediction accuracy of genomic selection for quantitative traits. To test this hypothesis, a set of candidate gene-based markers for yield and grain traits-related genes cloned across the rice genome were custom-designed. A multi-model, multi-locus genome-wide association study (GWAS) was performed using new genic markers developed to test their effectiveness for gene discovery. Two multi-locus models, FarmCPU and mrMLM, along with a single-locus mixed linear model (MLM), identified 28 significant marker-trait associations. These associations revealed novel causative alleles for grain weight and pleiotropic associations with other traits. For instance, the marker YD91 derived from the gene OsAAP3 on chromosome 1 was consistently associated with grain weight, while the gene has a significant effect on grain yield. Furthermore, nine genomic selection methods, including regression-based and machine learning-based models, were used to predict grain weight using a leave-one-out five-fold cross-validation approach to optimize the genomic selection model with genic markers. Among nine prediction models, Kernel Hilbert Space Regression (RKHS) is the best among regression-based models, and Random Forest Regression (RFR) is the best among machine learning-based models. Genomic prediction accuracies with and without GWAS significant markers were compared to assess the effectiveness of markers. The rapid decreases in prediction accuracy upon dropping GWAS significant markers indicate the effectiveness of new genic markers in genomic selection. Apart from that, the candidate gene-based markers were found to be more effective in genomic selection programs for better accuracy.

Stress responsive OsHyPRP16 promoter driven early expression of resistance gene Pi54 potentiate the resistance against Magnaporthe oryzae in transgenic rice.

The rice Hybrid Proline Rich Protein (HyPRP) encoding gene, OsHyPRP16 expression exhibit early upregulation in response to Magnaporthe oryzae inoculation. Here, we functionally characterized the OsHyPRP16 promoter through deletion analysis in transgenic Arabidopsis using GUS (ß-glucuronidase) reporter assay. The promoter fragments, sequentially deleted from the 5' end could induce differential GUS activity in response to stresses induced by different hormones and abiotic stress conditions. In addition, a strong GUS induction was observed in M. oryzae inoculated transgenic Arabidopsis. Based on the insilico and stress-inducibility of D1 promoter fragment against various phytohormones and rice blast fungus, and with no basal activity under control conditions, we rationally selected D1 promoter fragment to drive the expression of a major rice blast resistance gene; Pi54 in the genetic background of blast susceptible TP309 rice line. The D1 promoter fragment was able to induce the expression of Pi54 at immediate-early stages of M. oryzae infection in transgenic rice. The transgenic plants with Pi54 under the control of D1 promoter fragment displayed complete resistance against M. oryzae infection as compared to control plants. The present study suggests that the D1 fragment of OsHyPRP16 promoter is a valuable tool for breeding and development of rice lines with early-inducible and pathogen-responsive enhanced disease resistance.

Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions.

Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice-M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.

Role of transporters in plant disease resistance.

Plants being sessile have evolved numerous mechanisms to meet the changing environmental and growth conditions. Plant pathogens are responsible for devastating disease epidemics in many species. Transporter proteins are an integral part of plant growth and development, and several studies have documented their role in pathogen disease resistance. In this review, we analyze the studies on genome-wide identifications of plant transporters like sugars will eventually be exported transporters (SWEET), multidrug and toxic compound extrusion (MATE) transporters, ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (NRAMP), and sugar transport proteins (STPs), all having a significant role in plant disease resistance. The mechanism of action of these transporters, their solute specificity, and the potential application of recent molecular biology approaches deploying these transporters for the development of disease-resistant plants are also discussed. The applications of genome editing tools, such as CRIPSR/Cas9, are also presented. Altogether the information included in this article gives a better understanding of the role of transporter proteins during plant-pathogen interaction.

Functional validation of the Pi54 gene by knocking down its expression in a blast-resistant rice line using RNA interference and its effects on other traits.

Rice blast disease caused by Magnaporthe oryzae is one of the major diseases affecting the rice (Oryza sativa L.) crop. A major blast resistance gene, Pi54, has already been cloned and deployed in different rice varieties. To understand the role of Pi54 in providing rice blast resistance, we used the RNA interferences (RNAi) approach to knock down the expression of this gene. We showed a high frequency of Agrobacterium tumefaciens-mediated transformation of rice line Taipei 309 containing a single gene (Pi54) for blast resistance. Pi54 RNAi leads to a decreased level of Pi54 transcripts, leading to the susceptibility of otherwise M. oryzae-resistant rice lines. However, among the RNAi knockdown plants, the severity of blast disease varied between the lines. Histochemical analysis of the leaves of knockdown plants inoculated with M. oryzae spores also showed typical cell death and blast lesions. Additionally, Pi54 RNAi also showed an effect on the Hda3 gene, a florigen gene playing a role in rice flowering. By using the RNAi technique, for the first time, we showed that the directed degradation of Pi54 transcripts results in a significant reduction in the rice blast resistance response, suggesting that RNAi is a powerful tool for functional validation of genes.