A virus-derived short hairpin RNA confers resistance against sugarcane mosaic virus in transgenic sugarcane

Genetic Engineering for Enhancing Sugarcane Tolerance to Biotic and Abiotic Stresses

Sugarcane, a vital cash crop, contributes significantly to the world's sugar supply and raw materials for biofuel production, playing a significant role in the global sugar industry. However, sustainable productivity is severely hampered by biotic and abiotic stressors. Genetic engineering has been used to transfer useful genes into sugarcane plants to improve desirable traits and has emerged as a basic and applied research method to maintain growth and productivity under different adverse environmental conditions. However, the use of transgenic approaches remains contentious and requires rigorous experimental methods to address biosafety challenges. Clustered regularly interspaced short palindromic repeat (CRISPR) mediated genome editing technology is growing rapidly and may revolutionize sugarcane production. This review aims to explore innovative genetic engineering techniques and their successful application in developing sugarcane cultivars with enhanced resistance to biotic and abiotic stresses to produce superior sugarcane cultivars.

Construction of high-quality genomes and gene catalogue for culturable microbes of sugarcane (Saccharum spp.)

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies.

Factors affecting the production of sugarcane yield and sucrose accumulation: suggested potential biological solutions

Environmental stresses are the main constraints on agricultural productivity and food security worldwide. This issue is worsened by abrupt and severe changes in global climate. The formation of sugarcane yield and the accumulation of sucrose are significantly influenced by biotic and abiotic stresses. Understanding the biochemical, physiological, and environmental phenomena associated with these stresses is essential to increase crop production. This review explores the effect of environmental factors on sucrose content and sugarcane yield and highlights the negative effects of insufficient water supply, temperature fluctuations, insect pests, and diseases. This article also explains the mechanism of reactive oxygen species (ROS), the role of different metabolites under environmental stresses, and highlights the function of environmental stress-related resistance genes in sugarcane. This review further discusses sugarcane crop improvement approaches, with a focus on endophytic mechanism and consortium endophyte application in sugarcane plants. Endophytes are vital in plant defense; they produce bioactive molecules that act as biocontrol agents to enhance plant immune systems and modify environmental responses through interaction with plants. This review provides an overview of internal mechanisms to enhance sugarcane plant growth and environmental resistance and offers new ideas for improving sugarcane plant fitness and crop productivity.

Expression of Chitinase and shRNA Gene Exhibits Resistance to Fungi and Virus

With the increasing global population, saving crops from diseases caused by different kinds of bacteria, fungi, viruses, and nematodes is essential. Potato is affected by various diseases, destroying many crops in the field and storage. In this study, we developed potato lines resistant to fungi and viruses, Potato Virus X (PVX) and Potato Virus Y (PVY), by inoculating chitinase for fungi and shRNA designed against the mRNA of the coat protein of PVX and PVY, respectively. The construct was developed using the pCAMBIA2301 vector and transformed into AGB-R (red skin) potato cultivar using Agrobacterium tumefaciens. The crude protein extract of the transgenic potato plant inhibited the growth of Fusarium oxysporum from ~13 to 63%. The detached leaf assay of the transgenic line (SP-21) showed decreased necrotic spots compared to the non-transgenic control when challenged with Fusarium oxysporum. The transgenic line, SP-21, showed maximum knockdown when challenged with PVX and PVY, i.e., 89 and 86%, while transgenic line SP-148 showed 68 and 70% knockdown in the PVX- and PVY-challenged conditions, respectively. It is concluded from this study that the developed transgenic potato cultivar AGB-R showed resistance against fungi and viruses (PVX and PVY).

Critical points for the design and application of RNA silencing constructs for plant virus resistance

Control of plant virus diseases is a big challenge in agriculture as is resistance in plant lines to infection by viruses. Recent progress using advanced technologies has provided fast and durable alternatives. One of the most promising techniques against plant viruses that is cost-effective and environmentally safe is RNA silencing or RNA interference (RNAi), a technology that could be used alone or along with other control methods. To achieve the goals of fast and durable resistance, the expressed and target RNAs have been examined in many studies, with regard to the variability in silencing efficiency, which is regulated by various factors such as target sequences, target accessibility, RNA secondary structures, sequence variation in matching positions, and other intrinsic characteristics of various small RNAs. Developing a comprehensive and applicable toolbox for the prediction and construction of RNAi helps researchers to achieve the acceptable performance level of silencing elements. Although the attainment of complete prediction of RNAi robustness is not possible, as it also depends on the cellular genetic background and the nature of the target sequences, some important critical points have been discerned. Thus, the efficiency and robustness of RNA silencing against viruses can be improved by considering the various parameters of the target sequence and the construct design. In this review, we provide a comprehensive treatise regarding past, present and future prospective developments toward designing and applying RNAi constructs for resistance to plant viruses.

Genetic engineering: an efficient approach to mitigating biotic and abiotic stresses in sugarcane cultivation

Abiotic stresses are the foremost limiting factors for crop productivity. Crop plants need to cope with adverse external pressure caused by various environmental conditions with their intrinsic biological mechanisms to keep their growth, development, and productivity. Climate-resilient, high-yielding crops need to be developed to maintain sustainable food supply. Over the last decade, understanding of the genetic complexity of agronomic traits in sugarcane has prompted the integrated application of genetic engineering to address specific biological questions. Genes for adaptation to environmental stress and yield enhancement traits are being determined and introgressed to develop elite sugarcane cultivars with improved characteristics through genetic engineering approaches. Here, we discuss the advancement to provide a reference for future sugarcane (Saccharum spp.) genetic engineering.

Sugarcane multitrophic interactions: Integrating belowground and aboveground organisms

Sugarcane is a crop of major importance used mainly for sugar and biofuel production, and many additional applications of its byproducts are being developed. Sugarcane cultivation is plagued by many insect pests and pathogens that reduce sugarcane yields overall. Recently emerging studies have shown complex multitrophic interactions in cultivated areas, such as the induction of sugarcane defense-related proteins by insect herbivory that function against fungal pathogens that commonly appear after mechanical damage. Fungi and viruses infecting sugarcane also modulate insect behavior, for example, by causing changes in volatile compounds responsible for insect attraction or repelling natural vector enemies via a mechanism that increases pathogen dissemination from infected plants to healthy ones. Interestingly, the fungus Fusarium verticillioides is capable of being vertically transmitted to insect offspring, ensuring its persistence in the field. Understanding multitrophic complexes is important to develop better strategies for controlling pathosystems affecting sugarcane and other important crops and highlights the importance of not only studying binary interactions but also adding as many variables as possible to effectively translate laboratory research to real-life conditions.

Foliar Infiltration of Virus-Derived Small Hairpin RNAs Triggers the RNAi Mechanism against the Cucumber Mosaic Virus

Post-transcriptional gene silencing (PTGS) is an evolutionarily conserved plant defense mechanism against viruses. This paper aimed to evaluate a dsDNA construct (77 bp) as a template for in vitro production of virus-derived artificial small hairpin RNAs (shRNAs) and test for their potential to trigger the RNAi mechanism in Nicotiana benthamiana plants against CMV after their foliar infiltration. This approach allowed for the production of significant amounts of shRNAs (60-mers) quickly and easily. The gene silencing was confirmed using polymerase chain reaction (PCR), immunological-based assays, and real-time PCR (qPCR). The highest levels of gene silencing were recorded for mRNAs coding for replication protein (ORF1a), the viral suppressor of RNA silencing (ORF2b), and the capsid protein (ORF3b), with 98, 94, and 70% of total transcript silencing, respectively. This protocol provides an alternative to producing significant shRNAs that can effectively trigger the RNAi mechanism against CMV.

Sugarcane Mosaic Disease: Characteristics, Identification and Control

Mosaic is one of the most important sugarcane diseases, caused by single or compound infection of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and/or Sugarcane streak mosaic virus (SCSMV). The compound infection of mosaic has become increasingly serious in the last few years. The disease directly affects the photosynthesis and growth of sugarcane, leading to a significant decrease in cane yield and sucrose content, and thus serious economic losses. This review covers four aspects of sugarcane mosaic disease management: first, the current situation of sugarcane mosaic disease and its epidemic characteristics; second, the pathogenicity and genetic diversity of the three viruses; third, the identification methods of mosaic and its pathogen species; and fourth, the prevention and control measures for sugarcane mosaic disease and potential future research focus. The review is expected to provide scientific literature and guidance for the effective prevention and control of mosaic through resistance breeding in sugarcane.

Genetic Engineering Approaches for Enhanced Insect Pest Resistance in Sugarcane

Sugarcane (Saccharum officinarum), a sugar crop commonly grown for sugar production all over the world, is susceptible to several insect pests attack in addition to bacterial, fungal and viral infections leading to substantial reductions in its yield. The complex genetic makeup and lack of resistant genes in genome of sugarcane have made the conventional breeding a difficult and challenging task for breeders. Using pesticides for control of the attacking insects can harm beneficial insects, human and other animals and the environment as well. As alternative and effective strategy for control of insect pests, genetic engineering has been applied for overexpression of cry proteins, vegetative insecticidal proteins (vip), lectins and proteinase inhibitors (PI). In addition, the latest biotechnological tools such as host-induced gene silencing (HIGS) and CRISPR/Cas9 can be employed for sustainable control of insect pests in sugarcane. In this review overexpression of the cry, vip, lectins and PI genes in transgenic sugarcane and their disease resistance potential is described.

Induction of resistance to sugarcane mosaic virus by RNA interference targeting coat protein gene silencing in transgenic sugarcane

Sugarcane mosaic virus (SCMV) is a serious disease of monocotyledonous plants, including sugarcane, causing deterioration in both growth and productivity. RNA interference (RNAi) inhibits gene expression through RNA-mediated sequence-specific interactions and is considered an effective approach to control viral infection in plants. In this study, the SCMVCp gene encoding the coat protein (CP) was inserted into the pGreen-0179 plasmid in both sense and antisense orientations. Cauliflower mosaic virus (CaMV) and Zea mays ubiquitin (Ubi) promoters were selected to drive the transcription of the intron-hairpin constructs, called HpSCMVCp-CaMV and HpSCMVCp-Ubi, respectively. Transgenic sugarcane expressing these constructs was generated through Agrobacterium-mediated transformation. This transformation method produced a high percentage of transgenic plants for both HpSCMVCp-CaMV and HpSCMVCp-Ubi, as confirmed by PCR analysis. Southern blotting revealed a single stable insertion of the DNA target in the genome of transgenic sugarcane lines. After artificial virus infection, lines that developed mosaic symptoms were classified as susceptible, whereas those that remained green without symptoms were classified as resistant at 42 days post-inoculation. Immunoblotting revealed CP expression at 37 kDa in susceptible and non-transgenic sugarcane, but not in resistant lines. RT-PCR analysis confirmed viral Cp and Nib gene expression in susceptible lines and their absence in resistant lines. Interestingly, upon comparison of effectivity, CaMV and Ubi promoter-driven gene expression resulted in 57.69% and 82.35% resistant sugarcane lines, respectively. Thus, we concluded that RNAi is effective for inducing resistance against SCMV and that the Ubi promoter is an effective promoter for producing transgenic sugarcane.

Genetic Transformation of Sugarcane, Current Status and Future Prospects

Sugarcane (Saccharum spp.) is a tropical and sub-tropical, vegetative-propagated crop that contributes to approximately 80% of the sugar and 40% of the world's biofuel production. Modern sugarcane cultivars are highly polyploid and aneuploid hybrids with extremely large genomes (>10 Gigabases), that have originated from artificial crosses between the two species, Saccharum officinarum and S. spontaneum. The genetic complexity and low fertility of sugarcane under natural growing conditions make traditional breeding improvement extremely laborious, costly and time-consuming. This, together with its vegetative propagation, which allows for stable transfer and multiplication of transgenes, make sugarcane a good candidate for crop improvement through genetic engineering. Genetic transformation has the potential to improve economically important properties in sugarcane as well as diversify sugarcane beyond traditional applications, such as sucrose production. Traits such as herbicide, disease and insect resistance, improved tolerance to cold, salt and drought and accumulation of sugar and biomass have been some of the areas of interest as far as the application of transgenic sugarcane is concerned. Although there have been much interest in developing transgenic sugarcane there are only three officially approved varieties for commercialization, all of them expressing insect-resistance and recently released in Brazil. Since the early 1990's, different genetic transformation systems have been successfully developed in sugarcane, including electroporation, Agrobacterium tumefaciens and biobalistics. However, genetic transformation of sugarcane is a very laborious process, which relies heavily on intensive and sophisticated tissue culture and plant generation procedures that must be optimized for each new genotype to be transformed. Therefore, it remains a great technical challenge to develop an efficient transformation protocol for any sugarcane variety that has not been previously transformed. Additionally, once a transgenic event is obtained, molecular studies required for a commercial release by regulatory authorities, which include transgene insertion site, number of transgenes and gene expression levels, are all hindered by the genomic complexity and the lack of a complete sequenced reference genome for this crop. The objective of this review is to summarize current techniques and state of the art in sugarcane transformation and provide information on existing and future sugarcane improvement by genetic engineering.

Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential

Sugarcane (Saccharum spp.), a C₄ grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.

Tackling Aging by Using miRNA as a Target and a Tool

miRNA is a class of short noncoding RNA that regulates gene expression at the post-transcriptional level. Evidence of age-associated changes in miRNA expression has been collected in models ranging from nematodes to humans; however, there has been little discussion of how to turn our knowledge of miRNA biology into antiaging therapy. This opinion article provides a snapshot of our current understanding of the roles of miRNA in modulating the aging process. We discuss major chemical techniques for modifying the miRNA structure as well as developing delivery systems for intervention. Finally, technical needs to be met for bench-to-clinic translation of miRNA-based interventions are highlighted for future research.

High-degree and broad-spectrum resistance mediated by a combination of NIb siRNA and miRNA suppresses replication of necrotic and common strains of potato virus Y

In plants, viral replication can be inhibited through gene silencing, which is mediated by short interfering RNA (siRNA) or microRNA (miRNA). However, under natural conditions, viruses are extremely susceptible to mutations that may decrease the efficiency of cleavage of these small RNAs (sRNAs). Therefore, a single sRNA may not provide a sufficient degree of viral resistance to transgenic plants. Potato virus Y necrotic strain (PVYN) and Potato virus Y common strain (PVYO) are the two major PVY strains that cause systemic necrosis and mottling, respectively, in tobacco. In this study, we designed specific siRNAs and miRNAs to target two regions of the PVYO replicase gene (NIb). Eight plant expression vectors containing one or two sRNAs were constructed. Luciferase activity assays showed that the designed sRNAs successfully cleaved the NIb gene of PVYO and PVYN, and the vector carrying a combined siRNA- and miRNA-based short hairpin RNA (shRNA) demonstrated the strongest inhibitory effect. These effects were confirmed through the acquisition of PVYO and PVYN resistance in transgenic sRNA-expressing Nicotiana tabacum plants. This phenomenon could be related to a plant defense mechanism in which siRNA and miRNA pathways are complementary and interact to achieve gene silencing. Furthermore, there is a tendency for the homologous small RNA sequences (PVYO) to be more effective in conferring resistance than those with imperfect homology (PVYN). Overall, these findings confirm that the use of a combined siRNA- and miRNA-based shRNAs is a promising approach for introducing viral resistance to plants through genetic engineering.

Full sequence of the coat protein gene is required for the induction of pathogen-derived resistance against sugarcane mosaic virus in transgenic sugarcane

Sugarcane mosaic virus (SCMV) is a plant pathogenic virus of the family Potyviridae that causes chlorosis, stunting and significantly reduced sugar productivity in sugarcane. Pathogen-derived resistance is a method used to develop SCMV-resistant sugarcane by overexpression of viral DNA. In this study, the gene encoding the coat protein (CP) of SCMV was amplified by reverse transcriptase PCR from symptomatic sugarcane leaves and used to generate transgenic sugarcane. Nucleotide sequence analysis of amplified cDNA indicated that the 998-bp-long cDNA, termed ScMVCp cDNA, codes for the CP of SCMV from the PS881 isolate. The ScMVCp cDNA was inserted into the binary vector pRI101-ON with two constructs, a full nucleotide sequence (p927) and a sequence coding for N-terminally truncated protein (p702). The constructs were then introduced into sugarcane using Agrobacterium-mediated transformation. Southern blot analysis showed a single hybridized DNA copy inserted into the genome of transgenic sugarcane lines. The inserted genes were expressed at both the RNA transcript and protein levels in the transgenic sugarcane. The highest expression was found in transgenic lines 10, 11 and 13 from the p927 construct. Artificial infection by the virus showed that p927 generated a higher resistance to virus compared with p702. This resistance was passed on to the second generation of transgenic sugarcane with 100 and 20-40% levels of resistance in the p927 and p702 transgenic lines, respectively. This report shows that the full sequence of the CP gene is required to disrupt viral assembly and packaging, thereby generating resistance to SCMV infection.