The early transcriptome response of cassava (Manihot esculenta Crantz) to mealybug (Phenacoccus manihoti) feeding

Comparative analysis of salicylic acid levels and gene expression in resistant, tolerant, and susceptible cassava varieties following whitefly-mediated SLCMV infection

Sri Lankan cassava mosaic virus (SLCMV), the primary pathogen responsible for cassava mosaic disease in cassava plantations, is transmitted via infected cutting stems and the whitefly vector, Bemisia tabaci. To obtain better insights into the defense mechanism of cassava against SLCMV, whiteflies were used to induce SLCMV infection for activating the salicylic acid (SA) signaling pathway, which triggers the innate immune system. The study aimed to investigate the specific interactions between viruliferous whiteflies and SA accumulation in resistant (C33), tolerant (Kasetsart 50; KU50), and susceptible (Rayong 11) cassava cultivars by infecting with SLCMV. Leaf samples were collected at various time points, from 1 to 7 days after inoculation (dai). The SA levels were quantified by gas chromatography-mass spectrometry and validated by quantitative reverse transcription polymerase chain reaction. The SA levels increased in KU50 and C33 plants at 2 and 3 dai, respectively, but remained undetected in Rayong11 plants. The expression of PR-9e, PR-7f5, SPS1, SYP121, Hsf8, and HSP90 increased in infected C33 plants at 4 dai, whereas that of KU50 plants decreased immediately at 2 dai, and that of Rayong11 plants increased at 1 dai but gradually decreased thereafter. These findings strongly indicate that SA plays a crucial role in regulating antiviral defense mechanisms, especially in SLCMV-resistant plants. Altogether, the findings provide valuable insights into the mechanisms underlying the activation of SA-mediated anti-SLCMV defense pathways, and the resistance, tolerance, and susceptibility of cassava, which can aid future breeding programs aimed at enhancing SLCMV resistance.

Exogenous methyl jasmonate induced cassava defense response and enhanced resistance to Tetranychus urticae

Exogenous application of methyl jasmonate (MeJA) could activate plant defense response against the two-spotted spider mite (TSSM), Tetranychus urticae Koch, in different plants. However, whether MeJA can also serve as an elicitor in cassava (Manihot esculenta Crantz) remains unknown. In this study, induced defense responses were investigated in TSSM-resistant cassava variety C1115 and TSSM-susceptible cassava variety KU50 when applied with MeJA. The performance of TSSM feeding on cassava plants that were pre-treated with various concentrations of MeJA was first evaluated. Subsequently, the activities of antioxidative enzymes (superoxide dismutase and catalase), detoxification enzymes (glutathione S-transferase, cytochrome P450 and carboxylesterase) and digestive enzymes (protease, amylase and invertase) in TSSM were analyzed at days 1, 2, 4 and 8 post-feeding. The results showed that MeJA treatment can induce cassava defense responses to TSSM in terms of reducing egg production and adult longevity as well as slowing development and prolonging the egg stage. Noticeably, C1115 exhibited stronger inhibition of TSSM development and reproduction than KU50. In addition, the activities of all the tested enzymes were induced in both C1115 and KU50, the most in C1115. We conclude that exogenous methyl jasmonate can induce cassava defense responses and enhance resistance to TSSM.

Current status and impending progress for cassava structural genomics

We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

The Roles of Cassava in Marginal Semi-Arid Farming in East Nusa Tenggara—Indonesia

Risk and uncertainty in grain crop production are common in marginal semi-arid environments, such as East Nusa Tenggara province. Growing root and tuber crops in a mixed-cropping system is one of the strategies developed by smallholder farmers to substitute food grains and minimize risk. Nevertheless, root and tuber crops are not prioritized for food production systems since food crops in Indonesia are based more on grain and wetland rice production systems. This paper reviews cassava crops, which are widely cultivated by smallholder farmers. This paper contributes to understanding the roles of cassava for smallholder farmers, the diversity of the cassava germ plasm, the progress made to increase cassava productivity, and the potency of cassava crops to improve farmers’ incomes. This paper highlights that, in the low and erratic rainfall of dominant semi-arid regions, the development of cassava is pivotal to secure the harvest of food crops or food availability and income generation for marginal farmers.

Cyanogenesis in cassava and its molecular manipulation for crop improvement

While cassava is one of the most important staple crops worldwide, it has received the least investment per capita consumption of any of the major global crops. This is in part due to cassava being a crop of subsistence farmers that is grown in countries with limited resources for crop improvement. While its starchy roots are rich in calories, they are poor in protein and other essential nutrients. In addition, they contain potentially toxic levels of cyanogenic glycosides which must be reduced to safe levels before consumption. Furthermore, cyanogens compromise the shelf life of harvested roots due to cyanide-induced inhibition of mitochondrial respiration, and associated production of reactive oxygen species that accelerate root deterioration. Over the past two decades, the genetic, biochemical, and developmental factors that control cyanogen synthesis, transport, storage, and turnover have largely been elucidated. It is now apparent that cyanogens contribute substantially to whole-plant nitrogen metabolism and protein synthesis in roots. The essential role of cyanogens in root nitrogen metabolism, however, has confounded efforts to create acyanogenic varieties. This review proposes alternative molecular approaches that integrate accelerated cyanogen turnover with nitrogen reassimilation into root protein that may offer a solution to creating a safer, more nutritious cassava crop.

The future of cassava in the era of biotechnology in Southern Africa

Cassava (Manihot esculenta) is a major staple food and the world's fourth source of calories. Biotechnological contributions to enhancing this crop, its advances, and present issues must be assessed regularly. Functional genomics, genomic-assisted breeding, molecular tools, and genome editing technologies, among other biotechnological approaches, have helped improve the potential of economically important crops like cassava by addressing some of its significant constraints, such as nutrient deficiency, toxicity, poor starch quality, disease susceptibility, low yield capacity, and postharvest deterioration. However, the development, improvement, and subsequent acceptance of the improved cultivars have been challenging and have required holistic approaches to solving them. This article provides an update of trends and gaps in cassava biotechnology, reviewing the relevant strategies used to improve cassava crops and highlighting the potential risk and acceptability of improved cultivars in Southern Africa.

Expression profiling of pathogenesis-related Protein-1 (PR-1) genes from Solanum tuberosum reveals its critical role in phytophthora infestans infection

Pathogen-related (PR) proteins are an integral part of plants' defense mechanisms against various types of biotic and abiotic stresses. A little is known about the importance of these PR proteins in potato defense mechanisms. In the current study, a total of 22 pathogenesis-related 1 genes were identified in the potato genome. All identified proteins possessed the CAP superfamily domain with some other motifs. The cis-acting elements analysis identified several stress-responsive elements, including MYB, ABRE, and MeJRE. The gene duplication events demonstrated purifying and positive selection pressure. Expression profiling showed high transcripts level in root compared to other tissues; however, some genes have tissue-specific expression. Furthermore, the PR-1-5 gene is transcriptionally induced under Phytophthora infestans stress and hormonal (ABA and IAA) treatments. The Real-Time qPCR analysis also validated the RNA-seq data results of genes with maximum expression in roots compared to leaves and stems. The current study results provided basic data for functional characterization and can also use as a reference study for other important crops.

Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding

Herbivorous insects use plant volatile compounds to find their host plants for feeding and egg deposition. The monophagous beetle Agasicles hygrophila uses a volatile (E)-4,8-dimethyl-1,3,7-nonanetriene (DMNT) to recognize its host plant Alternanthera philoxeroides. Alternanthera philoxeroides releases DMNT in response to A. hygrophila attack and nerolidol synthase (NES) is a key enzyme in DMNT biosynthesis; however, the effect of A. hygrophila on NES expression remains unclear. In this study, the A. philoxeroides transcriptome was sequenced and six putative NES genes belonging to the terpene synthase-g family were characterized. The expression of these NES genes was assayed at different times following A. hygrophila contact, feeding or mechanical wounding. Results showed that A. hygrophila contact and feeding induced NES expression more rapidly and more intensely than mechanical wounding alone. This may account for a large release of DMNT following A. hygrophila feeding in a previous study and subsequently facilitate A. hygrophila to find host plants. Our research provides a powerful genetic platform for studying invasive plants and lays the foundation for further elucidating the molecular mechanisms of the interaction between A. philoxeroides and its specialist A. hygrophila.

Ento(o)mics: the intersection of 'omic' approaches to decipher plant defense against sap-sucking insect pests

Plants are constantly challenged by insect pests that can dramatically decrease yields. Insects with piercing-sucking mouthparts, for example, aphids, whiteflies, and leaf hoppers, seemingly cause less physical damage to tissues, however, they feed on the plant's sap by piercing plant tissue and extracting plant fluids, thereby transmitting several plant-pathogenic viruses as well. As a counter-defense, plants activate an array of dynamic defense machineries against insect pests including the rapid reprogramming of the host cell processes. For a holistic understanding of plant-sap-sucking insect interactions, there is a need to call for techniques with the capacity to concomitantly capture these dynamic changes. Recent progress with various 'omic' technologies possess this capacity. In this review, we will provide a concise summary of application of 'omic' technologies and their utilization in plant and sap-sucking insect interaction studies. Finally, we will provide a perspective on the integration of 'omics' data in uncovering novel plant defense mechanisms against sap-sucking insect pests.

Enhancing of anthracnose disease resistance indicates a potential role of antimicrobial peptide genes in cassava

Cassava (Manihot esculenta Crantz.) is an important economic crop in tropical countries. Demands for using cassava in food, feed and biofuel industries have been increasing worldwide. Cassava anthracnose disease, caused by Colletotrichum gloeosporioides f.sp. manihotis (CAD), is considered a major problem in cassava production. To minimize the effects of such disease, this study investigated the response of cassava to attack by CAD and how the plants defend themselves against this threat. Genome-wide identification of antimicrobial peptide genes (AMPs) and their expression in response to fungal infection was performed in the resistant cassava cultivar (Huay Bong 60; HB60) in comparison with the highly susceptible cultivar (Hanatee; HN). A total of 114 gene members of AMP were identified in the cassava genome database. Fifty-six gene members were selected for phylogenetic tree construction and analysis of putative cis-acting elements in their promoter regions. Differential expression profiles of six candidate genes were observed in response to CAD infection of both cassava cultivars. Upregulation of snakins, MeSN1 and MeSN2 was found in HB60, whereas MeHEL, Me-AMP-D2 and MeLTP2 were highly induced in HN. The MeLTP1 gene was not expressed in either cultivar. HB60 showed a reduced severity rating in comparison to HN after CAD infection. The biomembrane permeability test of fungal CAD was strongly affected after treatment with protein extract derived from CAD-infected HB60. Altogether, these findings suggest that snakins have a potential function in the CAD defense response in cassava. These results could be useful for cassava improvement programs to fight fungal pathogen.

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

Background

Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors.

Results

The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families.

Conclusions

This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.

Differential expression of the Hsf family in cassava under biotic and abiotic stresses

Heat shock transcription factors (Hsfs) are important regulators of biotic and abiotic stress responses in plants. Currently, the Hsf gene family is not well understood in cassava, an important tropical crop. In the present study, 32 MeHsf genes were identified from the cassava genome database, which were divided into three types based on functional domain and motif distribution analyses. Analysis of the differential expression of the genes belonging to the Hsf family in cassava was carried out based on published cassava transcriptome data from tissues/organs (leaf blade, leaf midvein, lateral buds, organized embryogenic structures, friable embryogenic callus, fibrous roots, storage roots, stem, petiole, shoot apical meristem, and root apical meristem) under abiotic stress (cold, drought) or biotic stress (mealybugs. cassava brown streak disease, cassava bacterial blight). The results show the expression diversity of cassava Hsfs genes in various tissues/organs. The transcript levels of MeHsfB3a, MeHsfA6a, MeHsfA2a, and MeHsfA9b were upregulated by abiotic and biotic stresses, such as cold, drought, cassava bacterial blight, cassava brown streak disease, and mealybugs, indicating their potential roles in mediating the response of cassava plants to environment stresses. Further interaction network and co-expression analyses suggests that Hsf genes may interact with Hsp70 family members to resist environmental stresses in cassava. These results provide valuable information for future studies of the functional characterization of the MeHsf gene family.

Transcriptomic and proteomic response of Manihot esculenta to Tetranychus urticae infestation at different densities

Tetranychus urticae (Acari: Tetranychidae) is an extremely serious cassava (Manihot esculenta) pest. Building a genomic resource to investigate the molecular mechanisms of cassava responses to T. urticae is vital for characterizing cassava resistance to mites. Based on the tolerance of cassava varieties to mite infestation (focusing on mite development rate, fecundity and physiology), cassava variety SC8 was selected to analyze transcriptomic and proteomic changes after 5 days of T. urticae feeding. Transcriptomic analysis revealed 698 and 2140 genes with significant expression changes under low and high mite infestation, respectively. More defense-related genes were found in the enrichment pathways at high mite density than at low density. In addition, iTRAQ-labeled proteomic analysis revealed 191 proteins with significant expression changes under low mite infestation. Differentially expressed genes and proteins were mainly found in the following defense-related pathways: flavonoid biosynthesis, phenylpropanoid biosynthesis, and glutathione metabolism under low-density mite feeding and plant hormone signal transduction and plant-pathogen interaction pathways under high-density mite feeding. The plant hormone signal transduction network, involving ethylene, jasmonic acid, and salicylic acid transduction pathways, was explored in relation to the M. esculenta response to T. urticae. Correlation analysis of the transcriptome and proteome generated a Pearson correlation coefficients of R = 0.2953 (P < 0.01), which might have been due to post-transcriptional or post-translational regulation resulting in many genes being inconsistently expressed at both the transcript and protein levels. In summary, the M. esculenta transcriptome and proteome changed in response to T. urticae, providing insight into the general activation of plant defense pathways in response to mite infestation.