Deep Sequencing Reveals a Divergent Ugandan cassava brown streak virus Isolate from Malawi.
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ABSTRACT:
SUBMITTER: Mbewe W
PROVIDER: S-EPMC5604781 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of 'translational elongation', 'translation factor activity', 'ribosomal subunit' and 'phosphorelay signal transduction', were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga's resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.
| S-EPMC5575035 | biostudies-literature
Project description:Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.
| S-EPMC4595453 | biostudies-literature
Project description:Small RNA sequences for Ugandan cassava brown streak virus in Cassava genotype 60444
| PRJNA352341 | ENA
Project description:Cassava brown streak disease (CBSD), caused by Cassava brown streak Uganda virus (CBSUV) and Cassava brown streak virus (CBSV), is of new epidemic importance to cassava (Manihot esculenta Crantz) production in East Africa, and an emerging threat to the crop in Central and West Africa. This study demonstrates that at least one of these two ipomoviruses, CBSUV, can be efficiently controlled using RNA interference (RNAi) technology in cassava. An RNAi construct targeting the near full-length coat protein (FL-CP) of CBSUV was expressed constitutively as a hairpin construct in cassava. Transgenic cassava lines expressing small interfering RNAs (siRNAs) against this sequence showed 100% resistance to CBSUV across replicated graft inoculation experiments. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed the presence of CBSUV in leaves and some tuberous roots from challenged controls, but not in the same tissues from transgenic plants. This is the first demonstration of RNAi-mediated resistance to the ipomovirus CBSUV in cassava.
| S-EPMC6640337 | biostudies-literature
Project description:Artificial miRNAs (amiRNA) were generated targeting conserved sequences within the genomes of the two causal agents of Cassava brown streak disease (CBSD): Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Transient expression studies on ten amiRNAs targeting 21nt conserved sequences of P1(CBSV and UCBSV), P3(CBSV and UCBSV), CI(UCBSV), NIb(CBSV and UCBSV), CP(UCBSV) and the un-translated region (3'-UTR) were tested in Nicotiana benthamiana. Four out of the ten amiRNAs expressed the corresponding amiRNA at high levels. Transgenic N. benthamiana plants were developed for the four amiRNAs targeting the P1 and NIb genes of CBSV and the P1 and CP genes of UCBSV and shown to accumulate miRNA products. Transgenic plants challenged with CBSV and UCBSV isolates showed resistance levels that ranged between ∼20-60% against CBSV and UCBSV and correlated with expression levels of the transgenically derived miRNAs. MicroRNAs targeting P1 and NIb of CBSV showed protection against CBSV and UCBSV, while amiRNAs targeting the P1 and CP of UCBSV showed protection against UCBSV but were less efficient against CBSV. These results indicate a potential application of amiRNAs for engineering resistance to CBSD-causing viruses in cassava.
| S-EPMC4819903 | biostudies-literature
Project description:Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.
| S-EPMC6523400 | biostudies-literature
Project description:Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world's largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i ). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSD rs ) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSD ri ) and CBSD rs (r = 0.90***). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s ) and CBSD foliar incidence at 6 months (CBSD6i ) (r = 0.77***), CBSD3s and CBSD rs (r = 0.35***). Fresh root weight (Fresh RW ) negatively correlated with CBSD ri and CBSD rs , respectively (r = -0.21*** and r = -0.22***). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s ) and 6 months (CMD6s ), respectively (r = -0.25*** and r = -0.21***). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties.
| S-EPMC8646096 | biostudies-literature
Project description:The genetic and symptom diversity of six virus isolates causing cassava brown streak disease (CBSD) in the endemic (Kenya, Mozambique, and Tanzania) and the recently affected epidemic areas (Uganda) of eastern Africa was studied. Five cassava varieties; Albert, Colombian, Ebwanateraka, TMS60444 (all susceptible) and Kiroba (tolerant) were graft inoculated with each isolate. Based on a number of parameters including the severity of leaf and root symptoms, and the extent of virus transmission by grafting, the viruses were classified as either severe or relatively mild. These results were further confirmed by the mechanical inoculation of 13 herbaceous hosts in which the virulent isolates caused plant death in Nicotiana clevelandii and N. benthamiana whereas the milder isolates did not. Phylogenetic analysis of complete coat protein gene sequences of these isolates together with sequences obtained from 14 other field-collected samples from Kenya and Zanzibar, and reference sequences grouped them into two distinct clusters, representing the two species of cassava brown streak viruses. Put together, these results did not suggest the association of a hypervirulent form of the virus with the current CBSD epidemic in Uganda. Identification of the severe and milder isolates, however, has further implications for disease management and quarantine requirements.
| S-EPMC3290829 | biostudies-literature
Project description:Growing cassava in Africa requires resistance against the viruses causing cassava mosaic disease (CMD) and the viruses causing cassava brown streak disease (CBSD). A dominant CMD2 resistance gene from a West African cassava landrace provides strong resistance against the cassava mosaic viruses. However, resistance against cassava brown streak viruses is limited to cassava varieties that show tolerance to the disease. A recently identified cassava germplasm that cannot be infected with cassava brown streak viruses provides a new source of the resistance required to protect cassava from CBSD. We present a synopsis of the status of virus resistance in cassava and report on the research to combine resistance against CBSD and CMD. We improve the lengthy and erratic screening for CBSD resistance by proposing a virus infection and screening protocol for the viruses causing CBSD and CMD, which allows a rapid and precise assessment of cassava resistance under controlled conditions. Using this approach, we classified the virus responses of cassava lines from Africa and South America and identified truly virus-resistant clones that cannot be infected with any of the known viruses causing CBSD even under the most stringent virus infections. A modification of this protocol was used to test seedlings from cassava crosses for resistance against both diseases. A broad-spectrum resistance was identified in a workflow that lasted 9 months from seed germination to the identification of virus resistance. The workflow we propose dramatically reduces the evaluation and selection time required in a classical breeding workflow to reach the advanced field trial stage in only 9 months by conducting selections for virus resistance and plant multiplication in parallel. However, it does not bypass field evaluations; cassava resistance assessment prior to the field limits the evaluation to candidates with virus resistance defined as the absence of symptoms and the absence of the virus. The transfer of our virus screening workflow to cassava breeding programs enhances the efficiency by which resistance against viruses can be selected. It provides a precise definition of the plant's resistance response and can be used as a model system to tackle resistance in cassava against other diseases.
| S-EPMC9909537 | biostudies-literature
Project description:Robustness, a naïve property of biological systems, enables organisms to maintain functions during perturbation and is crucial for improving the resilience of crops to prevailing stress conditions and diseases, guaranteeing food security. Most studies of robustness in crops have focused on genetic superiority based upon individual genes, overlooking the collaborative actions of multiple responsive genes and the regulatory network topology. This research aims to uncover patterns of gene cooperation leading to organismal robustness by studying the topology of gene co-expression networks (GCNs) of both CBSV virus resistant and susceptible cassava cultivars. The resulting GCNs show higher topological clustering of cooperative genes in the resistant cultivar, suggesting that the network architecture is central to attaining robustness. Despite a reduction in the number of hub genes in the resistant cultivar following the perturbation, essential biological functions contained in the network were maintained through neighboring genes that withstood the shock. The susceptible cultivar seemingly coped by inducing more gene actions in the network but could not maintain the functions required for plant growth. These findings underscore the importance of regulatory network architecture in ensuring phenotypic robustness and deepen our understanding of transcriptional regulation.
| S-EPMC8041763 | biostudies-literature