Cassava Brown Streak Disease Research Articles

Gene action controlling cassava brown streak disease resistance and storage root yield in cassava

Cassava (Manihot esculenta Crantz) brown streak disease (CBSD) is currently one of the major constraints to sustained cassava production in Malawi. Its economic impact is mainly manifested in the storage roots where it causes pitting, necrosis and constriction. CBSD can effectively be managed by using resistant varieties as well as early harvesting especially if the varieties are early bulking (high storage root yield). However, development of resistant and high storage root bulking varieties requires an understanding of gene action controlling inheritance of the two traits. Currently, there is very little information in Malawi regarding the inheritance pattern and relative importance of general (GCA) and specific combining ability (SCA) of these two traits. Therefore, a study was conducted to determine mode of gene action as well as importance of GCA and SCA in the genetic control of CBSD resistance and storage root yield. Information generated is essential in the selection of parents and breeding strategies for an effective breeding programme. Thirty-six crosses were generated using a 6 × 6 North Carolina Design II and later evaluated for CBSD resistance and storage root bulking at two locations using a triple square lattice design. Data for the progenies were analysed using REML in Genstat (17th ed.) while family (crosses) data were analysed using a PROC Mixed procedure performed in SAS® 9.3 Software. The GCAf × location, GCAm × location and SCA × location interaction effects were highly significant (P < 0.01) for CBSDS and CBSDI. Pooled analysis across two locations showed highly significant (P < 0.01) variance among GCA due to females (GCAf) and GCA due to males (GCAm) for FSRY. These GCAf, GCAm and female × male interaction (SCA) effects accounted for 19.8, 33.4 and 46.7% of the sum of squares for CBSDS, respectively. The results suggested that additive gene effects predominantly controlled CBSD resistance and high storage root bulking. Four parental genotypes (Silira, Mulola, Phoso and Mkondezi) were identified as the best general combiners for the CBSD, high storage root bulking and other traits. Thirteen progenies exhibiting CBSD resistance and high storage root bulking were identified and selected for advancement.

Exchanging and managing in-vitro elite germplasm to combat Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) in Eastern and Southern Africa

Cassava varieties resistant to cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are needed for the food and income security of the rural poor in eastern and southern Africa (ESA). The International Institute of Tropical Agriculture led five national cassava breeding programs (Malawi, Mozambique, Kenya, Tanzania and Uganda) in virus-cleaning and exchanging elite cassava germplasm resistant to both diseases. This paper documents the experiences and lessons learned from the process. Thirty-one clones (25 elite, two standard and four national) were submitted by the five breeding programs to the Natural Resources Institute and Kenya Plant Health Inspectorate Services for virus cleaning and indexing. Subsequently, ca 75 in-vitro virus-indexed plantlets per clone were sent to Genetic Technologies International Limited (GTIL), a private tissue culture (TC) lab in Kenya, and micro-propagated to produce ≥1500 plantlets. After fulfilling all the formal procedures of germplasm exchange between countries ≥300 plantlets per clone were sent to each partner country. National check clones susceptible to CMD/CBSD were sent only to their countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transferred to clean isolated sites for field multiplication. All the clones were cleaned of the viruses, except Tomo. The cleaning process was slow for F19-NL, NASE1, and Kibandameno and TC micro-propagation at GTIL was less efficient for Pwani, Tajirika, NASE1, and Okhumelela than for the other clones. Difficulties in cleaning recalcitrant clones affected the timeline for establishing the multi-site evaluation trials in target countries. The initiative is the one of the kind to successfully clean and exchange elite germplasm as a joint action to combat CBSD in ESA. Adequate preparation in terms of infrastructure and personnel are critical to successfully receiving and adapting the indexed in-vitro plants as new germplasm.

Plot based heritability estimates and categorization of cassava genotype response to cassava brown streak disease

Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is a threat to food security in sub-Saharan Africa, where the disease persistently reduces overall root quality and quantity resulting in up to 100% yield losses. Complexities in CBSD symptom expression and the damage caused on leaves, stems and roots throughout the 12 months of cassava growth require that appropriate ways of categorizing genotype response and optimal stages of evaluation be identified. This study aimed at: 1) determining plot based heritability of CBSD based on symptom expression and 2) categorizing genotype resistance to CBSD based on symptom expression. Herein, 41 genotypes were evaluated for two years at Namulonge with an additional evaluation conducted across three locations. Evaluations were done at three, six, nine and twelve months after planting. Genotype responses to CBSD varied significantly. High broad sense heritability estimates of up to 0.81 (incidence) and 0.71 (severity) were obtained.Average disease severity scores had higher broad sense heritability estimates (0.53 and 0.65) than maximum disease severity scores (0.33 and 0.61) for root and foliar severities respectively. These findings are important in choosing an appropriate evaluation method for CBSD. Genotypes displayed differing CBSD responses in type, locality and severity of symptoms. This suggested that genotypes had differences in mechanisms of resistance that can be exploited in CBSD resistance breeding.

Cassava Brown Streak Disease and Ugandan cassava brown streak virus Reported for the First Time in Zambia.

A diagnostic survey was conducted in July 2017 in two northern districts of Zambia to investigate presence or absence of cassava brown streak disease (CBSD) and its causal viruses. In total, 29 cassava fields were surveyed and cassava leaf samples were collected from 116 plants (92 symptomatic and 24 nonsymptomatic). CBSD prevalence was approximately 79% (23 of 29) across fields. Mean CBSD incidence varied across fields but averaged 32.3% while mean disease severity was 2.3 on a 1-to-5 rating scale. Reverse-transcription polymerase chain reaction screening of all 116 samples with one generic and two species-specific primer pairs yielded DNA bands of the expected sizes from all symptomatic plants with the generic (785 bp) and Ugandan cassava brown streak virus (UCBSV)-specific (440 bp) primers. All 24 nonsymptomatic samples were negative for UCBSV and all samples tested negative with primers targeting Cassava brown streak virus. The complete genome of a representative isolate of UCBSV (WP282) was determined to be 9,050 nucleotides in length, minus the poly A tail. A comparative analysis of this isolate with global virus isolates revealed its nature as a sequence variant of UCBSV sharing 94 and 96% maximum complete polyprotein nucleotide and amino acid identities, respectively, with isolates from Malawi (MF379362) and Tanzania (FJ039520). This is the first report of CBSD and UCBSV in Zambia, thus expanding the geographical distribution of the disease and its causal virus and further reinforcing the need to strengthen national and regional phytosanitary programs in Africa.

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

Cassava (Manihot esculenta Crantz) is an important security crop that faces severe yield loses due to cassava brown streak disease (CBSD). Motivated by the slow progress of conventional breeding, genetic improvement of cassava is undergoing rapid change due to the implementation of quantitative trait loci mapping, Genome-wide association mapping (GWAS), and genomic selection (GS). In this study, two breeding panels were genotyped for SNP markers using genotyping by sequencing and phenotyped for foliar and CBSD root symptoms at five locations in Uganda. Our GWAS study found two regions associated to CBSD, one on chromosome 4 which co-localizes with a Manihot glaziovii introgression segment and one on chromosome 11, which contains a cluster of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. We evaluated the potential of GS to improve CBSD resistance by assessing the accuracy of seven prediction models. Predictive accuracy values varied between CBSD foliar severity traits at 3 months after planting (MAP) (0.27–0.32), 6 MAP (0.40–0.42) and root severity (0.31–0.42). For all traits, Random Forest and reproducing kernel Hilbert spaces regression showed the highest predictive accuracies. Our results provide an insight into the genetics of CBSD resistance to guide CBSD marker-assisted breeding and highlight the potential of GS to improve cassava breeding.

Genetic inheritance of pulp colour and selected traits of cassava (Manihot esculenta Crantz) at early generation selection.

The early generation selection of cassava quantitative and qualitative traits saves breeding resources as it can shorten breeding schemes. Inheritance analysis provides important breeding information for developing new improved varieties. This study aimed at developing an F1 segregating cassava population and determining mode of gene action of pulp colour and selected traits at early generation selection (F1 seedling and clones). The 15 families exhibited significant (P < 0.05) phenotypic variation between offspring. The general combining ability (GCA) was significant for all traits except cassava brown streak disease on leaves, whereas specific combining ability (SCA) was significant for all evaluated traits. The Garukansubire and Gitamisi genotypes were the best general combiners for improving fresh storage root yield, while G1 and G2 were the best general combiners for improved carotenoid (yellow/orange pulp colour) and delayed physiological postharvest deterioration. The pulp colour had the highest GCA/SCA ratio and percent sum of squares due to GCA. The 15 F1 families exhibited essential genetic diversity for cassava improvement. The expression of most cassava traits was controlled by both additive and non-additive gene action. The study elucidated the role of dominance effects over the additive effects for the evaluated traits. However, the pulp colour was predominantly controlled by additive gene action. This implies the possibility of improving cassava through conventional breeding using recurrent selection for most traits. © 2017 Society of Chemical Industry.

Cassava brown streak disease: historical timeline, current knowledge and future prospects

SummaryCassava is the second most important staple food crop in terms of per capita calories consumed in Africa and holds potential for climate change adaptation. Unfortunately, productivity in East and Central Africa is severely constrained by two viral diseases: cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). CBSD was first reported in 1936 from northeast Tanzania. For approximately 70 years, CBSD was restricted to coastal East Africa and so had a relatively low impact on food security compared with CMD. However, at the turn of the 21st century, CBSD re‐emerged further inland, in areas around Lake Victoria, and it has since spread through many East and Central African countries, causing high yield losses and jeopardizing the food security of subsistence farmers. This recent re‐emergence has attracted intense scientific interest, with studies shedding light on CBSD viral epidemiology, sequence diversity, host interactions and potential sources of resistance within the cassava genome. This review reflects on 80 years of CBSD research history (1936–2016) with a timeline of key events. We provide insights into current CBSD knowledge, management efforts and future prospects for improved understanding needed to underpin effective control and mitigation of impacts on food security.

Considering behaviour to ensure the success of a disease control strategy.

The success or failure of a disease control strategy can be significantly affected by the behaviour of individual agents involved, influencing the effectiveness of disease control, its cost and sustainability. This behaviour has rarely been considered in agricultural systems, where there is significant opportunity for impact. Efforts to increase the adoption of control while decreasing oscillations in adoption and yield, particularly through the administration of subsidies, could increase the effectiveness of interventions. We study individual behaviour for the deployment of clean seed systems to control cassava brown streak disease in East Africa, noting that high disease pressure is important to stimulate grower demand of the control strategy. We show that it is not necessary to invest heavily in formal promotional or educational campaigns, as word-of-mouth is often sufficient to endorse the system. At the same time, for improved planting material to have an impact on increasing yields, it needs to be of a sufficient standard to restrict epidemic spread significantly. Finally, even a simple subsidy of clean planting material may be effective in disease control, as well as reducing oscillations in adoption, as long as it reaches a range of different users every season.

Unusual occurrence of a DAG motif in the Ipomovirus Cassava brown streak virus and implications for its vector transmission.

Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector. With the advent of next generation sequencing, researchers are generating whole genome sequences for both CBSV and UCBSV from throughout eastern Africa. Our initial goal for this study was to characterize U/CBSV whole genomes from CBSD symptomatic cassava plants sampled in Kenya. We have generated 8 new whole genomes (3 CBSV and 5 UCBSV) from Kenya, and in the process of analyzing these genomes together with 26 previously published sequences, we uncovered the aphid transmission associated DAG motif within coat protein genes of all CBSV whole genomes at amino acid positions 52–54, but not in UCBSV. Upon further investigation, the DAG motif was also found at the same positions in two other Ipomoviruses: Squash vein yellowing virus (SqVYV), Coccinia mottle virus (CocMoV). Until this study, the highly-conserved DAG motif, which is associated with aphid transmission was only noticed once, in SqVYV but discounted as being of minimal importance. This study represents the first comprehensive look at Ipomovirus genomes to determine the extent of DAG motif presence and significance for vector relations. The presence of this motif suggests that aphids could potentially be a vector of CBSV, SqVYV and CocMov. Further transmission and ipomoviral protein evolutionary studies are needed to confirm this hypothesis.

Cassava brown streak disease in Rwanda, the associated viruses and disease phenotypes.

Cassava brown streak disease (CBSD) was first observed on cassava (Manihot esculenta) in Rwanda in 2009. In 2014 eight major cassava‐growing districts in the country were surveyed to determine the distribution and variability of symptom phenotypes associated with CBSD, and the genetic diversity of cassava brown streak viruses. Distribution of the CBSD symptom phenotypes and their combinations varied greatly between districts, cultivars and their associated viruses. The symptoms on leaf alone recorded the highest (32.2%) incidence, followed by roots (25.7%), leaf + stem (20.3%), leaf + root (10.4%), leaf + stem + root (5.2%), stem + root (3.7%), and stem (2.5%) symptoms. Analysis by RT‐PCR showed that single infections of Ugandan cassava brown streak virus (UCBSV) were most common (74.2% of total infections) and associated with all the seven phenotypes studied. Single infections of Cassava brown streak virus (CBSV) were predominant (15.3% of total infections) in CBSD‐affected plants showing symptoms on stems alone. Mixed infections (CBSV + UCBSV) comprised 10.5% of total infections and predominated in the combinations of leaf + stem + root phenotypes. Phylogenetic analysis and the estimates of evolutionary divergence, using partial sequences (210 nt) of the coat protein gene, revealed that in Rwanda there is one type of CBSV and an indication of diverse UCBSV. This study is the first to report the occurrence and distribution of both CBSV and UCBSV based on molecular techniques in Rwanda.

English

Cassava is an important food security crop in Western and Coastal counties of Kenya. As a food security crop, it is continuously cultivated with minimal inputs. Its production is constrained by factors like declining soil fertility, poor agronomic practices, pests and diseases. Cassava brown streak disease (CBSD) is a viral infection attacking the cassava crop causing yield losses of up to 100%. The current study was intended to determine the effect of planting technologies on the prevalence of CBSD in two agro-ecological zones of Western Kenya: lower midland (LM1) and upper midland (UM1). Various spacing arrangements, four fertilizer regimes, legume intercrop and improved cassava cultivars were tested in a randomised complete block design (RCBD) with each site as a replicate. Data was collected on pathogen population and disease incidences and severity, and cassava and legumes yields. Results showed no effect of modified spacing and legume intercrop on CBSD incidence. However, incidences varied by cassava cultivar (9 to 59%) and fertilizer application (3 to 41%). Low CBSD incidences (3 to 16%) were observed over time in management strategies involving fertilizer NPK 17:17:17 suggesting that vigour enhancement may have contributed to low CBSD incidences. Low incidence of CBSD on improved cultivars indicates that CBSD can be mitigated through crop improvement technologies such as breeding for resistance to diseases. Intercropping cassava with beans and modification of spacing did not demonstrate an effect on CBSD incidence. However, 2 m× 0.5 m spacing arrangement can compensate for rising land pressure in Western Kenya and areas facing similar problem. Key words: Cassava, cropping arrangements, intercrop, yields, cassava brown streak disease (CBSD), Western Kenya.

WITHDRAWN: Variation in starch quality of carotenoids-rich cassava clones that exhibit resistance to cassava brown streak disease

• Cassava brown streak disease resulted into reduction in starch amylopectin content, but not amylose content.

Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing.

Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa.

RT-PCR-based detection and partial genome sequencing indicate high genetic diversity between CBSV and UCBSV in Kenya

Cassava is grown by small-scale farmers and consumed by over 200 million people in sub-Saharan Africa mainly as staple food. An emerging viral disease Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), has severely affected cassava production and resulted in poor quality tubers. The disease severely affecting root quality both for domestic use and marketing and has become a real threat to the livelihoods of the millions of poor in both eastern and southern African countries. There is also increase in the number of CBSV and UCBSV sequences available now, and a need to have primers that would detect all isolates of CBSV and UCBSV is required, particularly for field surveys. Two sets of virus-specific primers, CBSVF2 &amp; CBSVR7 and CBSVF2 &amp; CBSVR8, were developed to specifically detect CBSV and UCBSV respectively on six glass house maintained isolates and field collected samples from coastal Kenya. Positive samples produced expected PCR products of 345 bp and 441 bp using CBSVF2 &amp; CBSVR7 and CBSVF2 &amp; CBSVR8, respectively. In addition, our study further confirmed the genetic diversity of these viruses by sequencing over 41 new samples from Kenya as well as Tanzania and Zanzibar. The coat protein, partial HAM1 and 3' UTR regions of CBSV and UCBSV were amplified using CBSVF2 &amp; CBSVR1 and CBSVF2 &amp; CBSVR2, respectively. The PCR products of ~1.6 Kb obtained were extracted from gel, cloned and sequenced. The sequences of the UCBSV and CBSV isolates varied in length; 1678 nucleotide for UCBSV isolates and 1615 nucleotide for CBSV isolates. CBSV and UCBSV sequences were used to the construct phylogenetic trees by comparing with other sequences from GenBank. The phylogenetic tree clustered the CBSD isolates in two groups reflecting the two virus species causing CBSD. Based on the available sequences (~1600 bases), the CBSV group shared 93.7% nucleotide identities, UCBSV 93.1%, and there was ~70% identity between the two groups. However, the percentage nucleotide identities for coat protein nucleotide sequences were slightly greater than those observed for the sequences involving partial HAM1 and 3'UTR region. CBSV group shared 94.4% nucleotide identity, UCBSV 93.5% and ~74% identity between the two groups. In conclusion, this study has shown the genetic diversity between CBSV and UCBSV isolates collected from Kenya with those from Tanzania and Zanzibar.Keywords: Brown streak virus, cassava, Kenya

RT-PCR-based detection and partial genome sequencing indicate high genetic diversity between CBSV and UCBSV in Kenya

Cassava is grown by small-scale farmers and consumed by over 200 million people in sub-Saharan Africa mainly as staple food. An emerging viral disease Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), has severely affected cassava production and resulted in poor quality tubers. The disease severely affecting root quality both for domestic use and marketing and has become a real threat to the livelihoods of the millions of poor in both eastern and southern African countries. There is also increase in the number of CBSV and UCBSV sequences available now, and a need to have primers that would detect all isolates of CBSV and UCBSV is required, particularly for field surveys. Two sets of virus-specific primers, CBSVF2 &amp; CBSVR7 and CBSVF2 &amp; CBSVR8, were developed to specifically detect CBSV and UCBSV respectively on six glass house maintained isolates and field collected samples from coastal Kenya. Positive samples produced expected PCR products of 345 bp and 441 bp using CBSVF2 &amp; CBSVR7 and CBSVF2 &amp; CBSVR8, respectively. In addition, our study further confirmed the genetic diversity of these viruses by sequencing over 41 new samples from Kenya as well as Tanzania and Zanzibar. The coat protein, partial HAM1 and 3' UTR regions of CBSV and UCBSV were amplified using CBSVF2 &amp; CBSVR1 and CBSVF2 &amp; CBSVR2, respectively. The PCR products of ~1.6 Kb obtained were extracted from gel, cloned and sequenced. The sequences of the UCBSV and CBSV isolates varied in length; 1678 nucleotide for UCBSV isolates and 1615 nucleotide for CBSV isolates. CBSV and UCBSV sequences were used to the construct phylogenetic trees by comparing with other sequences from GenBank. The phylogenetic tree clustered the CBSD isolates in two groups reflecting the two virus species causing CBSD. Based on the available sequences (~1600 bases), the CBSV group shared 93.7% nucleotide identities, UCBSV 93.1%, and there was ~70% identity between the two groups. However, the percentage nucleotide identities for coat protein nucleotide sequences were slightly greater than those observed for the sequences involving partial HAM1 and 3'UTR region. CBSV group shared 94.4% nucleotide identity, UCBSV 93.5% and ~74% identity between the two groups. In conclusion, this study has shown the genetic diversity between CBSV and UCBSV isolates collected from Kenya with those from Tanzania and Zanzibar.Keywords: Brown streak virus, cassava, Kenya

Deep Learning for Image-Based Cassava Disease Detection.

Cassava is the third largest source of carbohydrates for human food in the world but is vulnerable to virus diseases, which threaten to destabilize food security in sub-Saharan Africa. Novel methods of cassava disease detection are needed to support improved control which will prevent this crisis. Image recognition offers both a cost effective and scalable technology for disease detection. New deep learning models offer an avenue for this technology to be easily deployed on mobile devices. Using a dataset of cassava disease images taken in the field in Tanzania, we applied transfer learning to train a deep convolutional neural network to identify three diseases and two types of pest damage (or lack thereof). The best trained model accuracies were 98% for brown leaf spot (BLS), 96% for red mite damage (RMD), 95% for green mite damage (GMD), 98% for cassava brown streak disease (CBSD), and 96% for cassava mosaic disease (CMD). The best model achieved an overall accuracy of 93% for data not used in the training process. Our results show that the transfer learning approach for image recognition of field images offers a fast, affordable, and easily deployable strategy for digital plant disease detection.

Spectral separability and mapping potential of cassava leaf damage symptoms caused by whiteflies (Bemisia tabaci).

BACKGROUNDThis study examines whether leaf spectra can be used to measure damage to cassava plants from whitefly (Bemisia tabaci), and the potential to translate measurements from leaf to landscape scale in eastern Africa. Symptoms of the cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) viruses, and sooty mould (SM) blackening of lower leaves from whiteflies feeding on the upper leaves, were measured at the leaf scale with a high‐resolution spectroradiometer and a single photon avalanche diode (SPAD) meter, which retrieves relative chlorophyll concentration. Spectral measurements were compared to the five‐level visual scores used to assess the severity of each of the three damaging agents in the field, and also to leaf chemistry data.RESULTSLeaves exhibiting severe CBSD and CMD were spectrally indistinguishable from leaves without any symptoms. Severe SM was spectrally distinctive but is likely to be difficult to map because of its occurrence in the lower crown. SPAD measurements were highly correlated with most foliar chemistry measurements and field scores of disease severity. Regression models between simulated Sentinel 2 bands, field scores and SPAD measurements were strongest using wavelengths with high importance weightings in random forest models.CONCLUSIONSPAD measurements are highly correlated to many foliar chemistry parameters, and should be considered for use in mapping disease severity over larger areas. Remaining challenges for mapping relate to the subtle expression of symptoms, the spatial distribution of disease severity within fields, and the small size and complex structure of the cassava fields themselves. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genotype by environment interactions in identifying cassava (Manihot esculenta Crantz) resistant to cassava brown streak disease

Cassava landraces were evaluated for resistance to cassava brown streak disease (CBSD) for two cropping seasons at a disease hotspot area in Naliendele, Tanzania. Based on reactions to CBSD, several landraces including Chimaje, Mfaransa and Supa B were considered to be resistant to the disease while Kikwada, Mbuyu, and Nyoka were tolerant. ANOVA revealed that the largest sum of squares (SS) (41.9–86.7%) was attributed to the genotype of the cassava landraces, while a smaller proportion of SS (8.1–38.2%) was due to genotype by environment interactions for all traits tested, which included disease symptoms, root weight, number of roots per plant and dry matter content. Environment accounted for the smallest effect (0.01–26.3%), however, the mean squares was nonetheless significant for a few genotypes, which indicated that their disease expression was indeed influenced by the environment. Increased CBSD severity was associated with low temperatures and rainfall. Increased rainfall towards harvesting led to higher root weight but lower dry matter content in the first cropping season. Correlation analysis showed that the presence of CBSD symptoms reduces the amount of usable roots, total root weight, and root dry matter content. Many resistant/tolerant landraces also had high root weight and dry matter content, and they can be used by farmers to reduce CBSD losses. The landraces described here form novel sources of CBSD resistance that can be used for breeding disease-resistant cassava varieties with superior agronomic characteristics.

Crops that feed the world: Production and improvement of cassava for food, feed, and industrial uses

Cassava (Manihot esculenta Crantz) is one of the oldest root and tuber crops, used by humans to produce food, feed and beverages. Currently, cassava is produced in more than 100 countries and fulfils the daily caloric demands of millions of people living in tropical America, Africa, and Asia. Its importance as a food security crop is high in Western, Central and Eastern Africa due to its ability to produce reasonable yields (~10 t/ha) in poor soils and with minimal inputs. Traditionally a famine reserve and a subsistence crop, the status of cassava is now evolving fast as a cash crop and as raw material in the production of starch (and starch based products), energy (bio-ethanol) and livestock feed in the major producing countries. Cassava leaves, which are rich in protein and beta-carotenoids, are also used as a vegetable and forage (fresh or dehydrated meal) in various parts of the world. In recent years, some of the problems in the production of cassava have been increasing infection with cassava mosaic disease (CMD), cassava brown streak disease (CBSD) and cassava bacterial blight (CBB). Inherent post-harvest physiological disorder (PPD) and cyanogenic glycosides (CG) are some of the most prominent challenges for scientists, producers and consumers in the post-production systems. Collaborative research in participatory plant breeding is ongoing at leading international research institutes such as IITA and CIAT to improve crop resistance to virus diseases, reduce PPD and CG, and improve the overall nutritional characteristics. Further research should also focus on post-production systems by developing enhanced storage and transportation techniques, mechanisation (peeling, size reduction, drying and dewatering) and improved packaging. Moreover, a robust national policy, market development, and dissemination and extension program are required to realise the full potential of innovations and technologies in cassava production and processing.

A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

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.