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Tackling agriculturally relevant diseases in the staple
crop cassava (Manihot esculenta)
Emily J McCallum, Ravi B Anjanappa and Wilhelm Gruissem
Cassava is an important staple food crop for millions of people
in tropical regions across Africa, South America and Asia. Viral,
bacterial and fungal diseases impact cassava yield in all three
regions. The viruses causing cassava mosaic disease and
cassava brown streak disease have been particularly
devastating to cassava production in Africa. Improved farming
practices and disease monitoring can reduce the impact of
cassava diseases in the field. The availability of disease
resistant cassava varieties developed through breeding or
genetic engineering is key to tackling disease incidence and
severity.
Address
Department of Biology, Plant Biotechnology, ETH Zurich, CH-8092
Zurich, Switzerland
Corresponding author: Gruissem, Wilhelm (wgruissem@ethz.ch)
Current Opinion in Plant Biology 2017, 38:50–58
This review comes from a themed issue on Biotic interactions
Edited by Silke Robatzek and Sarah Lebeis
For a complete overview see the Issue and the Editorial
Available online 3rd May 2017
http://dx.doi.org/10.1016/j.pbi.2017.04.008
1369-5266/ã 2017 Elsevier Ltd. All rights reserved.
Cassava production and implications of
disease impacts
Cassava is grown across tropical regions in South America,
Africa and Asia. It is a major staple food for an estimated
800 million people who mostly eat the starchy storage root
[1]. In Africa, cassava is an important food security crop for
small-scale subsistence farming families who grow the
crop on agriculturally marginal lands with minimal inputs.
Cassava is also utilized for animal feed and its starch for
industrial purposes. Many farmers favor cassava because
it has high carbohydrate yields relative to land area and
labor, tolerance to abundant rainfall, drought and poor
soils, and it is amenable to crop rotation. Agricultural
limitations of cassava include postharvest physiological
deterioration of storage roots, low yields (particularly in
parts of Sub-Saharan Africa) due to limited inputs such as
fertilizer, pesticides and herbicides, and susceptibility to a
variety of diseases and pests that can decimate cassava
crops and yields. The impact of diseases on cassava
Current Opinion in Plant Biology 2017, 38:50–58
farming has been identified as a key strategic research
and development activity by the FAO Global Cassava
Development Strategy, which stresses the importance of
identifying disease resistance in existing cassava germ-
plasm and isolation of resistance genes for breeding or
engineering resistant farmer-preferred varieties [2].
The potential social and economic consequences of cas-
sava diseases are broad ranging. Storage root yield losses
can result in food shortages or even famine. In Africa,
where cassava is typically consumed by some of the
poorest rural households, cassava leaves are important
sources of protein and vitamins that are not present in
sufficient amounts in storage roots [3]. Many cassava
diseases affect leaves most severely, thus increasing
potentially negative impacts on nutrition and health. A
robust cassava value chain has been identified as a driver
of economic development in poorer, rural African com-
munities and a major source of income for cassava farming
families who are at high risk to economic stress [4]. Thus,
losses resulting from cassava diseases are not merely an
agricultural issue, but pose a severe threat to the food
security and livelihoods of millions of people in Sub-
Saharan Africa. Here we review important agriculturally-
relevant cassava diseases and discuss options to tackle
them in farmer-preferred cultivars.
Cassava mosaic disease
Cassava mosaic disease (CMD) is a well-known and
widespread viral disease affecting cassava in Africa, India
and Sri Lanka [5,6]. CMD is caused by a family of
single-strand DNA cassava mosaic geminiviruses (CMGs)
(genus Begomovirus; family Geminiviridae) comprised of
11 species [7] and transmitted by the whitefly Bemisia
tabaci as well as infected stem cuttings. Typical CMD
infected leaves have twisted leaflets with mosaic pattern
of chlorosis (Figure 1) [8]. African cassava mosaic virus
and East African cassava mosaic virus-Uganda causes an
average loss of 82% root yield [9] and is seventh among
the top ten economically important plant viruses [10].
Geminiviruses, including CMGs, evolve rapidly in the
field through recombination and replicative errors [11].
Recent reports of the disease spreading to other cassava-
growing regions in the world indicate that it must be
tackled with high priority [12].
The development and deployment of CMD-resistant
varieties is currently the most widely adopted strategy
to control the disease. CMD resistance is not present in
cultivated cassava species (Manihot esculenta) but was
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 Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta) McCallum, Anjanappa and Gruissem 51

Figure 1

Cassava Cassava
Bacterial Blight Mosaic Disease

Cassava
Anthracnose Disease

Cassava Cassava
Frogskin Disease Brown Streak Disease

Current Opinion in Plant Biology

Major cassava diseases and representation of typical symptoms. Cassava bacterial blight (top left) is caused by Xanthomonas axonopodis pv.
manihotis. The pathogen causing frogskin disease (bottom left) has not been identified. Cassava mosaic disease (top right) is caused by single-
strand DNA geminiviruses. Anthracnose disease (center right) is caused by the fungus Colletotrichum gloeosporioides f.sp. manihotis. Cassava
brown streak disease (bottom right) is caused by (+)-single-strand RNA viruses. The diseases are discussed in more detail in the text.

identified in wild relatives (Manihot glaziovii) [13] and
African cassava landraces [14]. This provided opportu-
nities for resistance breeding using either the polygenic
recessive CMD1, the recently identified CMD3, and the
dominant monogenic CMD2 loci [15]. CMD2-type vari-
eties have high resistance to CMD [14,16]. Recent
screening of West- and East-African breeding germplasm
has failed to identify additional CMD resistance loci [17].
This creates a precarious situation considering the fast-
paced evolutionary rate of CMGs and the currently
unknown functionality of available resistance loci. Cas-
sava plants engineered for CMD resistance have a
reduced virus load [18,19], but these transgenic lines
have not been widely tested for field performance.
Alternatives to CMD2-type resistance need to be devel-
oped via breeding or transgenic approaches for small-
holder and commercial cassava production in the affected
countries. A better understanding of host susceptibility
factors promoting CMG replication, for example using
comparative transcriptomics [20,21] may facilitate the
identification of targets for resistance. Similarly, identify-
ing cassava homologs to begomovirus resistance alleles in
other plant species, such as the recently discovered RDRg

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52 Biotic interactions
gene (Ty-1 and Ty-3 allele) [22] could also be a useful
strategy. New resistance genes could be important targets
for new technologies (such as CRISPR/Cas9) to build
resistance in susceptible varieties.
Cassava brown streak disease
Cassava brown streak disease (CBSD) was first reported
in Eastern Africa during the 1930s and causes up to 70%
losses in cassava root yields [23]. Typical CBSD symp-
toms are leaf chlorosis, brown streaks on stems and dry
hard rot in roots thus affecting both the quality and
quantity of edible storage roots (Figure 1). CBSD is
caused by cassava brown streak (+)-ssRNA viruses
(CBSVs) (genus Ipomovirus; family Potyviridae) comprised
of the two phylogenetically distinct species CBSV and
Ugandan CBSV (UCBSV) [24,25]. CBSVs are mostly
transmitted by infected stem cuttings and also by white-
flies, although at a very low rate [26,27]. Recent reports of
CBSD occurrence in central African regions [28,29] indi-
cates that the virus is spreading to other cassava growing
regions.
Screening for CBSD-resistant cassava genotypes started
in 1937 and continues today. Early breeding of CBSD-
resistant cassava varieties was based on interspecific
crosses between M. esculenta and M. glaziovii or
M. melanobasis [30]. Engineering CBSV resistance in
cassava varieties has been shown to provide resistance
in greenhouse and field trials [31,32,33,34,35]. How-
ever, engineering CBSD resistance in CMD2 varieties is
complicated because the dominant CMD2 resistance
breaks down during somatic embryogenesis, an essential
step for cassava transformation [15]. Nevertheless,
genetic engineering approaches based on RNA interfer-
ence (RNAi), in combination with breeding cycles, still
represent the best option in cases where natural resistance
sources are not available. Alternatively, RNAi approaches
to silence genes in the insect vector can reduce virus
infections [36]. Deployment of double-strand RNA
(dsRNA) sprays, as demonstrated for cowpea challenged
with cucumber mosaic virus and Nicotiana tabacum cv.
Xanthi challenged with pepper mild mottle virus, are also
promising strategies [37]. Such dsRNA sprays can be
regularly updated to keep pace with newly evolved virus
isolates. The recent identification of elite breeding lines
resistant to virulent CBSV isolates is an important
advance towards dissecting the molecular mechanisms
involved in natural CBSD resistance [38]. Transcriptome
characterization of CBSD-resistant and susceptible cas-
sava varieties has led to a greater understanding of this
pathosystem and the identification of intriguing targets
for further study [39].
Considering the enormous impact of viral diseases on
cassava yield, virus resistance is an essential requirement
for the deployment of other trait improvements such as
Current Opinion in Plant Biology 2017, 38:50–58
pro-vitamin A [40] and vitamin B6 [41] biofortification in
cassava.
Cassava bacterial blight
Cassava bacterial blight (CBB) is caused by Xanthomonas
axonopodis pv. manihotis (Xam) and is the most predomi-
nant and agriculturally relevant bacterial disease in cas-
sava farming with yield losses of up to 75% [42]. Several
other bacterial pathogens have been reported to infect
cassava in the field, including Xanthomonas campestris pv.
cassavae, Erwinia carotovora pv. carotovora, Agrobacterium
tumefaciens [43] and Enterobacter cloacae [44] (Table 1).
However, the incidence and agronomic impact of these
bacterial diseases appears to be relatively low. CBB
symptoms include angular leaf spots, leaf wilting, gum
exudates, vascular necrosis of the stem and shoot dieback
(Figure 1) [45]. Transmission of CBB in fields is typi-
cally by rain splash and infected farming tools, and
between farms via infected cuttings. Disease incidence
and severity are largely driven by environmental factors,
primarily associated with periods of high rainfall. Inter-
cropping, crop rotation, fallow, late planting and weeding
decrease CBB severity [46] and treatment of suspected
infected seeds is possible [45].
Physical mechanisms of Xam infection in susceptible and
resistant cassava are known [45] and the Xam genome
encodes a suite of effectors commonly found in other
Xanthomonas plant pathogens [47,48]. Several of these
effectors promote virulence in cassava infection [49–52].
Cassava varieties with tolerance to bacterial blight exist
although tolerance frequently breaks down due to unsta-
ble genotype x environment interactions [53,54]. A num-
ber of quantitative trait loci (QTLs) have been identified
[55–57] including some strain-specific markers. Tran-
script profiling following CBB infection has revealed a
number of genes which are differentially regulated
through early, mid and late infection stages [42,58–60].
Two putative resistance genes, RXam1 and RXam2 have
been reported [61], however relatively little is understood
regarding the specific genetic mechanisms of resistance to
CBB in tolerant cassava varieties [42]. CBB resistance is
likely polygenic and additive, spread across several weak
alleles in tolerant varieties, further complicating efforts to
identify genetic determinants of resistance. CBB resistance
is thought to have been introgressed into cultivated cassava
via crosses with M. glaziovii or other wild relatives [45].
The cassava germplasm bank at the International Center
for Tropical Agriculture (CIAT) (http://genebank.ciat.
cgiar.org/genebank/language.do?collection=cass) contains
more than 30 Manihot species and more than 800 wild
genotypes, which may be a rich source of CBB resistance
genes that could be further explored. The application of
new technologies such as resistance gene enrichment
sequencing [62,63] may also lead to the discovery of targets
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 Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta) McCallum, Anjanappa and Gruissem 53
Table 1
Diseases of cassava, causal agent/s and typical disease symptoms. Data compiled from published literature [43,44,85] and field
guidebooks for cassava disease symptom identification [86–88]
Disease name
Viral
Cassava mosaic disease (CMD)
Cassava brown streak disease (CBSD)
Cassava common mosaic disease
Cassava vein mosaic disease
Cassava green mottle disease
Cassava symptomless diseases
No disease name specified
No disease name specified
Bacterial
Cassava bacterial blight (CBB)
Cassava bacterial angular leaf spot
(or Cassava bacterial necrosis)
Cassava bacterial stem rot
Cassava bacterial wilt
Cassava bacterial stem gall
Cassava sudden wilt
No disease name specified
Fungal
Cassava anthracnose disease (CAD)
Cassava blight (or diffuse) leaf spot
Cassava brown leaf spot
Cassava white leaf spot
Cassava (concentric) ring leaf spot
Cassava superelongation disease
Cassava ash disease (powdery mildew)
Cassava rust
Cassava stem rot
Cassava (soft) root rot
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Causal agent Typical symptoms
African cassava mosaic virus (ACMV) Patchy yellow/chlorotic mosaic pattern on leaves,
East African mosaic virus (EACMV) mild-severe leaf deformation, stunted shoot growth
South African cassava mosaic virus (SACMV)
Indian cassava mosaic virus (ICMV)
Sri Lankan cassava mosaic virus (SLCMV)
Cassava brown streak virus (CBSV) Mild-severe necrosis of storage roots, mild patchy
Ugandan brown streak virus (UCBSV) yellow mosaic pattern on leaves, elongated brown
lesions on young green stems
Cassava common mosaic virus Mild yellow/chlorotic mosaic pattern on leaves, leaf
deformation
Cassava vein mosaic virus Chevron or ringspot pattern vein yellowing and
chlorosis, leaf deformation
Cassava green mottle virus Yellow spots and mottled mosaic pattern, slight leaf
deformation, occasionally stunted shoot growth and
small, woody storage roots
Cassava virus X No reported symptoms for any of these viruses
Cassava symptomless virus
Cassava Colombian symptomless virus
Cassava American latent virus
Cassava Ivorian bacilliform virus
Cassava Kumi viruses (A and B) Pronounced leaf mottle
Cassava virus C or Cassava Q virus Pronounced leaf fleck
Xanthomonas axonopodis (campestris) Angular leaf spots, leaf wilting, gum exudates, stem
pv. manihotis vascular necrosis, shoot dieback
Xanthomonas campestris pv. cassavae Angular leaf spots, leaf lesions and yellowing, gum
(Xanthomonas cassavae) exudates, primarily leaf symptoms
Erwinia carotovora sp. carotovora Pungent soft rotting of stems, stem cankers, leaf
wilting
Erwinia herbicola Soft rotting of affected tissues
Agrobacterium tumefaciens Crown galls on older lignified stem regions
Ralstonia (Pseudomonas) solanacearum Leaf wilting, leaf loss
Enterobacter cloacae Necrotic lesions with chlorotic halo, leaf wilting and
loss
Colletotrichum gloeosporioides Spots at tips of young leaf lobes followed by necrosis
Colletotrichum graminicola of affected tissues, stem cankers and visible fruiting
bodies, shoot dieback
Cercospora vicosae Large leaf spots without well-defined borders, leaf loss
Cercospora (Cercosporidium) henningsii Angular brown spots often with yellow halo, leaf
yellowing, leaf loss
Cercospora caribaea Small sunken, circular-angular white/yellowish brown
(Phaeoramularia manihotis) spots
Phoma (Phyllosticta) spp. Concentric rings, necrotic veins radiating from lesions,
cankers at base of petiole, leaf loss, shoot dieback
Sphaceloma manihoticola Extremely elongated stem internodes, think and weak
Elsinoe brasiliensis stem, cankers, occasionally leaf loss and shoot
dieback
Erisyphe manihotis Pale yellow lesions forming brown angular spots
Oidium manihotis
Uromyces spp. Orange-light brown pustules causing distortion of
veins, petioles and green stems
Cochliobolus lunatus Discoloration and increasing decay of affected stem
Botryodiplodia theobromae tissues, visible fruiting bodies
Fusarium spp. Sudden leaf wilting, severe leaf loss, roots exuding
Phytophthora spp. pungent watery liquid, complete decomposition of
Polyporus sulphureus roots
Leptoporus lignosus
Phaeolus manihotis
Rhizoctonia solani
Botryodiplodia theobromae
Sclerotium rolfsii (Corticium rolfsii)
Current Opinion in Plant Biology 2017, 38:50–58
54 Biotic interactions
Table 1 (Continued )
Disease name Causal agent
Fungal
Cassava dry (black) root rot Rosellinia necatrix
Armillariella mellea
Rigidoprous microporus (Fomes lignosus)
Scytalidium sp.
Cassava stem and root rot Diplodia manihotis
Sphaerostilbe repens
Verticillium dahlia
Cassava bud necrosis Uncharacterized fungus
Other or unknown
Cassava antholysis Mycoplasma-like organism
Cassava witches’ broom (CWB) Mycoplasma-like organism
Cassava frogskin disease (CFSD) Phytoplasma? Phytoreolike virus?
for breeding or development of transgenic CBB resistant
farmer-preferred varieties.
Successful transgenic approaches engineered in other
Xanthomonas-host interaction models may also prove suc-
cessful for generating durable tolerance to CBB. The
broad-spectrum microbe-associated molecular pattern
(MAMP) resistance gene elongation factor Tu receptor
(EFR) from Arabidopsis [64] blocks infection by several
bacterial pathogens when expressed in Nicotiana
benthamiana and tomato [65]. EFR could potentially
impart resistance to a suite of bacterial pathogens in
cassava as well. The resistance genes Xa21 from rice,
and Bs2 and Pflp from Capsicum annuum have been used
successfully to engineer resistance in the field to Xantho-
monas pathogens of rice [66], tomato [67] and banana [68],
respectively. These genes could also be successful in
resistance strategies against Xam in cassava. It should
be noted, however that host-pathogen resistance mecha-
nisms are complex and successful resistance approaches
in one host-pathogen interaction are not always success-
fully recreated in heterologous systems.
Other cassava diseases
There are relatively few reports and little research regard-
ing many viral and fungal cassava diseases, and several
diseases exist with uncertain or unknown causal agents
(Table 1). These diseases are seemingly less frequent or
devastating to cassava farming, or alternatively are under-
diagnosed and under-reported in comparison to the virus
and bacterial infections discussed above. Fungal diseases,
especially cassava anthracnose disease (CAD) that is
caused by the fungus Colletotrichum gloeosporioides f.sp.
manihotis (Figure 1), are more frequent in areas of high
humidity and seasons of higher rainfall but can be con-
trolled through fungicides and improved farm hygiene.
CAD molecular markers and QTLs have been identified
Current Opinion in Plant Biology 2017, 38:50–58
Typical symptoms
Black coloration of affected tissues, canker-like root
lesions, leaf yellowing and wilting, leaf loss, shoot
dieback
Similar symptoms to stem rot and root rot, also gum
exudates, leaf wilting and shoot dieback
Brown or grey fungal patches on the stem often
covering auxiliary buds
Greening of floral tepals and conversion into leafy
structures
Small leaves, stunted shoots, shortened stem
internodes, excessive branching, small leaves
Surface ridges and raised lip-shaped fissures on
storage roots, thin storage roots, occasionally mild
mosaic patterning on leaves
from several CAD resistant varieties [69,70] and the
first studies investigating the underlying molecular
mechanisms of CAD infection have identified a number
of CAD responsive cassava transcripts [71] and identified
specific cassava miRNAs and target genes involved in
CAD infection [72]. The insect Pseudotheraptus devastans
is a vector of CAD transmission [73]. Cassava witches’
broom (CWB) disease (Figure 1), thought to be caused by
the Candidatus phytoplasma [74], is an emerging problem
for farmers in South-East Asia and research is currently
ongoing to determine the mechanisms of transmission,
practices for control and treatment of infected material,
and sources of resistance to CWB for use in breeding
programs [75]. The causal agent of cassava frogskin
disease (CFSD) (Figure 1), which is an economically
important disease in Central and South America, is still
unknown and could be attributed to a phytoplasma or
viral agent [76,77].
Cassava disease control at field and farm
levels
Disease incidence and severity in cassava farming can be
reduced by using clean planting material and manage-
ment of insect vectors that spread many of the most
common and devastating diseases impacting cassava
fields. Farmer awareness of disease symptoms and the
need for controlled movement of infected cuttings is
essential. Early symptom identification and removal of
infected plants, especially for diseases such as CBSD that
causes devastating storage root losses but show only mild
symptoms in aerial tissues, is pivotal to disease control.
Increased capacity and implementation of rapid and
reliable field testing and surveillance programs will help
farmers to ensure accurate and timely monitoring and
reporting of cassava disease outbreaks (or their insect
vectors) at both regional and national levels. Increased
research and development of diagnostic assays for
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 Tackling agriculturally relevant diseases in the staple crop cassava (Manihot esculenta) McCallum, Anjanappa and Gruissem 55
economically important cassava diseases in South Amer-
ica and Asia, including CWB and CFSD, should also be
encouraged, as outbreaks may become more frequent and
widespread.
Farmers can employ disease control methods including
intercropping, crop rotation, fallow, planting timing and
weeding, which are effective in reducing disease severity
and incidence. Improvements in field practices, such as
spacing of plantings, handling of cuttings and field
hygiene are also recommended to improve disease out-
comes [78]. Cassava is a vegetatively propagated crop,
thus clean planting material of disease resistant or tolerant
varieties that are certified disease-free and multiplied
through in vitro meristem cultures should be made avail-
able to farmers each season. Broad availability of clean
cassava seed would greatly reduce the movement of
infected cuttings between farms and reduce disease load
and transmission through insect vectors. The recent
expansion of CBSD has been at least partially attributed
to increased whitefly vector populations [79].
Farmers should be educated on the benefits and encour-
aged to establish sustainable integrated pest management
strategies, through intercropping and biological control as
recommended by FAO [1]. Climate change models pre-
dict significantly increased temperatures in Africa by
2050 [80]. Although some cassava producing countries
will likely experience increases in pest incidence and the
emergence of more virulent cassava viruses, increased
temperatures are predicted to boost cassava productivity
in many African regions and even reduce cassava pests
and their distribution [81].
Both breeding and transgenic approaches must be
deployed in order to develop improved cassava varieties
with increased disease resistance, ideally to multiple
diseases. Understanding the underlying mechanisms of
susceptibility and resistance in each cassava pathosystem
will significantly contribute to breeding and transgenic
efforts, through identification of causal genes, QTLs and
genetic mapping of molecular markers [82]. QTLs and
molecular markers have assisted cassava breeding efforts,
however, even today the mode of inheritance of resis-
tance to the well-studied CMD viruses is still unclear
[83]. Employment of new methods such as induced
early flowering, high-throughput phenotyping, genomic
selection, development of double haploids, and other
accelerated and targeted breeding technologies can help
to build more robust resistance and facilitate develop-
ment of new disease-resistant varieties [83]. Inbreeding
depression is commonly observed in cassava breeding
[83], thus transgenic and genome editing strategies,
as well as introduction of disease resistance genes from
heterologous species, will also play a major role in the
development of pyramiding resistance to multiple cassava
diseases [84].
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Conclusions
Our understanding of the causal agents, molecular mech-
anisms of infection and disease progression, as well as
identification of genes underlying resistance has led to the
release of new disease resistant cassava varieties devel-
oped through breeding programs. Field testing of trans-
genic disease resistance traits is underway. As new and
increasingly virulent disease strains are identified and the
incidence of multiple disease infections rises in the field,
the need for development of varieties with strong, dura-
ble resistance to multiple pathogens is increasingly
important to food security and economic development,
particularly in Africa. Continued discovery of new resis-
tance mechanisms and breeding stocks, as well as
increased acceptance of transgenic technologies, will be
essential to tackle cassava diseases in the future.
Conflict of interest
There is no conflict of interest relating to this article.
Acknowledgements
We thank Prof. Hervé Vanderschuren (University of Liège, Belgium), Dr.
Hernan Ceballos and Dr. Paul Chavarriaga (CIAT, Colombia) for providing
images of cassava bacterial blight and cassava frogskin disease. Cassava
research in our laboratory is supported by the Bill & Melinda Gates
Foundation, the Swiss National Science Foundation, and ETH Zurich.
RBA was supported by the Research Fellow Partnership Programme of
ETH Global. We apologize to all colleagues whose relevant work could not
be cited because of space limitations.
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