Cassava ( Manihot esculenta Crantz) stem and root rot caused by Fusarium falciforme is a major constraint to production. This study characterised rhizoplane bacteriome shifts across agroecosystems with contrasting disease incidence and identified microbial indicators and potential biocontrol agents using 16S rRNA gene amplicon sequencing, culture-dependent isolation, and functional assays. Microbial richness was highest in diseased wetlands (Chao1: 601.60 ± 10.37), followed by healthy wetlands (581.20 ± 14.39) and uplands (547.97 ± 5.74), while evenness remained comparable among ecosystems. Pseudomonadota dominated all sites (~ 64%). Bacteroidota, Planctomycetota, and Actinomycetota were enriched in healthy wetlands but declined in diseased sites, whereas Verrucomicrobiota increased in diseased roots (7.35%). Pseudomonas dominated uplands (29.7%), while Aeromonas, Salmonella, and Devosia were associated with disease. The conserved core microbiome comprised Aquicella, Enterobacter, Klebsiella, Sodalis , and Salmonella. Network analysis identified Geminigeraceae as a keystone taxon and revealed predominantly cooperative interactions between bacteria and fungi. Among 195 isolates, Bacillus subtilis ULB_36 and Bacillus stercoris ULB_12 exhibited strong inhibition of F. falciforme (83.33% and 78.52%), significantly reduced disease severity, and enhanced plant growth, comparable to fungicide treatments. These findings demonstrate that cassava stem and root rot are associated with disruption of the rhizoplane bacteriome and the loss of beneficial taxa. Agroecosystem-specific microbial signatures and core bacteriome members provide insights into cassava–microbe interactions, while native Bacillus strains offer promising niche-adapted biocontrol solutions for sustainable management of cassava stem and root rot.

Cassava mosaic disease (CMD) is a major threat to cassava production, causing significant disruptions in photosynthesis, carbohydrate metabolism, and leaf structure, severely reducing crop productivity. This study investigates CMD's physiological, biochemical, and structural impacts across five cassava genotypes, revealing substantial differences in CMD susceptibility. Genotypes such as Sree Visakham and Sree Vijaya exhibited greater tolerance, maintaining higher chlorophyll content, enhanced non-photochemical quenching, and less severe structural alterations, suggesting tolerance mechanisms against CMD. In contrast, Sree Athulya showed rapid viral accumulation and steep declines in photosynthetic efficiency, stomatal function, and carbohydrate synthesis. The study highlights CMD's disruption of source-sink dynamics, with significant reductions in starch content and altered sugar accumulation in susceptible varieties, indicating impaired carbon allocation. Confocal and scanning electron microscopy analyses provided direct evidence of CMD-induced chloroplast damage and distortions in the epidermal structure, further compounding the physiological stress. These findings emphasize the need for breeding strategies incorporating CMD tolerance traits, such as enhanced photosynthetic efficiency and structural resilience, to develop resistant cassava varieties. Such efforts are critical for ensuring food security in regions dependent on cassava as a staple crop.

Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.

Sweetpotato is an important tropical tuber crop and serve as a rich source of essential nutrients vitamins C and E, B, iron, zinc, potassium and fiber. In spite of its nutritional value and agricultural importance as a food crop sweetpotato weevil infestation remains as a threat which leads to 80–90

Sri Lankan cassava mosaic virus (SLCMV) is a major cause for mosaic infections in cassava leaves, resulting in significant economic losses in southern India. SLCMV leads to growth retardation, leaf curl, and chlorosis in the host, with rapid transmission through whitefly insect vectors. Detecting SLCMV promptly is crucial, and the study introduces a novel and efficient colorimetric Loop-mediated isothermal amplification (LAMP) assay for successful detection in 60 min. Three primer sets were designed to target the conserved region of the SLCMV genome, specifically the coat protein gene, making the assay highly specific. The LAMP assay offers rapid and sensitive detection, completing within 60 min in a temperature-controlled water bath or thermal cycler. Compared to PCR techniques, it demonstrates 100 times superior sensitivity. The visual inspection of LAMP tube results using a nucleic acid dye and observing ladder-like pattern bands in a 2 % agarose gel confirms the presence of SLCMV. The assay is specific to SLCMV, showing no false positives or contaminations when tested against other virus. The standardized SLCMV LAMP assay proves technically efficient, providing a rapid, specific, simple, and low-cost solution, streamlining the detection and management of SLCMV.

Small RNA (sRNA) mediated gene regulation during Sri Lankan Cassava Mosaic Virus (SLCMV) infection was studied from the Indian Cassava Cultivar H226. Our study generated high throughput sRNA dataset of 23.64 million reads from the control and SLCMV infected H226 leaf libraries. mes-miR9386 was detected as the most prominent miRNA expressed in control and infected leaf. Among the differentially expressed miRNAs, mes-miR156, mes- miR395 and mes-miR535a/b showed significant down regulation in the infected leaf. Genome-wide analysis of the three small RNA profiles revealed critical role of virus-derived small RNAs (vsRNAs) from the infected leaf tissues of H226. The vsRNAs were mapped to the bipartite SLCMV genome and high expression of siRNAs generated from the virus genomic region encoding AV1/AV2 genes in the infected leaf pointed towards the susceptibility of H226 cultivars to SLCMV. Furthermore, the sRNA reads mapped to the antisense strand of the SLCMV ORFs was higher than the sense strand. These vsRNAs were potential to target key host genes involved in virus interaction such as aldehyde dehydrogenase, ADP-ribosylation factor1 and ARF1-like GTP-binding proteins. The sRNAome-assisted analysis also revealed the origin of virus-encoded miRNAs from the SLCMV genome in the infected leaf. These virus-derived miRNAs were predicted to have hair-pin like secondary structures, and have different isoforms. Moreover, our study revealed that the pathogen sRNAs play a critical role in the infection process in H226 plants.

Cassava is one of the most important food and industrial crops in Asia, Africa, and South America. Cassava mosaic disease (CMD), caused by cassava mosaic geminivirus, is one of the major constraints to cassava cultivation. In Asia, the disease is caused by the Indian cassava mosaic virus and Sri Lankan cassava mosaic virus . Phytosanitation, vector control, breeding, and genetic engineering strategies have been widely adopted to manage the disease. This study provides a comprehensive review of the disease spread, the development of diagnostic methods, and various approaches employed for the management of CMD in South and Southeast Asia.

Hsp70 proteins function as molecular chaperones, regulating various cellular processes in plants. In this study, a genome-wide analysis led to the identification of 22 Hsp70 ( MeHsp70 ) genes in cassava. Phylogenetic relationship studies with other Malpighiales genomes ( Populus trichocarpa, Ricinus communis and Salix purpurea ) classified MeHsp70 proteins into eight groups (Ia, Ib, Ic, Id, Ie, If, IIa and IIb). Promoter analysis of MeHsp70 genes revealed the presence of tissue-specific, light, biotic and abiotic stress-responsive cis -regulatory elements showing their functional importance in cassava. Meta-analysis of publically available RNA-seq transcriptome datasets showed constitutive, tissue-specific, biotic and abiotic stress-specific expression patterns among MeHsp70s in cassava. Among 22 Hsp70, six MeHsp70s viz., MecHsp70-3, MecHsp70-6, MeBiP-1, MeBiP-2, MeBiP-3 and MecpHsp70-2 displayed constitutive expression, while three MecHsp70s were induced under both drought and cold stress conditions. Five MeHsp70s , MecHsp70-7 , MecHsp70-11 , MecHsp70-12 , MecHsp70-13 , and MecHsp70-14 were induced under drought stress conditions. We predicted that 19 MeHsp70 genes are under the regulation of 24 miRNAs. This comprehensive genome-wide analysis of the Hsp70 gene family in cassava provided valuable insights into their functional roles and identified various potential Hsp70 genes associated with stress tolerance and adaptation to environmental stimuli.

Viruses are a serious threat to crop production, causing heavy economic losses and threatening food security. Accurate diagnosis is the first stage in identifying the disease causing virus. The occurrence of different symptoms, latent infection, the emergence of new viral strains, and the rapid spread of viruses demands convenient diagnostic methods. Hence, a simple, specific, and sensitive method is crucial for diagnosing the pathogen. Nucleic acid-based detection has proven its advantages over the conventional methods. Isothermal-based detection methods like LAMP and RCA plays a major role in detecting geminiviruses. High-throughput sequencing methods speed up virus detection, including of novel viruses, and in addition sequence information can be used for further characterization. Developing integrated diagnostic methods will play a crucial role in the detection of viruses and implementation of appropriate management practices.

Elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson), is an important edible tropical tuber crop, belonging to the family Araceae. Corms produced by this plant is very big and they are rich in starch, protein, mineral, vitamins, and dietary fiber but has acridity problem. This crop is susceptible to virus and phytoplasma diseases which affects crop growth and corm yield. Even though this crop has high commercial value, the problems like susceptibility to viral diseases, acridity problems, and lack of genetic diversity made hindrance in their exploitation. These issues can be resolved only by improving the characters through genetic transformation. To achieve genetic transformation in this important crop, a study was conducted to optimize various parameters for efficient Agrobacterium-mediated genetic transformation using embryogenic calli with vectors having gus reporter gene. Calli were developed using petiole and leaves of in vitro plantlets of elephant foot yam cultivar Gajendra and experiments were conducted to evaluate the sensitivity of calli to different doses of antibiotics viz. geneticin, hygromycin, ticarcillin. It was observed that complete death and discoloration of the calli were obtained with 25 mgl−1 geneticin and 10 mgl−1 hygromycin. The lowest lethal concentration of ticarcillin against Agrobacterium growth was found to be 500 mgl−1 which did not affect calli growth. Optimized parameters for efficient transformation in elephant foot yam include 100 μM acetosyringone concentration with 2 days of co-cultivation at temperature 22 °C using LBA4404 strain. The putative transformants were characterized for the integration of the gus gene using PCR and nucleic acid spot hybridization. The optimized protocol is simple and reproducible and may be adapted for other cultivars also.

Sweet potato ( Ipomoea batatus L. (Lam), Family Convolvulaceae) is one of the most important tuber crops providing nutritional security because of its high consumption value and medicinal properties, and numerous agro-industrial uses. Sweet potato feathery mottle disease caused by Sweet potato feathery mottle virus (SPFMV) is one of the serious constrains in sweet potato cultivation in India. Effective diagnostic methods need to be developed to solve the problem due to these viruses. As part of the study, infected leaf samples from fields were collected, positive samples were screened for SPFMV using DAC-ELISA and confirmed through PCR. Coat protein gene of SPFMV was PCR amplified, cloned into TA cloning vector and then transformed into Escherichia coli DH5α cells. Positive clones were sub cloned into expression vector pET28A(+) and transformed into DH5α cells. Plasmid DNA from positive clones were isolated and transformed into BL21DE3 cells (NiCo21-DE3 cells). Positive clones were identified and confirmed in-frame position through sequence analysis. Selected colony was grown in Luria both medium at 37 o C. Cells were collected and solubility of SPFMV coat protein (CP) was checked through SDS PAGE. Various standardisations were carried out for optimising expression of SPFMV CP and it was observed that 4 hr induction of 1.5 mM IPTG at 25 o C gives maximum yield. Using these conditions, cells were grown on large scale and purified the protein (SPFMV CP) using Ni-NTA resin affinity chromatography. Purified protein was checked using SDS PAGE, confirmed the expression using Western Blotting and given for immunization into two New Zealand white rabbits for polyclonal antibody production. Serological tests like ELISA and DIBA were done for confirming the sensitivity and specificity of the raised antibody using field samples of SPFMV infected sweet potato along with healthy plants. Tested samples gave strong positive reactions at dilutions of 1:500 up to 1:6000. Also antibody reacted specifically at a dilution of 1:6000 in ELISA and DIBA. This is the first report of development of polyclonal antiserum against CP of SPFMV through recombinant technology in India and can be useful for the detection of virus from the field-grown samples.

Tropical root and tuber crops are gaining more importance presently due to their climate-the word climate resilience is very important for tuber crops resilient nature and irreplaceable role in assuring food security, especially in the developing countries. The major tropical root and tuber crops are cassava/tapioca (Manihot esculenta), sweet potato (Ipomoea batatas), yams (Dioscorea spp.), taro (Colocasia esculenta), elephant foot yam (Amorphophallus paeonifolius) and tania (Xanthosoma sagittifolium). Storage ability of tubers provides an opportunity to market the product, safeguards year-round supply and helps the growers realize better prices. Many viruses and fungi infection of tuber crops cause great loss to growers. The postharvest invasion of various pathogens takes the lead in increasing the loss. Postharvest pathogens make their way to the tuber through wounds or injury that occurs during harvest, transportation, packaging operations and storage processes. The pathogens belonging to the genera Alternaria, Aspergillus, Botrytis, Fusarium, Geotrichum, Gloeosporium, Mucor, Monilinia, Penicillium and Rhizopus cause the most important postharvest diseases in tuber crops. Many physical methods, chemicals, bioagents and botanicals are being utilized for minimizing and managing postharvest diseases. Tuber crops are clonally propagated and thus storage is an essential factor. Minimizing postharvest losses increases food availability to the growing human population, decreases the area needed for production and conserves natural resources. Correct information is essential in formulating an effective and eco-friendly management strategy and thus ensuring tubers that are safe to eat at affordable prices. Precise identification of the pathogens responsible for various diseases, preharvest and postharvest environmental conditions that favour the disease along with proper handling and curing helps in alleviating the huge postharvest loss encountered.

Cassava Mosaic Disease caused by cassava mosaic virus is one of the most devastating crop diseases affecting cassava cultivation. Bioinformatics approach was applied to search cassava ( Manihot esculenta Crantz.) miRNAs that targeted the cassava mosaic virus genome. Nucleotide sequences representing the genome of cassava mosaic virus were screened against a set of mature cassava miRNAs. Efficacy of cassava miRNAs against putative viral mRNA targets was analysed based on complementarity of miRNA-mRNA target pairing. This study revealed 14 cassava miRNA families to have putative targets in the cassava mosaic virus with nearly perfect complementarity. These miRNAs when artificially designed may have the potential to confer effective resistance against cassava mosaic disease infection in transformed cassava

Sri Lankan Cassava Mosaic Virus (SLCMV) causes mosaic disease in cassava in India, Sri Lanka and south east Asian countries. Among the 98 plants species/ cultivars belonging to seven families screened/ tested against the virus, SLCMV was transmitted to 42 species of plants belonging to Solanaceae and 4 species of plants belonging to Euphorbiaceae through whitefly inoculation. The incubation period for symptom appearance varied from 6-49 days depending on the species. Presence or absence of SLCMV in the host was confirmed through PCR.

The distribution of Sri Lankan cassava mosaic virus (SLCMV) in the buds regenerated from the nodes of stem cuttings varied with different varieties. Using different diagnostic techniques (ELISA, PCR and NASH), the SLCMV distribution in 8 varieties of cassava viz., Sree Sahya, Sree Prakash, Sree Visakham, Sree Padmanabha, Sree Vijaya, M-4, H-165 and H-226 were diagnosed. Top portions (one third of total stem used for planting) of the stems in all the varieties tested had maximum virus accumulation except Sree Padmanabha, which showed high virus accumulation in bottom portion. Similar results were obtained from the diagnosis of bark samples of all the varieties with variation in the virus accumulation level.

Silverleaf whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), is one of the most notorious invasive insect pests, infesting more than 900 species of plants and spreading more than 200 viral diseases. This polyphagous agricultural pest harbours diverse bacterial communities in its gut, which perform multiple functions in whiteflies, including nutrient provisioning, amino acid biosynthesis, and virus transmission. The present exploratory study compares the bacterial communities associated with silverleaf whitefly infesting cassava, also known as cassava whitefly, collected from two different zones (zone P: plains; zone H: high ranges), from Kerala, India, using next-generation sequencing of 16S rDNA. The data sets for these two regions consisted of 1 321 906 and 690 661 high-quality paired-end sequences with mean length of 150 bp. Highly diverse bacterial communities were present in the sample, containing approximately 3513 operational taxonomic units (OTUs). Sequence analysis showed a marked difference in the relative abundance of bacteria in the populations. A total of 16 bacterial phyla, 27 classes, 56 orders, 91 families, 236 genera, and 409 species were identified from the P population, against 16, 31, 60, 88, 225, and 355, respectively, in the H population. Arsenophonus sp. (Enterobacteriaceae), which is important for virus transmission by whiteflies, was relatively abundant in the P population, whereas in the H population Bacillus sp. was the most dominant group. The association of whitefly biotypes and secondary symbionts suggests a possible contribution of these bacteria to host characteristics such as virus transmission, host range, insecticide resistance, and speciation.

We here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus , Yam mild mosaic virus and Yam chlorotic necrosis virus . A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach. The full-length genome sequence of yam chlorotic necrosis virus was determined using Sanger sequencing, which enabled determination of the coverage and sequencing accuracy of the MinION technology. Whereas the total mean sequencing error rate of yam chlorotic necrosis virus-related MinION reads was 11.25%, we show that the consensus sequence obtained either by de novo assembly or after mapping the MinION reads on the virus genomic sequence was >99.8% identical with the Sanger-derived reference sequence. From the perspective of potential plant disease diagnostic applications of MinION sequencing, these degrees of sequencing accuracy demonstrate that the MinION approach can be used to both reliably detect and accurately sequence nearly full-length positive-sense single-strand polyadenylated RNA plant virus genomes.

The most reliable and competent explant for producing transgenic lines were identified in farmer preferred Indian cassava variety, H226, utilizing four different tissue types viz., apical meristem (AM) young cotyledon (YC), compact embryogenic structures (CES) and friable embryogenic callus (FEC) through transformation with Agrobacterium tumefaciens strain, AGL0 harbouring the plant transformation vector pOYE153 having uidA gene conferring GUS activity and Npt II marker (AGL0/ pOYE153). The transgenic lines were confirmed for the presence and expression of transferred selectable marker gene Npt II as well as visual marker gene GUS by molecular analysis (PCR and Nucleic Acid Spot Hybridisation (NASH)) and GUS histochemical assay. This study reported maximum frequency of GUS gene expression (64%) in cotyledon explants, producing six putative transgenic lines and it was followed by CES explants, producing two lines in selection medium. Although FEC GUS assay proved positive for 43% of the tested samples, only one transgenic line was regenerated and the recovery was quite difficult. In the present study, young cotyledon was identified as the most suitable target tissue for Agrobacterium mediated genetic transformation of cassava variety, H226.