Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

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.

Historical Review of Sugarcane Streak Mosaic Virus that Has Recently Emerged in Africa

Sugarcane streak mosaic virus (SCSMV), now assigned to the genus Poacevirus of the family Potyviridae, was reported for the first time in 1932 in Louisiana and was believed to be strain F of sugarcane mosaic virus (SCMV) for more than six decades. SCMV-F was renamed SCSMV in 1998 after partial sequencing of its genome and phylogenetic investigations. Following the development of specific molecular diagnostic methods in the 2000s, SCSMV was recurrently found in sugarcane exhibiting streak mosaic symptoms in numerous Asian countries but not in the Western hemisphere or in Africa. In this review, we give an overview of the current knowledge on this disease and the progression in research on SCSMV. This includes symptoms, geographical distribution and incidence, diagnosis and genetic diversity of the virus, epidemiology, and control. Finally, we highlight future challenges, as sugarcane streak mosaic has recently been found in Africa, where this disease represents a new threat to sugarcane production.

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.

TCOD: an integrated resource for tropical crops

Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.

Heat and Wheat: Adaptation strategies with respect to heat shock proteins and antioxidant potential; an era of climate change

Extreme changes in weather including heat-wave and high-temperature fluctuations are predicted to increase in intensity and duration due to climate change. Wheat being a major staple crop is under severe threat of heat stress especially during the grain-filling stage. Widespread food insecurity underscores the critical need to comprehend crop responses to forthcoming climatic shifts, pivotal for devising adaptive strategies ensuring sustainable crop productivity. This review addresses insights concerning antioxidant, physiological, molecular impacts, tolerance mechanisms, and nanotechnology-based strategies and how wheat copes with heat stress at the reproductive stage. In this study stress resilience strategies were documented for sustainable grain production under heat stress at reproductive stage. Additionally, the mechanisms of heat resilience including gene expression, nanomaterials that trigger transcription factors, (HSPs) during stress, and physiological and antioxidant traits were explored. The most reliable method to improve plant resilience to heat stress must include nano-biotechnology-based strategies, such as the adoption of nano-fertilizers in climate-smart practices and the use of advanced molecular approaches. Notably, the novel resistance genes through advanced molecular approach and nanomaterials exhibit promise for incorporation into wheat cultivars, conferring resilience against imminent adverse environmental conditions. This review will help scientific communities in thermo-tolerance wheat cultivars and new emerging strategies to mitigate the deleterious impact of heat stress.

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1-8 and 1-10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

Mass Spectrometry-Based Investigation of Sugarcane Exposed to Five Different Pesticides

The use of agrochemicals has become a standard practice worldwide to ensure the productivity and quality of sugarcane crops. This study aimed to analyze the metabolic changes in sugarcane culms treated with five different nematicides. The experimental design was randomized in blocks, and agro-industrial and biometric variables were evaluated. The samples were extracted and then analyzed using LC-MS, LC-MS/MS, and LC-HRMS. The data obtained were submitted to statistical methods (PCA and PLS). Fragmentation patterns, retention time, and UV absorptions of the main features were analyzed. The plantations treated with carbosulfan (T4) obtained higher agricultural productivity and total recoverable sugar (TRS), while the use of benfuracarb (T3) was associated with lower growth and lower TRS. Statistical analysis revealed the contribution of the features at m/z 353 and m/z 515, assigned as chlorogenic acids, which discriminated the groups. The MS profile also supported the occurrence of flavonoids (C-glycosides and O-glycosides) in the samples.

Metabolome profile variations in common bean (Phaseolus vulgaris L.) resistant and susceptible genotypes incited by rust (Uromyces appendiculatus)

The causal agent of rust, Uromyces appendiculatus is a major constraint for common bean (Phaseolus vulgaris) production. This pathogen causes substantial yield losses in many common bean production areas worldwide. U. appendiculatus is widely distributed and although there have been numerous breakthroughs in breeding for resistance, its ability to mutate and evolve still poses a major threat to common bean production. An understanding of plant phytochemical properties can aid in accelerating breeding for rust resistance. In this study, metabolome profiles of two common bean genotypes Teebus-RR-1 (resistant) and Golden Gate Wax (susceptible) were investigated for their response to U. appendiculatus races (1 and 3) at 14- and 21-days post-infection (dpi) using liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-qTOF-MS). Non-targeted data analysis revealed 71 known metabolites that were putatively annotated, and a total of 33 were statistically significant. Key metabolites including flavonoids, terpenoids, alkaloids and lipids were found to be incited by rust infections in both genotypes. Resistant genotype as compared to the susceptible genotype differentially enriched metabolites including aconifine, D-sucrose, galangin, rutarin and others as a defence mechanism against the rust pathogen. The results suggest that timely response to pathogen attack by signalling the production of specific metabolites can be used as a strategy to understand plant defence. This is the first study to illustrate the utilization of metabolomics to understand the interaction of common bean with rust.

Integrated Transcriptome and Metabolome Analysis to Identify Sugarcane Gene Defense against Fall Armyworm (Spodoptera frugiperda) Herbivory

Sugarcane is the most important sugar crop, contributing ≥80% to total sugar production around the world. Spodoptera frugiperda is one of the main pests of sugarcane, potentially causing severe yield and sugar loss. The identification of key defense factors against S. frugiperda herbivory can provide targets for improving sugarcane resistance to insect pests by molecular breeding. In this work, we used one of the main sugarcane pests, S. frugiperda, as the tested insect to attack sugarcane. Integrated transcriptome and metabolomic analyses were performed to explore the changes in gene expression and metabolic processes that occurred in sugarcane leaf after continuous herbivory by S. frugiperda larvae for 72 h. The transcriptome analysis demonstrated that sugarcane pest herbivory enhanced several herbivory-induced responses, including carbohydrate metabolism, secondary metabolites and amino acid metabolism, plant hormone signaling transduction, pathogen responses, and transcription factors. Further metabolome analysis verified the inducement of specific metabolites of amino acids and secondary metabolites by insect herbivory. Finally, association analysis of the transcriptome and metabolome by the Pearson correlation coefficient method brought into focus the target defense genes against insect herbivory in sugarcane. These genes include amidase and lipoxygenase in amino acid metabolism, peroxidase in phenylpropanoid biosynthesis, and pathogenesis-related protein 1 in plant hormone signal transduction. A putative regulatory model was proposed to illustrate the sugarcane defense mechanism against insect attack. This work will accelerate the dissection of the mechanism underlying insect herbivory in sugarcane and provide targets for improving sugarcane variety resistance to insect herbivory by molecular breeding.

A short review on sugarcane: its domestication, molecular manipulations and future perspectives

Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.

Sugarcane Metabolome Compositional Stability in Pretreatment Processes for NMR Measurements

Sugarcane is essential for global sugar production and its compressed juice is a key raw material for industrial products. Sugarcane juice includes various metabolites with abundances and compositional balances influencing product qualities and functionalities. Therefore, understanding the characteristic features of the sugarcane metabolome is important. However, sugarcane compositional variability and stability, even in pretreatment processes for nuclear magnetic resonance (NMR)-based metabolomic studies, remains elusive. The objective of this study is to evaluate sugarcane juice metabolomic variability affected by centrifugation, filtration, and thermal pretreatments, as well as the time-course changes for determining optimal conditions for NMR-based metabolomic approach. The pretreatment processes left the metabolomic compositions unchanged, indicating that these pretreatments are compatible with one another and the studied metabolomes are comparable. The thermal processing provided stability to the metabolome for more than 32 h at room temperature. Based on the determined analytical conditions, we conducted an NMR-based metabolomic study to discriminate the differences in the harvest period and allowed for successfully identifying the characteristic metabolome. Our findings denote that NMR-based sugarcane metabolomics enable us to provide an opportunity to collect a massive amount of data upon collaboration between multiple researchers, resulting in the rapid construction of useful databases for both research purposes and industrial use.

Integrated Analysis of Transcriptome and Metabolome Reveals the Regulation of Chitooligosaccharide on Drought Tolerance in Sugarcane (Saccharum spp. Hybrid) under Drought Stress

Sugarcane (Saccharum spp. hybrid) is an important crop for sugar and biofuels, and often suffers from water shortages during growth. Currently, there is limited knowledge concerning the molecular mechanism involved in sugarcane response to drought stress (DS) and whether chitooligosaccharide could alleviate DS. Here, we carried out a combined transcriptome and metabolome of sugarcane in three different treatment groups: control group (CG), DS group, and DS + chitooligosaccharide group (COS). A total of 12,275 (6404 up-regulated and 5871 down-regulated) differentially expressed genes (DEGs) were identified when comparing the CG and DS transcriptomes (T_CG/DS), and 2525 (1261 up-regulated and 1264 down-regulated) DEGs were identified in comparing the DS and COS transcriptomes (T_DS/COS). GO and KEGG analysis showed that DEGs associated with photosynthesis were significantly enriched and had down-regulated expression. For T_DS/COS, photosynthesis DEGs were also significantly enriched but had up-regulated expression. Together, these results indicate that DS of sugarcane has a significantly negative influence on photosynthesis, and that COS can alleviate these negative effects. In metabolome analysis, lipids, others, amino acids and derivatives and alkaloids were the main significantly different metabolites (SDMs) observed in sugarcane response to DS, and COS treatment reduced the content of these metabolites. KEGG analysis of the metabolome showed that 2-oxocarboxylic acid metabolism, ABC transporters, biosynthesis of amino acids, glucosinolate biosynthesis and valine, leucine and isoleucine biosynthesis were the top-5 KEGG enriched pathways when comparing the CG and DS metabolome (M_CG/DS). Comparing DS with COS (M_DS/COS) showed that purine metabolism and phenylalanine metabolism were enriched. Combined transcriptome and metabolome analysis revealed that pyruvate and phenylalanine metabolism were KEGG-enriched pathways for CG/DS and DS/COS, respectively. For pyruvate metabolism, 87 DEGs (47 up-regulated and 40 down-regulated) and five SDMs (1 up-regulated and 4 down-regulated) were enriched. Pyruvate was closely related with 14 DEGs (|r| > 0.99) after Pearson’s correlation analysis, and only 1 DEG (Sspon.02G0043670-1B) was positively correlated. For phenylalanine metabolism, 13 DEGs (7 up-regulated and 6 down-regulated) and 6 SDMs (1 up-regulated and 5 down-regulated) were identified. Five PAL genes were closely related with 6 SDMs through Pearson’s correlation analysis, and the novel.31257 gene had significantly up-regulated expression. Collectively, our results showed that DS has significant adverse effects on the physiology, transcriptome, and metabolome of sugarcane, particularly genes involved in photosynthesis. We further show that COS treatment can alleviate these negative effects.

Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum

BACKGROUND

Cell polarity establishment and maintenance is indispensable for plant growth and development. In plants, the YABBY transcription factor family has a distinct role in leaf asymmetric polarity establishment and lateral organ initiation. However, for the important sugar crop Saccharum, little information on YABBY genes is available.

RESULTS

In this study, a total of 20 sequences for 7 SsYABBY genes were identified in the sugarcane genome, designated as SsYABBY1-7 based on their chromosome locations, and characterized by phylogenetic analysis. We provided a high-resolution map of SsYABBYs' global expression dynamics during vegetative and reproductive organ morphogenesis and revealed that SsYABBY3/4/5 are predominately expressed at the seedling stage of stem and leaf basal zone; SsYABBY2/5/7 are highly expressed in ovules. Besides, cross-species overexpression and/or complementation verified the conserved function of SsYABBY2 in establishing leaf adaxial-abaxial polarity and ovules development. We found that the SsYABBY2 could successfully rescue the leaves curling, carpel dehiscence, and ovule abortion defects in Arabidopsis crc mutant.

CONCLUSIONS

Collectively, our study demonstrates that SsYABBY genes retained a conserved function in establishing and preserving leaf adaxial-abaxial polarity and lateral organ development during evolution.

Quantitative trait loci mapping of stem sugar content and stem diameter in sorghum recombinant inbred lines using genotyping-by-sequencing

BACKGROUND

Sweet sorghum is an important crop with sugary stem that can mainly be used for syrup, fodder and bio-fuel. Many sugar content QTLs have been discovered from different sources through breeding worldwide. Most of these QTLs are detected using exotic germplasm as a mapping population. This study aimed to detect and map QTLs for stem sugar content and stem diameter targeting Ethiopian recombinant inbred lines of sorghum using genotyping-by-sequencing.

METHODS AND RESULT

Genotyping-by-sequencing and phenotyping using 139 recombinant inbred lines of sorghum as mapping populations were conducted. A total of 1082 polymorphic and high quality SNP markers that are evenly distributed across the ten linkage groups of sorghum were selected to detect and map the trait of interest. A genetic linkage map using 1082 SNP markers was constructed and several QTLs associated with stem sugar content and stem diameter were identified. Phenotypic variation explained by qBrix4-1 and qBrix2-1 ranged from 6.33 to 14%, respectively. Over two seasons, four QTLs for stem sugar content (qBrix1-1, qBrix2-1, qBrix4-1 and qBrix4-2) and three QTLs for stem diameter (qSD1-1, qSD8-1 and qSD9-1) were detected.

CONCLUSION

QTLs that significantly associated with stem sugar content and stem diameter have been detected and mapped. This will help sorghum breeding program to develop superior sweet sorghum varieties through the use of appropriate crop improvement approaches like marker assisted breeding. This ultimately contributes to the current development plan to considerably improve food, feed and bio-fuel supply in developing countries like Ethiopia.

A Sugarcane G-Protein-Coupled Receptor, ShGPCR1, Confers Tolerance to Multiple Abiotic Stresses

Sugarcane (Saccharum spp.) is a prominent source of sugar and serves as bioenergy/biomass feedstock globally. Multiple biotic and abiotic stresses, including drought, salinity, and cold, adversely affect sugarcane yield. G-protein-coupled receptors (GPCRs) are components of G-protein-mediated signaling affecting plant growth, development, and stress responses. Here, we identified a GPCR-like protein (ShGPCR1) from sugarcane and energy cane (Saccharum spp. hybrids) and characterized its function in conferring tolerance to multiple abiotic stresses. ShGPCR1 protein sequence contained nine predicted transmembrane (TM) domains connected by four extracellular and four intracellular loops, which could interact with various ligands and heterotrimeric G proteins in the cells. ShGPCR1 sequence displayed other signature features of a GPCR, such as a putative guanidine triphosphate (GTP)-binding domain, as well as multiple myristoylation and protein phosphorylation sites, presumably important for its biochemical function. Expression of ShGPCR1 was upregulated by drought, salinity, and cold stresses. Subcellular imaging and calcium (Ca²⁺) measurements revealed that ShGPCR1 predominantly localized to the plasma membrane and enhanced intracellular Ca²⁺ levels in response to GTP, respectively. Furthermore, constitutive overexpression of ShGPCR1 in sugarcane conferred tolerance to the three stressors. The stress-tolerance phenotype of the transgenic lines corresponded with activation of multiple drought-, salinity-, and cold-stress marker genes, such as Saccharum spp. LATE EMBRYOGENESIS ABUNDANT, DEHYDRIN, DROUGHT RESPONSIVE 4, GALACTINOL SYNTHASE, ETHYLENE RESPONSIVE FACTOR 3, SALT OVERLY SENSITIVE 1, VACUOLAR Na+/H+ ANTIPORTER 1, NAM/ATAF1/2/CUC2, COLD RESPONSIVE FACTOR 2, and ALCOHOL DEHYDROGENASE 3. We suggest that ShGPCR1 plays a key role in conferring tolerance to multiple abiotic stresses, and the engineered lines may be useful to enhance sugarcane production in marginal environments with fewer resources.

Unveiling sugarcane defense response to Mythimna separata herbivory by a combination of transcriptome and metabolic analyses

BACKGROUND

Sugarcane is the most important sugar crop in the world. Like other crops, sugarcane suffers from herbivorous insect attack. The oriental armyworm Mythimna separata is a devastating pest of various crops in northeast Asia and an outbreak of this pest can result in substantial yield loss for sugarcane. However, the plant defense response situation is widely acquisition in model crops, but there is little information about how sugarcane plants defend themselves against this herbivore at the molecular and biochemical levels.

RESULTS

We combined transcriptome and metabolomic analysis to investigate the changes in gene expression and metabolic processes that occurred in sugarcane plants after continuous feeding by M. separata larvae for 12 and 24 h. We identified 13 662 genes and 55 metabolites that were differentially regulated in sugarcane plants fed on by M. separata. The genes involved in phytohormones, transcription factors, and kinase-related were activated and metabolism compounds such as carbohydrate, amino acid, ferulic substances and glutathione were detected regulated in sugarcane defense response. Comparable analyses showed a close correspondence relationship among pathways of phenylalanine metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis in transcript and metabolite profiles. Furthermore, a bioassay experiment was conducted to test the influence of up-regulated metabolites on M. separata growth and found chlorogenic acid had a lethal effect.

CONCLUSION

The results of our study greatly enhanced the understanding of the sugarcane-induced defense response mechanism against herbivore infestation at the transcriptional and metabolic levels. Also make contributions to provide clues for development of green pest control method. © 2021 Society of Chemical Industry.

Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review

Crop plants often have challenges of biotic and abiotic stresses, and they adapt sophisticated ways to acclimate and cope with these through the expression of specific genes. Changes in chromatin, histone, and DNA mostly serve the purpose of combating challenges and ensuring the survival of plants in stressful environments. Epigenetic changes, due to environmental stress, enable plants to remember a past stress event in order to deal with such challenges in the future. This heritable memory, called "plant stress memory", enables plants to respond against stresses in a better and efficient way, not only for the current plant in prevailing situations but also for future generations. Development of stress resistance in plants for increasing the yield potential and stability has always been a traditional objective of breeders for crop improvement through integrated breeding approaches. The application of epigenetics for improvements in complex traits in tetraploid and some other field crops has been unclear. An improved understanding of epigenetics and stress memory applications will contribute to the development of strategies to incorporate them into breeding for complex agronomic traits. The insight in the application of novel plant breeding techniques (NPBTs) has opened a new plethora of options among plant scientists to develop germplasms for stress tolerance. This review summarizes and discusses plant stress memory at the intergenerational and transgenerational levels, mechanisms involved in stress memory, exploitation of induced and natural epigenetic changes, and genome editing technologies with their future possible applications, in the breeding of crops for abiotic stress tolerance to increase the yield for zero hunger goals achievement on a sustainable basis in the changing climatic era.

Proteomic analysis of young sugarcane plants with contrasting salt tolerance

Soil salinity affects sugarcane (Saccharum officinale L.) production in arid and semiarid climates, severely reducing productivity. This study aimed to identify differentially regulated proteins in two cultivars that differ markedly in tolerance of saline soil. Plants were grown for 30 days and then subjected to treatments of 0 and 160 mM NaCl for 15 days. The tolerant cultivar showed a 3-fold upregulation of lipid metabolising enzymes, GDSL-motif lipases, which are associated with defence to abiotic stress, and which were not upregulated in the sensitive cultivar. Lipoxygenase was 2-fold upregulated in the tolerant cultivar but not in the sensitive cultivar, as were Type III chlorophyll a/b binding proteins. Other differences were that in the sensitive cultivar, the key enzyme of C4 photosynthesis, phosphoenolpyruvate carboxylase was downregulated, along with other chloroplast enzymes. Na+ concentrations had not reached toxic concentrations in either cultivar by this time of exposure to salt, so these changes would be in response to the osmotic effect of the soil salinity, and likely be in common with plants undergoing drought stress.

Transcriptional reprogramming of major defense-signaling pathways during defense priming and sugarcane-Colletotrichum falcatum interaction

Red rot caused by Colletotrichum falcatum poses a serious threat to sugarcane cultivation in many tropical and sub-tropical countries. Deciphering the molecular network of major defense-signaling pathways in sugarcane cultivars with varying red rot resistance is essential to elucidate the phenomenon of defense priming exerted by resistance inducers. Therefore, in this study, expression pattern of transcripts coding for major defense-signaling pathway regulatory genes was profiled during compatible and incompatible interactions and in response to defense priming using qRT-PCR. Candidate genes that were profiled are involved in or related to hypersensitive response and reactive oxygen species production (HR/ROS), salicylic acid (SA), and jasmonic acid/ethylene (JA/ET) pathways. For compatible and incompatible interactions, susceptible (CoC 671), field tolerant (Co 86032) and resistant (Co 93009) sugarcane cultivars were used, whereas for defense priming, benzothiadiazole (BTH) and the pathogen-associated molecular patterns (PAMPs) of C. falcatum viz., CfEPL1 (eliciting plant response-like) and CfPDIP1 (plant defense inducing protein) were used in CoC 671 cultivar. Results indicated that the master regulator of defense pathways, nonexpressor of pathogenesis-related genes 1 (NPR1) was highly upregulated in incompatible interactions (in both Co 86032 and Co 93009) than the compatible interaction along with SA pathway-associated genes. Similarly, in response to defense priming with BTH, CfEPL1 and CfPDIP1, only the SA pathway-associated genes showed considerable upregulation at 0 h post inoculation (hpi) and other intermittent time points. Overall, this study showed that SA-mediated defense pathway is the most predominant pathway reprogrammed during priming with BTH, CfEPL1 and CfPDIP1 and substantiated the earlier findings that these agents indeed induce systemic resistance against red rot of sugarcane.

Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum

RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stress-resistance genes in modern sugarcane cultivars (Saccharum spp.) were originated from wild species of Saccharum, for example S. spontaneum. Here, we used genome-wide analysis and a phylogenetic approach to identify four DCL, 21 AGO and 11 RDR genes in the S. spontaneum genome (termed SsDCL, SsAGO and SsRDR, respectively). Several genes, particularly some of the SsAGOs, appeared to have undergone tandem or segmental duplications events. RNA-sequencing data revealed that four SsAGO genes (SsAGO18c, SsAGO18b, SsAGO10e and SsAGO6b) and three SsRDR genes (SsRDR2b, SsRDR2d and SsRDR3) tended to have preferential expression in stem tissue, while SsRDR5 was preferentially expressed in leaves. qRT-PCR analysis showed that SsAGO10c, SsDCL2 and SsRDR6b expressions were strongly upregulated, whereas that of SsAGO18b, SsRDR1a, SsRDR2b/2d and SsRDR5 was significantly depressed in S. spontaneum plants exposed to PEG-induced dehydration stress or infected with Xanthomonas albilineans, causal agent of leaf scald disease of sugarcane, suggesting that these genes play important roles in responses of S. spontaneum to biotic and abiotic stresses.

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Adventitious root (AR) formation was enhanced following the treatment of sugarcane microshoots with indole-3-butyric acid (IBA) and 1-naphthalene acetic acid (NAA) combined, suggesting that auxin is a positive regulator of sugarcane microshoot AR formation. The transcriptome profile identified 1737 and 1268 differentially expressed genes (DEGs) in the basal tissues (5 mm) of sugarcane microshoots treated with IBA+NAA compared to nontreated control on the 3rd and 7th days post-auxin or water treatment (days post-treatment—dpt), respectively. To understand the molecular changes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. This analysis showed that DEGs associated with the pathways were associated with plant hormone signaling, flavonoid and phenylpropanoid biosyntheses, cell cycle, and cell wall modification, and transcription factors could be involved in sugarcane microshoot AR formation. Furthermore, qRT–PCR analysis was used to validate the expression patterns of nine genes associated with root formation and growth, and the results were consistent with the RNA-seq results. Finally, a hypothetical hormonal regulatory working model of sugarcane microshoot AR formation is proposed. Our results provide valuable insights into the molecular processes associated with auxin-induced AR formation in sugarcane.

Shaping Durum Wheat for the Future: Gene Expression Analyses and Metabolites Profiling Support the Contribution of BCAT Genes to Drought Stress Response

Global climate change, its implications for agriculture, and the complex scenario presented by the scientific community are of worldwide concern. Drought is a major abiotic stress that can restrict plants growth and yields, thus the identification of genotypes with higher adaptability to drought stress represents one of the primary goals in breeding programs. During abiotic stress, metabolic adaptation is crucial for stress tolerance, and accumulation of specific amino acids and/or as secondary metabolites deriving from amino acid metabolism may correlate with the increased tolerance to adverse environmental conditions. This work, focused on the metabolism of branched chain-amino acids (BCAAs) in durum wheat and the role of branched-chain amino acid aminotransferases (BCATs) in stress response. The role of BCATs in plant response to drought was previously proposed for Arabidopsis, where the levels of BCAAs were altered at the transcriptional level under drought conditions, triggering the onset of defense response metabolism. However, in wheat the role of BCAAs as a trigger of the onset of the drought defense response has not been elucidated. A comparative genomic approach elucidated the composition of the BCAT gene family in durum wheat. Here we demonstrate a tissue and developmental stage specificity of BCATs regulation in the drought response. Moreover, a metabolites profiling was performed on two contrasting durum wheat cultivars Colosseo and Cappelli resulting in the detection of a specific pattern of metabolites accumulated among genotypes and, in particular, in an enhanced BCAAs accumulation in the tolerant cv Cappelli further supporting a role of BCAAs in the drought defense response. The results support the use of gene expression and target metabolomic in modern breeding to shape new cultivars more resilient to a changing climate.

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.

Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.