Transgene-Free Genome Editing for Biotic and Abiotic Stress Resistance in Sugarcane: Prospects and Challenges

Overexpression of an NF-YB gene family member, EaNF-YB2, enhances drought tolerance in sugarcane (Saccharum Spp. Hybrid)

BACKGROUND

Drought is one of main critical factors that limits sugarcane productivity and juice quality in tropical regions. The unprecedented changes in climate such as monsoon failure, increase in temperature and other factors warrant the need for development of stress tolerant cultivars to sustain sugar production. Plant Nuclear factor (NF-Y) is one of the major classes of transcription factors that have a major role in plant development and abiotic stress response. In our previous studies, we found that under drought conditions, the nuclear factor NF-YB2 was highly expressed in Erianthus arundinaceus, an abiotic stress tolerant wild genus of Saccharum species. In this study, the coding sequence of NF-YB2 gene was isolated from Erianthus arundinaceus and overexpressed in sugarcane to develop drought tolerant lines. RESULTS : EaNF-YB2 overexpressing sugarcane (OE) lines had higher relative water content, chlorophyll content and photosynthetic efficiency compared to non-transgenic (NT) control. In addition, overexpressing lines had higher activity of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR), and higher proline content, lower malondialdehyde (MDA) and peroxide (H2O2) contents. The expression studies revealed that EaNF-YB2 expression was significantly higher in OE lines than NT control under drought stress. The OE lines had an elevated expression of abiotic stress responsive genes such as BRICK, HSP 70, DREB2, EDH45, and LEA3. The morphological analysis revealed that OE lines exhibited less wilting than NT under drought conditions.

CONCLUSION

This study provides insights into the role of the EaNF-YB2 gene in drought tolerance in sugarcane. Based on the findings of this study, the EaNF-YB2 gene can be potentially exploited to produce drought tolerant sugarcane cultivars to sustain sugarcane production under water deficit conditions.

Ectopic expression of choline oxidase (codA) gene from Arthrobacter globiformis confers drought stress tolerance in transgenic sugarcane

Drought is a serious problem that impacts sugarcane production and productivity worldwide. In this current investigation, a codon-optimized choline oxidase (codA) gene was transformed into Saccharum hybrid cultivar Co 86032 through Agrobacterium-mediated transformation. The transgenic events with the codA gene driven by the portubi882 (PD2) promoter accumulated elevated levels of glycine betaine (5 - 10µg/g) whereas untransformed control plants accumulated less than 1.5µg/g which in turn maintained the plant health by sustaining transpiration rate (4 - 5 µmol of H2O/cm2/s) and photosynthetic efficiency (30 - 34 µmol/Co2/s) whereas the control plants suffered from 50% reduction under water-deficit stress condition. Morpho-anatomic cross-sections of both transgenic events and control plants exhibited significant differences in the epidermal layer and sclerenchyma cells under stress conditions. The relative water content (71 - 76%) and chlorophyll fluorescence (0.60 - 0.72 Fv/Fm) were higher in transgenic events compared to control plants respectively recorded 59% and 0.50 respectively. In addition, significantly elevated activity of antioxidant enzymes viz., superoxide dismutase (95 - 102 U/g), catalase (65 - 73 umol/min/g), ascorbate peroxidase (1700 - 1900 umol/min/mg) and glutathione reductase (17 - 20 umol/min/mg) were observed in transgenic events along with reduced levels of hydrogen peroxide (14 - 16 µmol/g) and malondialdehyde (14 - 17 nmol/g) content. Transgenic events recorded significantly higher arial biomass content compared to untransformed plant after the drought stress. Overall, the increased expression levels of codA gene in sugarcane events resulted in an enhanced ability to withstand water-deficit conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04151-y.

Overexpression of EaALDH7, an aldehyde dehydrogenase gene from Erianthus arundinaceus enhances salinity tolerance in transgenic sugarcane (Saccharum spp. Hybrid)

Aldehyde Dehydrogenases (ALDH), a group of enzymes, are associated with the detoxification of aldehydes, produced in plants during abiotic stress conditions. Salinity remains a pivotal abiotic challenge that poses a significant threat to cultivation and yield of sugarcane. In this study, an Aldehyde dehydrogenase gene (EaALDH7) from Erianthus arundinaceus was overexpressed in the commercial sugarcane hybrid cultivar Co 86032. The transgenic lines were evaluated at different NaCl concentrations ranging from 0 mM to 200 mM for various morpho-physiological and biochemical parameters. The control plants, subjected to salinity stress condition, exhibited morphological changes in protoxylem, metaxylem, pericycle and pith whereas the transgenic events were on par with plants under regular irrigation. The overexpressing (OE) lines showed less cell membrane injury and improved photosynthetic rate, transpiration rate, and stomatal conductance than the untransformed control plants under stress conditions. Elevated proline content, higher activity of enzymatic antioxidants such as sodium dismutase (SOD), catalase (CAT), glutathione reductase (GR) and ascorbate peroxidase (APX) and low level of malondialdehyde MDA and hydrogen peroxide (H2O2) in the transgenic lines. The analysis of EaALDH7 expression revealed a significant upregulation in the transgenic lines compared to that of the untransformed control during salt stress conditions. The current study highlights the potentials of EaALDH7 gene in producing salinity-tolerant sugarcane cultivars.

Recent advances in genome editing strategies for balancing growth and defence in sugarcane (Saccharum officinarum)

Sugarcane (Saccharum officinarum ) has gained more attention worldwide in recent decades because of its importance as a bioenergy resource and in producing table sugar. However, the production capabilities of conventional varieties are being challenged by the changing climates, which struggle to meet the escalating demands of the growing global population. Genome editing has emerged as a pivotal field that offers groundbreaking solutions in agriculture and beyond. It includes inserting, removing or replacing DNA in an organism's genome. Various approaches are employed to enhance crop yields and resilience in harsh climates. These techniques include zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/associated protein (CRISPR/Cas). Among these, CRISPR/Cas is one of the most promising and rapidly advancing fields. With the help of these techniques, several crops like rice (Oryza sativa ), tomato (Solanum lycopersicum ), maize (Zea mays ), barley (Hordeum vulgare ) and sugarcane have been improved to be resistant to viral diseases. This review describes recent advances in genome editing with a particular focus on sugarcane and focuses on the advantages and limitations of these approaches while also considering the regulatory and ethical implications across different countries. It also offers insights into future prospects and the application of these approaches in agriculture.

Leveraging the sugarcane CRISPR/Cas9 technique for genetic improvement of non-cultivated grasses

Under changing climatic scenarios, grassland conservation and development have become imperative to impart functional sustainability to their ecosystem services. These goals could be effectively and efficiently achieved with targeted genetic improvement of native grass species. To the best of our literature search, very scant research findings are available pertaining to gene editing of non-cultivated grass species (switch grass, wild sugarcane, Prairie cordgrass, Bermuda grass, Chinese silver grass, etc.) prevalent in natural and semi-natural grasslands. Thus, to explore this novel research aspect, this study purposes that gene editing techniques employed for improvement of cultivated grasses especially sugarcane might be used for non-cultivated grasses as well. Our hypothesis behind suggesting sugarcane as a model crop for genetic improvement of non-cultivated grasses is the intricacy of gene editing owing to polyploidy and aneuploidy compared to other cultivated grasses (rice, wheat, barley, maize, etc.). Another reason is that genome editing protocols in sugarcane (x = 10-13) have been developed and optimized, taking into consideration the high level of genetic redundancy. Thus, as per our knowledge, this review is the first study that objectively evaluates the concept and functioning of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 technique in sugarcane regarding high versatility, target specificity, efficiency, design simplicity, and multiplexing capacity in order to explore novel research perspectives for gene editing of non-cultivated grasses against biotic and abiotic stresses. Additionally, pronounced challenges confronting sugarcane gene editing have resulted in the development of different variants (Cas9, Cas12a, Cas12b, and SpRY) of the CRISPR tool, whose technicalities have also been critically assessed. Moreover, different limitations of this technique that could emerge during gene editing of non-cultivated grass species have also been highlighted.

Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration

Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.

Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs.