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Secondary metabolites such as flavonoids play an important role in protecting plants from biological agents such as fungi, pathogens, bacteria and pests. Chalcone synthase (CHS) is the first enzyme in the plant flavonoid biosynthesis pathway, and is also a key enzyme and rate-limiting enzyme in the secondary metabolite production pathway, which has very important physiological significance in plants. Despite extensive characterization in various plants, the functions of CHS in cassava remain unknown. Here, MeCH S1, MeCHS 3 and MeCH S5 genes from Manihot esculenta Crantz were isolated and functionally analyzed. The results showed that the over-expression of the three MeCHS s were beneficial to control the further reproduction of Tetranychus cinnabarinus . At the same time, the transfer of MeCH S1, MeCHS 3 and MeCH S5 genes can promote the synthesis of more secondary metabolites in Arabidopsis thaliana . Heterologous expression in A. thaliana indicated the presence of different expression levels of the three MeCHS s in defense against T. cinnabarinus infestation. Correlation analysis showed that the expression of MeCHS s were positively correlated with the synthesis of secondary metabolites, and negatively correlated with survival rate of T. cinnabarinus . These results indicate that the different expression levels of MeCHS genes lead to the difference in the synthesis of secondary metabolites, and thus the resistance of A. thaliana to T. cinnabarinus is also different.

Whitefly species pose a major threat to cassava production in tropical regions causing direct plant damage and transmitting viruses that lead to devastating cassava diseases. Aleurotrachelus socialis whitefly is one of the pests that affect cassava in South America. Developing resistant cassava varieties is the most sustainable control strategy for managing whiteflies. This study aimed to map the quantitative trait loci (QTL) associated with resistance to A. socialis and develop molecular markers to facilitate marker-assisted selection. An F2 cassava population (N = 183) was generated by selfing a highly resistant F1 derived from a cross between ECU72 (resistant) and COL2246 (susceptible) landraces. Phenotyping was performed using an efficient glasshouse screening method and high throughput image analysis of infested leaves (Nymphstar). We identified QTL on chromosomes 1, 2, 5, 6, 8, 9, and 14, with a stable and highly significant QTL on chromosome 8 (MeF2WFly8.1), explaining 35.44% of the phenotypic variation. To enable efficient selection, high-throughput KASP markers were developed and validated across diverse genetic backgrounds. Three SNPs displayed the highest association with whitefly resistance, with Chr08_6483145 as the most effective marker for selection in diverse backgrounds. These markers are provided for improving the efficiency of whitefly resistance breeding in the global cassava community.

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are two viral diseases that threaten cassava production in the East and Central African countries. These diseases are spread by members of the cryptic species complex of the whitefly Bemisia tabaci sensu lato, and/or through the propagation of infected stem cuttings. This study aims to i) identify the B. tabaci s.l. species colonizing cassava in the north of the Democratic Republic of the Congo (DRC), ii) analyse their genetic diversity, and iii) examine how this diversity is geographically structured or influenced by invasions from neighbouring (eastern) countries with high CBSD prevalence. A comprehensive sampling survey was conducted across 43 sites from east to west in the DRC, spanning 1339 km. Both nuclear and mitochondrial markers were used to identify the species and study the genetic diversity and structuring of the populations. Three species of B. tabaci s.l. were found: B. tabaci SSA1-SG1 U SG2; B. tabaci SSA1-SG3, and B. tabaci SSA2 U SSA3. In the surveyed provinces, B. tabaci SSA1 SG1 U SG2 was the dominant species (94.91%). It was structured into two genetic clusters along the east-west transect, while B. tabaci SSA2 U SSA3 was restricted to the western provinces. The findings of this study confirm that B. tabaci SSA1-SG1 U SG2 is the most abundant and adapted species on cassava in the DRC. It is likely that this species is responsible for the spread of cassava virus diseases in the DRC. Furthermore, the results showed significant geographical structuring of B. tabaci SSA1-SG1 U SG2 populations, with potential movements of populations towards the west of the country. This highlights the increased risk of virus spread towards West Africa.

Background Cassava ( Manihot esculenta Crantz) is cultivated for its starchy root and mainly used as starch and biofuel feedstock in China. The red spider mite ( Tetranychus cinnabarinus Boisduval) is one of the main insect pests reducing cassava yields and becoming more and more serious with regard to the increasing continuous cropping years in China. Results The results indicated that SC205 (4×) was more resistant to T. cinnabarinus infestation than SC205 (2×) according to the leaf damage ingestion, nutrient substance and secondary metabolite results. The T. cinnabarinus infestation triggered the expression of many genes and various metabolic processes reaction. Under the mite feeding stress, SC205 (2×) and SC205 (4×) shared 4494 and 5849 differentially expressed genes (DEGs) at 2 and 8 days, respectively. The DEGs were found enriched in the defense pathways flavonoid biosynthesis (map00941) and the flavone and flavonol biosynthesis (map00944), while, differentially accumulated metabolites (DAMs) were also found enhanced in flavonol biosynthesis (map00944) and phenylpropanoid biosynthesis pathway (map00940). Integrative analysis revealed that under 8-day pest hazards, both DEGs and DAMs in SC205 (2×) and SC205 (4×) were significantly co-enriched in several key pathways, including alpha-linolenic acid metabolism, ABC transporters, galactose metabolism, ascorbate and aldarate metabolism, alanine, aspartate and glutamate metabolism, and tyrosine metabolism. These findings suggest that carbohydrate metabolism and amino acid metabolism play crucial roles in cassava’s resistance to T. cinnabarinus infection. Conclusions Our study reveal the mechanisms of how cassava diploid and its autopolyploid in response to the feeding of T. cinnabarinus and provides data support for the precise analysis of cassava resistance and mite resistance breeding in further research.

High populations of African cassava whitefly ( Bemisia tabaci ) have been associated with epidemics of two viral diseases in Eastern Africa. We investigated population dynamics and genetic patterns by comparing whiteflies collected on cassava in 1997, during the first whitefly upsurges in Uganda, with collections made in 2017 from the same locations. Nuclear markers and mtCOI barcoding sequences were used on 662 samples. The composition of the SSA1 population changed significantly over the 20-year period with the SSA1-SG2 percentage increasing from 0.9 to 48.6%. SSA1-SG1 and SSA1-SG2 clearly interbreed, confirming that they are a single biological species called SSA1. The whitefly species composition changed: in 1997, SSA1, SSA2 and B. afer were present; in 2017, no SSA2 was found. These data and those of other publications do not support the ‘invader’ hypothesis. Our evidence shows that no new species or new population were found in 20 years, instead, the distribution of already present genetic clusters composing SSA1 species have changed over time and that this may be in response to several factors including the introduction of new cassava varieties or climate changes. The practical implications are that cassava genotypes possessing both whitefly and disease resistances are needed urgently.

Projected climate changes are thought to promote emerging infectious diseases, though to date, evidence linking climate changes and such diseases in plants has not been available. Cassava is perhaps the most important crop in Africa for smallholder farmers. Since the late 1990’s there have been reports from East and Central Africa of pandemics of begomoviruses in cassava linked to high abundances of whitefly species within the Bemisia tabaci complex. We used CLIMEX, a process-oriented climatic niche model, to explore if this pandemic was linked to recent historical climatic changes. The climatic niche model was corroborated with independent observed field abundance of B. tabaci in Uganda over a 13-year time-series, and with the probability of occurrence of B. tabaci over 2 years across the African study area. Throughout a 39-year climate time-series spanning the period during which the pandemics emerged, the modelled climatic conditions for B. tabaci improved significantly in the areas where the pandemics had been reported and were constant or decreased elsewhere. This is the first reported case where observed historical climate changes have been attributed to the increase in abundance of an insect pest, contributing to a crop disease pandemic.

Cassava ( Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

The mealybug, Phenacoccus manihoti, is a leading pest of cassava (Manihot esculenta Crantz), damaging this crop globally. Although the biological control of this mealybug using natural predators has been established, resistance breeding remains an important means of control. Understanding plant responses to insect herbivory, by determining and identifying differentially expressed genes (DEGs), is a vital step towards the understanding of molecular mechanisms of defence responses in plants and the development of resistant cultivars by gene editing. Morphological and molecular analysis confirmed the mealybug identity as Phenacoccus manihoti (Matile-Ferrero). The transcriptome response of the green mite resistant cassava genotype AR23.1 was compared to P40/1 with no known resistance at 24 and 72 hours of mealybug infestation compared to non-infested mock. A total of 301 and 206 genes were differentially expressed at 24 and 72 of mealybug infestation for AR23.1 and P40/1 genotypes respectively, using a log2 fold change and P-value ≤ 0.05. Gene ontology functional classification revealed an enrichment of genes in the secondary metabolic process category in AR23.1 in comparison with P40/1, while genes in the regulation of molecular function, cellular component biogenesis and electron carrier categories were more significantly enriched in P40/1 than in AR23.1. Biological pathway analysis, based on KEGG, revealed a significant enrichment of plant-pathogen interaction and plant hormonal signal transduction pathways for a cohort of up-regulated and down-regulated DEGs in both genotypes. Defence-related genes such as 2-oxogluterate, gibberellin oxidase and terpene synthase proteins were only induced in genotype AR23.1 and not in P40/1, and subsequently validated by RT-qPCR. The study revealed a difference in response to mealybug infestation in the two genotypes studied, with AR23.1 showing a higher number of differentially expressed transcripts post mealybug infestation at 24 and 72 hours. Candidate defence-related genes that were overexpressed in the AR23.1 genotype post mealybug infestation will be useful in future functional studies towards the control of mealybugs.

Background Cassava whitefly outbreaks were initially reported in East and Central Africa cassava ( Manihot esculenta Crantz) growing regions in the 1990’s and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. Results In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring accessions of cassava, one susceptible and one resistant to whitefly. Quantitative differences between genotypes detected at pre-infestation stages were consistently observed at each time point throughout the course of the whitefly infestation. This prevalent differential feature suggests that inherent genotypic differences override the response induced by the presence of whitefly and that they are directly linked with the phenotype observed. The most significant quantitative changes relating to whitefly susceptibility were linked to the phenylpropanoid super-pathway and its linked sub-pathways: monolignol, flavonoid and lignan biosynthesis. These findings suggest that the lignification process in the susceptible variety is less active, as the susceptible accession deposits less lignin and accumulates monolignol intermediates and derivatives thereof, differences that are maintained during the time-course of the infestation. Conclusions Resistance mechanism associated to the cassava whitefly-resistant accession ECU72 is an antixenosis strategy based on reinforcement of cell walls. Both resistant and susceptible accessions respond differently to whitefly attack at biochemical level, but the inherent metabolic differences are directly linked to the resistance phenotype rather than an induced response in the plant.

To explore the role of protective enzymes in cassava ( Manihot esculenta Crantz) resistance to mites, transgenic cassava lines overproducing copper/zinc superoxide dismutase ( MeCu/ZnSOD ) and catalase ( MeCAT1 ) were used to evaluate and molecularly confirm cassava resistance to Tetranychus cinnabarinus. Laboratory evaluation demonstrated that, compared with the control cultivar TMS60444 (wild type, WT), the survival, reproduction, development and activities of SOD and CAT in T. cinnabarinus feeding on transgenic cassava lines SC2, SC4, and SC11 significantly inhibited. Furthermore, the activities of SOD and CAT in transgenic cassava lines SC2, SC4, and SC11 damaged by T. cinnabarinus significantly increased. These findings were similar to the results in the mite-resistant cassava cultivars. Besides, field evaluation indicated that the transgenic cassava lines SC2, SC4, and SC11 were slightly damaged as the highly mite-resistant control C1115, while the highly mite-susceptible WT was severely damaged by T. cinnabarinus . Laboratory and field evaluation demonstrated that transgenic cassava lines were resistant to T. cinnabarinus , which directly confirmed that the increase in SOD and CAT activities was positively related to cassava resistance to T. cinnabarinus . These results will help in understanding the antioxidant defense responses in the cassava–mite interaction and molecular breeding of mite-resistant cassava for effective pest control.