Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta)

Genetic engineering and genome editing technologies as catalyst for Africa's food security: the case of plant biotechnology in Nigeria

Many African countries are unable to meet the food demands of their growing population and the situation is worsened by climate change and disease outbreaks. This issue of food insecurity may lead to a crisis of epic proportion if effective measures are not in place to make more food available. Thus, deploying biotechnology towards the improvement of existing crop varieties for tolerance or resistance to both biotic and abiotic stresses is crucial to increasing crop production. In order to optimize crop production, several African countries have implemented strategies to make the most of this innovative technology. For example, Nigerian government has implemented the National Biotechnology Policy to facilitate capacity building, research, bioresource development and commercialization of biotechnology products for over two decades. Several government ministries, research centers, universities, and agencies have worked together to implement the policy, resulting in the release of some genetically modified crops to farmers for cultivation and Commercialization, which is a significant accomplishment. However, the transgenic crops were only brought to Nigeria for confined field trials; the manufacturing of the transgenic crops took place outside the country. This may have contributed to the suspicion of pressure groups and embolden proponents of biotechnology as an alien technology. Likewise, this may also be the underlying issue preventing the adoption of biotechnology products in other African countries. It is therefore necessary that African universities develop capacity in various aspects of biotechnology, to continuously train indigenous scientists who can generate innovative ideas tailored towards solving problems that are peculiar to respective country. Therefore, this study intends to establish the role of genetic engineering and genome editing towards the achievement of food security in Africa while using Nigeria as a case study. In our opinion, biotechnology approaches will not only complement conventional breeding methods in the pursuit of crop improvements, but it remains a viable and sustainable means of tackling specific issues hindering optimal crop production. Furthermore, we suggest that financial institutions should offer low-interest loans to new businesses. In order to promote the growth of biotechnology products, especially through the creation of jobs and revenues through molecular farming.

CPK1-HSP90 phosphorylation and effector XopC2-HSP90 interaction underpin the antagonism during cassava defense-pathogen infection

Cassava is one of the most important tropical crops, but it is seriously affected by cassava bacteria blight (CBB) caused by the bacterial pathogen Xanthomonas phaseoli pv manihotis (Xam). So far, how pathogen Xam infects and how host cassava defends during pathogen-host interaction remains elusive, restricting the prevention and control of CBB. Here, the illustration of HEAT SHOCK PROTEIN 90 kDa (MeHSP90.9) interacting proteins in both cassava and bacterial pathogen revealed the dual roles of MeHSP90.9 in cassava-Xam interaction. On the one hand, calmodulin-domain protein kinase 1 (MeCPK1) directly interacted with MeHSP90.9 to promote its protein phosphorylation at serine 175 residue. The protein phosphorylation of MeHSP90.9 improved the transcriptional activation of MeHSP90.9 clients (SHI-RELATED SEQUENCE 1 (MeSRS1) and MeWRKY20) to the downstream target genes (avrPphB Susceptible 3 (MePBS3) and N-aceylserotonin O-methyltransferase 2 (MeASMT2)) and immune responses. On the other hand, Xanthomonas outer protein C2 (XopC2) physically associated with MeHSP90.9 to inhibit its interaction with MeCPK1 and the corresponding protein phosphorylation by MeCPK1, so as to repress host immune responses and promote bacterial pathogen infection. In summary, these results provide new insights into genetic improvement of cassava disease resistance and extend our understanding of cassava-bacterial pathogen interaction.

Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance

Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.

Phenotypic Variability in Resistance to Anthracnose, White, Brown, and Blight Leaf Spot in Cassava Germplasm

Despite fungal diseases affecting the aerial parts of cassava (Manihot esculenta Crantz) and causing significant yield losses, there is a lack of comprehensive studies assessing resistance in the species' germplasm. This study aimed to evaluate the phenotypic diversity for resistance to anthracnose disease (CAD), blight leaf spot (BliLS), brown leaf spot (BLS), and white leaf spot (WLS) in cassava germplasm and to identify genotypes suitable for breeding purposes. A total of 837 genotypes were evaluated under field conditions across two production cycles (2021 and 2022). Artificial inoculations were carried out in the field, and data on yield and disease severity were collected using a standardized rating scale. The top 25 cassava genotypes were selected based on a selection index for disease resistance and agronomic traits. High environmental variability resulted in low heritabilities (h2) for CAD, WLS, and BLS (h2 = 0.42, 0.34, 0.29, respectively) and moderate heritability for BliLS (h2 = 0.51). While the range of data for disease resistance was narrow, it was considerably wider for yield traits. Cluster analysis revealed that increased yield traits and disease severity were associated with higher scores of the first and second discriminant functions, respectively. Thus, most clusters comprised genotypes with hybrid characteristics for both traits. Overall, there was a strong correlation among aerial diseases, particularly between BLS and BliLS (r = 0.96), while the correlation between CAD and other diseases ranged from r = 0.53 to 0.58. Yield traits showed no significant correlations with disease resistance. Although the mean selection differential for disease resistance was modest (between -2.31% and -3.61%), selection based on yield traits showed promising results, particularly for fresh root yield (82%), dry root yield (39%), shoot yield (49%), and plant vigor (26%). This study contributes to enhancing genetic gains for resistance to major aerial part diseases and improving yield traits in cassava breeding programs.

Cucumis sativus CsbZIP90 suppresses Podosphaera xanthii resistance by modulating reactive oxygen species

Resistance to disease in plants requires the coordinated action of multiple functionally related genes, as it is difficult to improve disease resistance with a single functional gene. Therefore, the use of transcription factors to regulate the expression of multiple resistance genes to improve disease resistance has become a recent focus in the field of gene research. The basic leucine zipper (bZIP) transcription factor family plays vital regulatory roles in processes, such as plant growth and development and the stress response. In our previous study, CsbZIP90 (Cucsa.134370) was involved in the defense response of cucumber to Podosphaera xanthii, but the relationship between cucumber and resistance to powdery mildew remained unclear. Herein, we detected the function of CsbZIP90 in response to P. xanthii. CsbZIP90 was localized to the cytoplasm and nucleus, and its expression was significantly induced during P. xanthii attack. Transient overexpression of CsbZIP90 in cucumber cotyledons resulted in decreased resistance to P. xanthii, while silencing CsbZIP90 increased resistance to P. xanthii. CsbZIP90 negatively regulated the expression of reactive oxygen species (ROS)-related genes and activities of ROS-related kinases. Taken together, our results show that CsbZIP90 suppresses P. xanthi resistance by modulating ROS. This study will provide target genes for breeding cucumbers resistant to P. xanthii.

LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava

Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.

The self-association of cytoplasmic malate dehydrogenase 1 promotes malate biosynthesis and confers disease resistance in cassava

Malate dehydrogenase (MDH) as an essential metabolic enzyme is widely involved in plant developmental processes. However, the direct relationship between its structural basis and in vivo roles especially in plant immunity remains elusive. In this study, we found that cytoplasmic cassava (Manihot esculenta, Me) MDH1 was essential for plant disease resistance against cassava bacterial blight (CBB). Further investigation revealed that MeMDH1 positively modulated cassava disease resistance, accompanying the regulation of salicylic acid (SA) accumulation and pathogensis-related protein 1 (MePR1) expression. Notably, the metabolic product of MeMDH1 (malate) also improved disease resistance in cassava, and its application rescued the disease susceptibility and decreased immune responses of MeMDH1-silenced plants, indicating that malate was responsible for MeMDH1-mediated disease resistance. Interestingly, MeMDH1 relied on Cys330 residues to form homodimer, which was directly related with MeMDH1 enzyme activity and the corresponding malate biosynthesis. The crucial role of Cys330 residue in MeMDH1 was further confirmed by in vivo functional comparison between overexpression of MeMDH1 and MeMDH1C330A in cassava disease resistance. Taken together, this study highlights that MeMDH1 confers improved plant disease resistance through protein self-association to promote malate biosynthesis, extending the knowledge of the relationship between its structure and cassava disease resistance.

Histone deacetylase 9 regulates disease resistance through fine-tuning histone deacetylation of melatonin biosynthetic genes and melatonin accumulation in cassava

Melatonin participates in plant growth and development and biotic and abiotic stress responses. Histone acetylation regulates many plant biological processes via transcriptional reprogramming. However, the direct relationship between melatonin and histone acetylation in plant disease resistance remains unclear. In this study, we identified cassava bacterial blight (CBB) responsive histone deacetylase 9 (HDA9), which negatively regulated disease resistance to CBB by reducing melatonin content. In addition, exogenous melatonin alleviated disease sensitivity of MeHDA9 overexpressed plants to CBB. Importantly, MeHDA9 inhibited the expression of melatonin biosynthetic genes through decreasing lysine 5 of histone 4 (H4K5) acetylation at the promoter regions of melatonin biosynthetic genes, thereby modulating melatonin accumulation in cassava. Furthermore, protein phosphatase 2C 12 (MePP2C12) interacted with MeHDA9 in vivo and in vitro, and it was involved in MeHDA9-mediated disease resistance via melatonin biosynthetic pathway. In summary, this study highlights the direct interaction between histone deacetylation and melatonin biosynthetic genes in cassava disease resistance via histone deacetylation, providing new insights into the genetic improvement of disease resistance via epigenetic regulation of melatonin level in tropical crops.

Histone acetyltransferase HAM1 interacts with molecular chaperone DNAJA2 and confers immune responses through salicylic acid biosynthetic genes in cassava

Cassava bacterial blight (CBB) is one of the most serious diseases in cassava production, so it is essential to explore the underlying mechanism of immune responses. Histone acetylation is an important epigenetic modification, however, its relationship with cassava disease resistance remains unclear. Here, we identified 10 histone acetyltransferases in cassava and found that the transcript of MeHAM1 showed the highest induction to CBB. Functional analysis showed that MeHAM1 positively regulated disease resistance to CBB through modulation of salicylic acid (SA) accumulation. Further investigation revealed that MeHAM1 directly activated SA biosynthetic genes' expression via promoting lysine 9 of histone 3 (H3K9) acetylation and lysine 5 of histone 4 (H4K5) acetylation of these genes. In addition, molecular chaperone MeDNAJA2 physically interacted with MeHAM1, and MeDNAJA2 also regulated plant immune responses and SA biosynthetic genes. In conclusion, this study illustrates that MeHAM1 and MeDNAJA2 confer immune responses through transcriptional programming of SA biosynthetic genes via histone acetylation. The MeHAM1 & MeDNAJA2-SA biosynthesis module not only constructs the direct relationship between histone acetylation and cassava disease resistance, but also provides gene network with potential value for genetic improvement of cassava disease resistance.

Cassava (Manihot esculenta Crantz): A Systematic Review for the Pharmacological Activities, Traditional Uses, Nutritional Values, and Phytochemistry

Cassava (Manihot esculenta Crantz) is considered one of the essential tuber crops, serving as a dietary staple food for various populations. This systematic review provides a comprehensive summary of the nutritional and therapeutic properties of cassava, which is an important dietary staple and traditional medicine. The review aims to evaluate and summarize the phytochemical components of cassava and their association with pharmacological activities, traditional uses, and nutritional importance in global food crises. To collect all relevant information, electronic databases; Cochrane Library, PubMed, Scopus, Web of Science, Google Scholar, and Preprint Platforms were searched for studies on cassava from inception until October 2022. A total of 1582 studies were screened, while only 34 were included in this review. The results of the review indicate that cassava has diverse pharmacological activities, including anti-bacterial, anti-cancer, anti-diabetic, anti-diarrheal, anti-inflammatory, hypocholesterolemic effects, and wound healing properties. However, more studies that aim to isolate the phytochemicals in cassava extracts and evaluate their pharmacological property are necessary to further validate their medical and nutritional values.

Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

BACKGROUND

Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem.

RESULTS

We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common.

CONCLUSIONS

Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.

Cassava Frogskin Disease: Current Knowledge on a Re-Emerging Disease in the Americas

Cassava frogskin disease (CFSD) is a graft-transmissible disease of cassava reported for the first time in the 1970s, in Colombia. The disease is characterized by the formation of longitudinal lip-like fissures on the peel of the cassava storage roots and a progressive reduction in fresh weight and starch content. Since its first report, different pathogens have been identified in CFSD-affected plants and improved sequencing technologies have unraveled complex mixed infections building up in plants with severe root symptoms. The re-emergence of the disease in Colombia during 2019–2020 is again threatening the food security of low-income farmers and the growing local cassava starch industry. Here, we review some results obtained over several years of CFSD pathology research at CIAT, and provide insights on the biology of the disease coming from works on symptoms’ characterization, associated pathogens, means of transmission, carbohydrate accumulation, and management. We expect this work will contribute to a better understanding of the disease, which will reflect on lowering its impact in the Americas and minimize the risk of its spread elsewhere.

Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses

Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles within MePOLD1. Genetic variation of MePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.

Genome-wide association study and selection for field resistance to cassava root rot disease and productive traits

Cassava root rot disease is caused by a complex of soil-borne pathogens and has high economic impacts because it directly affects the tuberous roots, which are the main commercial product. This study aimed to evaluate cassava genotypes for resistance to root rot disease in a field with a previous history of high disease incidence. It also aimed to identify possible genomic regions associated with field resistance based on genome-wide association studies. A total of 148 genotypes from Embrapa Mandioca and Fruticultura were evaluated over two years, including improved materials and curated germplasms. Analysis of phenotypic data was conducted, as well as a genomic association analysis, based on the general linear model, mixed linear model, and fixed and random model circulating probability unification. The observed high disease index (ω) was directly correlated with genotype survival, affecting plant height, shoot yield, and fresh root yield. The genotypes were grouped into five clusters, which were classified according to level of root rot resistance (i.e., extremely susceptible, susceptible, moderately susceptible, moderately resistant, and resistant). The 10 genotypes with the best performance in the field were selected as potential progenitors for the development of segregating progenies. Estimates of genomic kinship between these genotypes ranged from -0.183 to 0.671. The genotypes BGM-1171 and BGM-1190 showed the lowest degree of kinship with the other selected sources of resistance. The genotypes BGM-0209, BGM-0398, and BGM-0659 showed negative kinship values with most elite varieties, while BGM-0659 presented negative kinship with all landraces. A genome-wide association analysis detected five significant single nucleotide polymorphisms related to defense mechanisms against biotic and abiotic stresses, with putative association with fresh root yield in soil infested with root rot pathogens. These findings can be utilized to develop molecular selection for root rot resistance in cassava.

Modelling cassava production and pest management under biotic and abiotic constraints

We summarise modelling studies of the most economically important cassava diseases and arthropods, highlighting research gaps where modelling can contribute to the better management of these in the areas of surveillance, control, and host-pest dynamics understanding the effects of climate change and future challenges in modelling. For over 30 years, experimental and theoretical studies have sought to better understand the epidemiology of cassava diseases and arthropods that affect production and lead to considerable yield loss, to detect and control them more effectively. In this review, we consider the contribution of modelling studies to that understanding. We summarise studies of the most economically important cassava pests, including cassava mosaic disease, cassava brown streak disease, the cassava mealybug, and the cassava green mite. We focus on conceptual models of system dynamics rather than statistical methods. Through our analysis we identified areas where modelling has contributed and areas where modelling can improve and further contribute. Firstly, we identify research challenges in the modelling developed for the surveillance, detection and control of cassava pests, and propose approaches to overcome these. We then look at the contributions that modelling has accomplished in the understanding of the interaction and dynamics of cassava and its' pests, highlighting success stories and areas where improvement is needed. Thirdly, we look at the possibility that novel modelling applications can achieve to provide insights into the impacts and uncertainties of climate change. Finally, we identify research gaps, challenges, and opportunities where modelling can develop and contribute for the management of cassava pests, highlighting the recent advances in understanding molecular mechanisms of plant defence.

RXam2, a NLR from cassava (Manihot esculenta) contributes partially to the quantitative resistance to Xanthomonas phaseoli pv. manihotis

The overexpression of RXam2, a cassava NLR (nucleotide-binding leucine-rich repeat) gene, by stable transformation and gene expression induction mediated by dTALEs, reduce cassava bacterial blight symptoms. Cassava (Manihot esculenta) is a tropical root crop affected by different pathogens including Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of cassava bacterial blight (CBB). Previous studies have reported resistance to CBB as a quantitative and polygenic character. This study sought to validate the functional role of a NLR (nucleotide-binding leucine-rich repeat) associated with a QTL to Xpm strain CIO151 called RXam2. Transgenic cassava plants overexpressing RXam2 were generated and analyzed. Plants overexpressing RXam2 showed a reduction in bacterial growth to Xpm strains CIO151, 232 and 226. In addition, designer TALEs (dTALEs) were developed to specifically bind to the RXam2 promoter region. The Xpm strain transformed with dTALEs allowed the induction of the RXam2 gene expression after inoculation in cassava plants and was associated with a diminution in CBB symptoms. These findings suggest that RXam2 contributes to the understanding of the molecular basis of quantitative disease resistance.

Fine-tuning of pathogenesis-related protein 1 (PR1) activity by the melatonin biosynthetic enzyme ASMT2 in defense response to cassava bacterial blight

Melatonin is widely involved in plant disease resistance through modulation of immune responses. Pathogenesis-related (PR) proteins play important roles in plant immune responses. However, the direct association between melatonin biosynthetic enzyme and PR protein remains elusive in plants. In this study, we found that N-acetylserotonin O-methyltransferase 2 (MeASMT2) physically interacted with MePR1 in vitro and in vivo, thereby promoting the anti-bacterial activity of MePR1 against Xanthomonas axonopodis pv. manihotis (Xam). Consistently, MeASMT2 improved the effect of MePR1 on positively regulating cassava disease resistance. In addition, we found that type 2C protein phosphatase 1 (MePP2C1) interacted with MeASMT2 to interfere with MePR1-MeASMT2 interaction, so as to inhibiting the effect of MeASMT2 and MePR1 on positively regulating cassava disease resistance. In contrast to the increased transcripts of MeASMT2 and MePR1 in response to Xam infection, the transcript of MePP2C1 was decreased upon Xam infection. Therefore, disease activated MeASMT2 was released from disease inhibited MePP2C1, so as to improving the anti-bacterial activity of MePR1, resulting in improved immune response. In summary, this study illustrates the dynamic modulation of the MePP2C1-MeASMT2-MePR1 module on cassava defense response against cassava bacterial blight (CBB), extending the understanding of the correlation between melatonin biosynthetic enzyme and PR in plants.

Efficacy of Chitosan Nanoparticle Loaded-Salicylic Acid and -Silver on Management of Cassava Leaf Spot Disease

Leaf spot is one of the most important cassava diseases. Nanotechnology can be applied to control diseases and improve plant growth. This study was performed to prepare chitosan (CS) nanoparticle (NP)-loaded salicylic acid (SA) or silver (Ag) by the ionic gelation method, and to evaluate their effectiveness on reducing leaf spot disease and enhancing the growth of cassava plants. The CS (0.4 or 0.5%) and Pentasodium triphosphate (0.2 or 0.5%) were mixed with SA varying at 0.05, 0.1, or 0.2% or silver nitrate varying at 1, 2, or 3 mM to prepare three formulations of CS-NP-loaded SA named N1, N2, and N3 or CS-NP-loaded Ag named N4, N5, and N6. The results showed that the six formulations were not toxic to cassava leaves up to 800 ppm. The CS-NP-loaded SA (N3) and CS-NP-loaded Ag (N6) were more effective than the remaining formulations in reducing the disease severity and the disease index of leaf spot. Furthermore, N3 at 400 ppm and N6 at 200, 400, and 800 ppm could reduce disease severity (68.9–73.6% or 37.0–37.7%, depending on the time of treatment and the pathogen density) and enhance plant growth more than or equal to commercial fungicide or nano-fungicide products under net-house conditions. The study indicates the potential to use CS-NP-loaded SA or Ag as elicitors to manage cassava leaf spot disease.

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Background

Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome.

Results

We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB.

Conclusions

This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02524-7.

Overexpression of SCL30A from cassava (Manihot esculenta) negatively regulates salt tolerance in Arabidopsis

Soil salinity is a significant threat to sustainable agricultural production. Plants must adjust their developmental and physiological processes to deal with environmental salt conditions. We previously identified 18 serine-arginine-rich (SR) proteins from cassava (Manihot esculenta Crantz) that play pivotal roles in alternative splicing when encountering the external stress condition. However, functional characterisation of SR proteins is less reported in cassava, which is an important staple crop in the world. In the current study, we found that the expression of cassava spliceosomal component 35-like 30A (MeSCL30A) was significantly induced in response to drought and salt stress. The MeSCL30A overexpressing lines were also obtained in Arabidopsis thaliana L., which flowered earlier when compared with Col-0. Moreover, the MeSCL30A overexpressing lines were hypersensitive to salt and drought stress with lower germination and greening rate in comparison to Col-0. Importantly, soil-grown overexpression lines exhibited salt sensitivity through modulating the reactive oxygen species homeostasis and negatively regulating the gene expression that involved in ionic stress pathway. Therefore, these findings refined the SR protein-coding genes and provided novel insights for enhancing the resistance to environmental stress in plant.

Autophagy-related genes serve as heat shock protein 90 co-chaperones in disease resistance against cassava bacterial blight

Heat shock protein 90 (HSP90) is involved in plant growth and various stress responses via regulating protein homeostasis. Autophagy keeps cellular homeostasis by recycling the components of cellular cytoplasmic constituents. Although they have similar effects on cellular protein homeostasis, the direct association between HSP90 and autophagy signaling remains unclear in plants, especially in tropical crops. In this study, the correlation between HSP90 and autophagy signaling was systematically analyzed by protein-protein interaction in cassava, one of the most important economy fruit in tropic. In addition, their effects on plant disease response and underlying mechanisms in cassava were investigated by functional genomics and genetic phenotype assay. The potential MeHSP90.9-MeSGT1-MeRAR1 chaperone complex interacts with MeATGs and subsequently triggers autophagy signaling, conferring improved disease resistance to cassava bacterial blight (CBB). On the contrary, HSP90 inhibitor and autophagy inhibitor decreased disease resistance against CBB in cassava, and autophagy may be involved in the potential MeHSP90.9-MeSGT1-MeRAR1 chaperone complex-mediated multiple immune responses. This study highlights the precise modulation of autophagy signaling by potential MeHSP90.9-MeSGT1-MeRAR1 chaperone complex in autophagy-mediated disease resistance to CBB.

ARABIDOPSIS MUESTRA RESISTENCIA NO-HOSPEDERO CONSTITUTIVA CONTRA Xanthomonas phaseoli pv. manihotis

La bacteriosis vascular de la yuca, causada por la bacteria gram negativa Xanthomonas phaseoli pv. manihotis (Xpm), anteriormente conocida como Xanthomonas axonopodis pv. manihotis, es la principal enfermedad bacteriana que compromete su producción. Con la meta de generar una resistencia durable y de amplio espectro a la bacteriosis es posible explotar los mecanismos naturales presentes en plantas no-hospedero. Arabidopsis es una planta modelo extensamente estudiada, la cual es no-hospedero de Xpm. La meta de este estudio fue determinar si la resistencia no-hospedero de Arabidopsis es consecuencia de la presencia de barreras físicas o si esta depende de determinantes genéticos. En este trabajo se evaluó la capacidad de plantas de Arabidopsis de responder a la inoculación con Xpm. Ninguno de los ocho ecotipos de Arabidopsis evaluados mostraron una respuesta hipersensible a la inoculación con ocho diferentes cepas de Xpm. Aunque no se identificó la presencia de especies reactivas de oxígeno si se encontró un bloqueo en el crecimiento de Xpm en las plantas de Arabidopsis. En conjunto, los resultados aquí presentados sugieren que Arabidopsis no está activando una respuesta contra Xpm y que la resistencia observada puede ser consecuencia de las barreras físicas presentes en Arabidopsis que Xpm no es capaz de superar.

The dual interplay of RAV5 in activating nitrate reductases and repressing catalase activity to improve disease resistance in cassava

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Nitrate reductase (NR) plays an important role in plant nitrogen metabolism in plants. However, the in vivo role of NR and the corresponding signalling pathway remain unclear in cassava. In this study, we isolated MeNR1/2 and revealed their novel upstream transcription factor MeRAV5. We also identified MeCatalase1 (MeCAT1) as the interacting protein of MeRAV5. In addition, we investigated the role of MeCatalase1 and MeRAV5-MeNR1/2 module in cassava defence response. MeNRs positively regulates cassava disease resistance against CBB through modulation of nitric oxide (NO) and extensive transcriptional reprogramming especially in mitogen-activated protein kinase (MAPK) signalling. Notably, MeRAV5 positively regulates cassava disease resistance through the coordination of NO and hydrogen peroxide (H2 O2 ) level. On the one hand, MeRAV5 directly activates the transcripts of MeNRs and NO level by binding to CAACA motif in the promoters of MeNRs. On the other hand, MeRAV5 interacts with MeCAT1 to inhibit its activity, so as to negatively regulate endogenous H2 O2 level. This study highlights the precise coordination of NR activity and CAT activity by MeRAV5 through directly activating MeNRs and interacting with MeCAT1 in plant immunity.

Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava

Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.

Heat shock protein 90 co-chaperone modules fine-tune the antagonistic interaction between salicylic acid and auxin biosynthesis in cassava

Heat shock protein 90 (HSP90) is an important molecular chaperone in plants. However, HSP90-mediated plant immune response remains elusive in cassava. In this study, cassava bacterial blight (CBB) induces the expression of MeHsf8, which directly targets MeHSP90.9 to activate its expression and immune response. Further identification of SHI-related sequence 1 (MeSRS1) and MeWRKY20 as MeHSP90.9 co-chaperones revealed the underlying mechanism of MeHSP90.9-mediated immune response. MeHSP90.9 interacts with MeSRS1 and MeWRKY20 to promote their transcriptional activation of salicylic acid (SA) biosynthetic gene avrPphB Susceptible 3 (MePBS3) and tryptophan metabolic gene N-acetylserotonin O-methyltransferase 2 (MeASMT2), respectively, so as to activate SA biosynthesis but inhibit tryptophan-derived auxin biosynthesis. Notably, genetic experiments confirmed that overexpressing MePBS3 and MeASMT2 could rescue the effects of silencing MeHsf8-MeHSP90.9 on disease resistance. This study highlights the dual regulation of SA and auxin biosynthesis by MeHSP90.9, providing the mechanistic understanding of MeHSP90.9 client partners in plant immunity.

CAMTA3 negatively regulates disease resistance through modulating immune response and extensive transcriptional reprogramming in cassava

As one of the important crops in the world, cassava production is seriously threatened by Xanthomonas axonopodis pv. manihotis (Xam) all year round. Calmodulin-binding transcription activators (CAMTAs) play key roles in biotic stress and abiotic stress in plants, however, their roles in cassava remain elusive. In this study, six MeCAMTAs were identified, and MeCAMTA3 with the highest induction upon Xam infection was confirmed as a transcription factor that binds to the vCGCGb motif. MeCAMTA3 negatively regulates plant disease resistance against Xam. On the one hand, MeCAMTA3 negatively regulated endogenous salicylic acid and reactive oxygen species accumulation, pathogenesis-related genes MePRs' transcripts and callose deposition during cassava-Xam interaction but not under control conditions. On the other hand, RNA sequencing showed extensive transcriptional reprogramming by MeCAMTA3, especially 18 genes with a vCGCGb motif in the promoter region in hormone signaling, antioxidant signaling and other disease resistance signaling. Notably, chromatin immunoprecipitation-polymerase chain reaction showed that eight of these genes might be directly regulated by MeCAMTA3 through transcriptional repression. In summary, MeCAMTA3 negatively regulates plant disease resistance against cassava bacterial blight through modulation of multiple immune responses during cassava-Xam interaction and extensive transcriptional reprogramming.

Melatonin synthesis enzymes interact with ascorbate peroxidase to protect against oxidative stress in cassava

Melatonin is an important indole amine hormone in animals and plants. The enzymes that catalyse melatonin synthesis positively regulate plant stress responses through modulation of the accumulation of reactive oxygen species (ROS). However, the relationship between melatonin biosynthetic enzymes and ROS-scavenging enzymes has not been characterized. In this study, we demonstrate that two enzymes of the melatonin synthesis pathway in Manihot esculenta (MeTDC2 and MeASMT2) directly interact with ascorbate peroxidase (MeAPX2) in both in vitro and in vivo experiments. Notably, in the presence of MeTDC2 and MeASMT2, MeAPX2 showed significantly higher activity and antioxidant capacity than the purified MeAPX2 protein alone. These findings indicate that MeTDC2-MeAPX2 and MeASMT2-MeAPX2 interactions both activate APX activity and increase antioxidant capacity. In addition, the combination of MeTDC2, MeASMT2, and MeAPX2 conferred improved resistance to hydrogen peroxide in Escherichia coli. Moreover, this combination also positively regulates oxidative stress tolerance in cassava. Taken together, these findings not only reveal a direct interaction between MeTDC2, MeASMT2, and MeAPX2, but also highlight the importance of this interaction in regulating redox homoeostasis and stress tolerance in cassava.

The Cassava Source-Sink project: opportunities and challenges for crop improvement by metabolic engineering

Cassava (Manihot esculenta Crantz) is one of the important staple foods in Sub-Saharan Africa. It produces starchy storage roots that provide food and income for several hundred million people, mainly in tropical agriculture zones. Increasing cassava storage root and starch yield is one of the major breeding targets with respect to securing the future food supply for the growing population of Sub-Saharan Africa. The Cassava Source-Sink (CASS) project aims to increase cassava storage root and starch yield by strategically integrating approaches from different disciplines. We present our perspective and progress on cassava as an applied research organism and provide insight into the CASS strategy, which can serve as a blueprint for the improvement of other root and tuber crops. Extensive profiling of different field-grown cassava genotypes generates information for leaf, phloem, and root metabolic and physiological processes that are relevant for biotechnological improvements. A multi-national pipeline for genetic engineering of cassava plants covers all steps from gene discovery, cloning, transformation, molecular and biochemical characterization, confined field trials, and phenotyping of the seasonal dynamics of shoot traits under field conditions. Together, the CASS project generates comprehensive data to facilitate conventional breeding strategies for high-yielding cassava genotypes. It also builds the foundation for genome-scale metabolic modelling aiming to predict targets and bottlenecks in metabolic pathways. This information is used to engineer cassava genotypes with improved source-sink relations and increased yield potential.

Cornus macrophylla, the Antibacterial Activity of Organic Leaf Extracts and the Characterization of the More Lipophilic Components by GC/MS

In the present study, the antibacterial activity of Cornus macrophylla was examined. Organic solvent extracts of leaves were prepared using methanol, n-hexane, chloroform, and ethyl acetate. Antibacterial activity was examined by using a 100 mg/mL extract concentration. Penicillin was kept as a positive control while dimethyl sulfoxide was taken as a negative control. Methanolic extract exhibited a 21.5, 36.3, 25.3, and 23.7 mm inhibition zone diameter (IZD); n-hexane showed a 33, 40, 32.8, and 28.7 mm IZD; chloroform showed a 18.8, 29, 22.3, and 21.6 mm IZD; and ethyl acetate showed a 23.5, 30.2, 30, and 22.3 mm IZD against Erwinia carotovora, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas axonopodis, respectively. The n-hexane extract revealed high antibacterial activity against all bacterial species as compared with methanolic, chloroform, and ethyl acetate extract. Gas Chromatography Mass Spectrometry (GC/MS) analysis of n-hexane extract depicted the presence of 55 compounds. Out of these compounds, one compound, identified as α-amyrin (Mol. wt = 426), exhibited the maximum peak area (32.64%), followed by A'-Neogammacer-22(29)-en-3-ol, acetate, (3.beta.,21.beta.)- (Mol. wt = 468) and β-amyrin (Mol. wt = 426) having peak areas of 25.97 and 6.77%, respectively. It was concluded that the antibacterial activity observed during the present investigation may be due to these compounds.

A 7-Amino-Acid Motif of Rep Protein Essential for Virulence Is Critical for Triggering Host Defense Against Sri Lankan Cassava Mosaic Virus

Geminiviruses cause severe damage to agriculture worldwide. The replication (Rep) protein is the indispensable viral protein for viral replication. Although various functional domains of Rep protein in Geminivirus spp. have been characterized, the most carboxyl terminus of Rep protein was not available. We have reported the first cassava-infecting geminivirus, Sri Lankan cassava mosaic virus (SLCMV-HN7 strain), in China. In this study, we reported the second Chinese SLCMV strain, SLCMV-Col, and conducted comparative genomic analysis between these two SLCMV strains. The virulence of SLCMV-Col is much stronger than SLCMV-HN7, indicated by the higher virus titer, more severe symptoms, and more extent host defense. We functionally characterized that Rep protein, a 7-amino-acid motif at the most carboxyl terminus, is essential for Rep protein accumulation and virulence of SLCMV. We also provided evidence suggesting that the motif could also enhance triggering of salicylic acid (SA) defense against SLCMV infection in Nicotiana benthamiana. The significance of the balance between virulence and host SA defense responses in expanding invasions of SLCMV is also discussed.

Engineering Disease-Resistant Cassava

Manihot esculenta Crantz (cassava) is a food crop originating from South America grown primarily for its starchy storage roots. Today, cassava is grown in the tropics of South America, Africa, and Asia with an estimated 800 million people relying on it as a staple source of calories. In parts of sub-Saharan Africa, cassava is particularly crucial for food security. Cassava root starch also has use in the pharmaceutical, textile, paper, and biofuel industries. Cassava has seen strong demand since 2000 and production has increased consistently year-over-year, but potential yields are hampered by susceptibility to biotic and abiotic stresses. In particular, bacterial and viral diseases can cause severe yield losses. Of note are cassava bacterial blight (CBB), cassava mosaic disease (CMD), and cassava brown streak disease (CBSD), all of which can cause catastrophic losses for growers. In this article, we provide an overview of the major microbial diseases of cassava, discuss current and potential future efforts to engineer new sources of resistance, and conclude with a discussion of the regulatory hurdles that face biotechnology.

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

Background

Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown.

Results

We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars.

Conclusions

The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

Electronic supplementary material

The online version of this article (10.1186/s12915-019-0697-6) contains supplementary material, which is available to authorized users.

Evolution and ecology of plant viruses

The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.

The overexpression of RXam1, a cassava gene coding for an RLK, confers disease resistance to Xanthomonas axonopodis pv. manihotis

The overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136, suggesting that RXam1 might be implicated in strain-specific resistance. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) is a prevalent disease in all regions, where cassava is cultivated. CBB is a foliar and vascular disease usually controlled through host resistance. Previous studies have found QTLs explaining resistance to several Xam strains. Interestingly, one QTL called XM5 that explained 13% of resistance to XamCIO136 was associated with a similar fragment of the rice Xa21-resistance gene called PCR250. In this study, we aimed to further identify and characterize this fragment and its role in resistance to CBB. Screening and hybridization of a BAC library using the molecular marker PCR250 as a probe led to the identification of a receptor-like kinase similar to Xa21 and were called RXam1 (Resistance to Xam 1). Here, we report the functional characterization of susceptible cassava plants overexpressing RXam1. Our results indicated that the overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136. This suggests that RXAM1 might be implicated in strain-specific resistance to XamCIO136.

Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins

Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vectors, a set of mini binary T-DNA plasmids suitable for Type IIS restriction endonuclease- and overlap-based assembly methods. pLX vectors include replicons from compatible broad host range plasmids. Simultaneous usage of pBBR1- and RK2-based pLX vectors in a two-plasmid/one-Agrobacterium strain strategy allowed multigene delivery to plants. Adoption of pLX vectors will facilitate routine plant transformations and targeted mutagenesis, as well as complex part and circuit characterization.

Two Cassava Basic Leucine Zipper (bZIP) Transcription Factors (MebZIP3 and MebZIP5) Confer Disease Resistance against Cassava Bacterial Blight

Basic domain-leucine zipper (bZIP) transcription factor, one type of conserved gene family, plays an important role in plant development and stress responses. Although 77 MebZIPs have been genome-wide identified in cassava, their in vivo roles remain unknown. In this study, we analyzed the expression pattern and the function of two MebZIPs (MebZIP3 and MebZIP5) in response to pathogen infection. Gene expression analysis indicated that MebZIP3 and MebZIP5 were commonly regulated by flg22, Xanthomonas axonopodis pv. manihotis (Xam), salicylic acid (SA), and hydrogen peroxide (H₂O₂). Subcellular localization analysis showed that MebZIP3 and MebZIP5 are specifically located in cell nucleus. Through overexpression in tobacco, we found that MebZIP3 and MebZIP5 conferred improved disease resistance against cassava bacterial blight, with more callose depositions. On the contrary, MebZIP3- and MebZIP5-silenced plants by virus-induced gene silencing (VIGS) showed disease sensitive phenotype, lower transcript levels of defense-related genes and less callose depositions. Taken together, this study highlights the positive role of MebZIP3 and MebZIP5 in disease resistance against cassava bacterial blight for further utilization in genetic improvement of cassava disease resistance.