Road Map for Cassava Landraces in ESC Africa – Page 1

A Road Map for the Collection, Documentation, Evaluation and Preservation of

Cassava Landraces in East, South and Central Africa
Morag Ferguson1*, Adriana Alercia2, Gueye Badara3, Yona Baguma4, Simon Bigirimana5, Able Chalwe6, Clair
Hershey7, Edward Kanju8, Robert Kawuki9, Heneriko Kulembeka10, Lava Kumar3, James Legg11, Thandie Lupupa12,
Christopher Abu Omongo9, Mamie Makumbu Binzunga13, Victor Manyong11, Geoffrey Mkamilo14, Ivone Muocha
Chimene15, Zacchary Muthamia16, Godfrey Mwila17, Grace Nakabonge9, Lawrent Pungulani18, Nzola-Meso
Mahungu19, Pheneas Ntawuruhunga20, Danièle Ramiaramanana21, Rojo Aina Ravalisoa21, Vincent Weyengo22,
Anabela Zacarias23, Michael Abberton3 & Claude Fauquet24

1
IITA, Nairobi, Kenya, orcid.org/0000-0002-7763-5173
2
Bioversity International, Rome, Italy
3
IITA, Ibadan, Nigeria
4
NARO, Kampala, Uganda
5
Institut des Sciences Agronomiques, Bujumbura, Burundi
6
Mutanda Research Station, Solwezi, Zambia
7
CIAT, Cali, Colombia
8
IITA, Sendusu, Uganda
9
NARO, Kampala, Uganda
10
TARI, Ukiriguru, Tanzania
11
IITA, Dar es Salam, Tanzania
12
SADC Plant Genetic Resources Centre, Lusaka, Zambia
13
INERA, Mvuazi, DRC
14
TARI, Ilonga, Tanzania
15
Eduardo Mondlane University, Maputo, Mozambique
16
KALRO, Nairobi, Kenya
17
ARI, Lusaka, Zambia
18
Malawi Plant Genetic Resources Centre, Lilongwe, Malawi
19
IITA, Kinshasa, DRC
20
IITA, Lusaka, Zambia
21
FOFIFA, Fianarantsoa, Madagascar
22
KALRO, Kakamega, Kenya
23
ARI, Maputo, Mozambique
24
GCP21, Cali, Colombia,

*Corresponding author: m.ferguson@cgiar.org, +254 733 524685

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Introduction:

Global population growth is on a steep trajectory, and by 2070 most of the world's population growth
will take place in Africa. Of the 2.4 billion additional people projected between 2015 and 2050, 54% will
be added in Africa with the population expanding from 0.82 billion in 2000 to 2.53 billion in 2050, a
growth of 209% (United Nations, 2017). By 2100, five of the top 10 largest cities will be in Africa
(Hoornweg and Pope, 2017).

Cassava (Manihot esculenta Crantz), being a major root starch staple crop of Africa, will no doubt have a
critical role to play in feeding this burgeoning population in Africa. Described as the “classic food security
crop” (DeVries and Toenniessen 2001), cassava offers the advantage of a good secure harvest under
erratic climatic conditions and infertile soils. Its high starch content (20-40%) makes cassava an
important energy source both for human consumption and industrial purposes, e.g. animal feed,
industrial starch, and biofuel. In East, South and Central (ESC) Africa 90% of cassava is consumed on-
farm, or sold at local markets for local consumption.

Cassava has more total fresh tonnage production in sub-Saharan Africa than any other crop (exceeding
157 million tonnes in 2016 (FAOSTAT 2018)), including maize and plantain, and is the fourth most
important source of calories in the developing world after the cereal crops; wheat, maize, and rice.
Worldwide, it feeds an estimated 700 million people directly or indirectly. Despite the high fresh
tonnage of cassava on the continent, yields are low (on average nearly 10.7t/ha; 8t/ha in DRC, 12t/ha in
Kenya and 5t/ha in Tanzania) compared to those achieved in some South Asian countries (China
(16t/ha), Indonesia (23.5t/ha), Thailand (21t/ha) and India (22t/ha) (FAOSTAT 2018)). The low average
yields in Africa are caused by many factors including susceptibility of commonly grown farmer varieties
to major diseases and pests, inherently low yields of these landraces and generally no fertilizer input.
Breeding for improved pest and disease resistance, and yield, while taking into account farmer and
consumer preferences in terms of growth, appearance, taste, cooking and processing qualities, to
encourage adoption of new varieties, will be an important component of a wholistic strategy to feed the
expanding rural and urban populations in Africa. Progress in plant breeding depends on access to
appropriate genetic variability upon which selection pressure can be applied.

The International Institute of Tropical Agriculture (IITA), with its headquarters in Ibadan, Nigeria, is
mandated for the improvement of cassava in Africa. It’s Genetic Resources Centre (GRC) holds
approximately 3,500 accessions of cassava for addressing current and future challenges to food
production and security. The vast majority of these are landraces from West Africa. Less than 2% of
cassava accessions are from ESC Africa and CIAT does not have any accessions from that region. There is
no substantial cassava germplasm conserved in regional/national genebanks in ESC Africa.
Cassava has existed in ESC Africa since it was introduced from the Americas, its center of origin and
domestication, by the Portuguese traders during the 16 th century (Carter et al. 1995). Its’ cultivation was
encouraged by early administrators in the region, and it spread rapidly. Over the past 400 years it has
adapted to a range of soil and climate conditions in the region and has been selected by farmers
according to their local preferences. In addition, some landraces have evolved alongside prevalent pests
and diseases, such cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Some of
these local landraces probably harbor valuable sources of pest and disease resistance as well as
‘adaptive gene complexes’ to both environmental conditions and farmer preferences. An example from
West Africa is the qualitative ‘CMD2’ type resistance, which confers high levels of resistance to cassava

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mosaic disease (CMD) and was first identified in landraces. It is now widely adopted in CMD resistance
breeding programs (Rabbi et al. 2014).
There are numerous compelling reasons why it is vital to collect and conserve cassava landraces from
ESC Africa, and make them available to researchers and breeders. Cassava in the region is subject to
heavy virus disease pressure, with two diseases predominating; CBSD and CMD. The majority of
landraces are known to be highly susceptible to both CMD and CBSD. Due to severe reduction in yields
and decline in performance of planting material, farmers are abandoning cultivation of the more
susceptible landraces which is resulting in loss of cassava genetic diversity. Most landraces in
Madagascar were lost during a severe CMD epidemic in 1934–36 (Cours et al. 1997). A similar epidemic
struck Uganda in the 1990s and led to the substantial elimination of the most susceptible landraces
(Legg et al. 2011). This drove the adoption of improved CMD resistant varieties from West Africa (mainly
NASE 1, 2 and 3). These improved cultivars were good for making flour (ugali) but were not appropriate
for consumption of boiled roots. As the pandemic abated, farmers gradually went back to growing their
traditional varieties which were still available and which had preferable organoleptic and cooking
qualities.
CBSD had previously been confined to coastal regions of southern and eastern Africa, where it caused
moderate yield losses (Nichols 1950; Hillocks 2003; Legg and Thresh 2003). Since 2003-04 it spread
rapidly and reached pandemic proportions especially around the Great Lakes regions in East Africa (Legg
et al. 2011; Alicai et al. 2007, Mulimbi et al. 2012; IITA 2012; Bigirimana et al. 2011; Tomlinson et al.
2013). It is feared that if the disease is not brought under control quickly, it may spread through central
Africa and even invade West Africa. For a review of CBSD, see Patil et al. (2014). In Africa, CMD occurs in
almost all cassava growing regions where it causes a yellow chlorotic mosaic together with leaf
deformation and plant stunting (Storey 1936). Legg et al. (2006) reported an estimate for total loss due
to CMD in Africa of 34 million Mt (in 2005). The causal viruses of both CBSD and CMD are spread by the
whitefly Bemisia tabaci Gennadius (Dubern 1994, 1979) and use of infected stem cuttings as planting
material. Susceptible landraces, which may harbor other valuable traits, are under threat of extinction
from virus pandemics and/or replacement by improved varieties. In addition, lack of access to
germplasm hinders progress in research, breeding and crop improvement.
For all these reasons, it is urgent that the cassava community act together to collect, evaluate,
identifying and preserve this valuable germplasm and indigenous knowledge for the benefit of farmers
and to allow breeders to improve cassava productivity in the ESC Africa region. This need is expressed by
Kawuki et al. (2013) who studied the genetic diversity at 26 simple sequence repeat (SSR) loci in 1401
cassava landraces and farmer varieties from Tanzania (270 genotypes), Uganda (268), Kenya (234),
Rwanda (184), Democratic Republic of Congo (DRC; 177), Madagascar (186) and Mozambique (82). They
found moderate genetic variation in the region with some differentiation among countries in both
varieties and landraces, with germplasm from Tanzania occupying a central position. Few if any of these
genotypes are conserved in any kind of repository.
Cassava viruses play a pivotal role in cassava breeding in ESC Africa, and in how germplasm is, or could
be, accessed and managed. Due to the virus problems in ESC Africa, particularly CBSD, movement of
cassava stakes (stem pieces) is rightly regulated by phytosanitary requirements, for example cassava
stakes cannot be moved from the Coastal Zone to the Lake Zone in Tanzania without a phytosanitary
certificate verifying their virus-free status. However, exchange of germplasm between countries is
important for access to diversity in breeding (Tumwegamire, 2018). This has been a major constraint to
progress in breeding. In addition, access to virus-free stocks of improved varieties for pre-basic seed has
hampered the development of a clean seed system in the region.

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Production of virus-free germplasm can be a relatively long process and involves complex procedures
including meristem tip culture, and chemo- and thermo-therapies. Tumwegamire et al. (2018) describes
one of the first efforts to eliminate viruses from, and distribute among countries in ESC Africa, the best
CMD/CBSD resistant/tolerant landraces and breeding lines from the region.
Under the auspices of the Global Cassava Partnership for the 21 st Century (GCP21), a recognized global
organization within the cassava community, and IITA, a workshop was held in Dar-es-Salaam, Tanzania,
with the goal to establish a Road Map for the collection, evaluation, documentation, preservation and
use of cassava landraces in ESC Africa, supported by all participants. This meeting brought together
specialists in cassava breeding and conservation from the region, as well as experts in the various
disciplines required to conserve, document and share cassava germplasm and associated farmer
knowledge in the region. Workshop discussions focused on how to efficiently acquire, conserve and
exchange cassava germplasm, and document and disseminate knowledge and farmer preferences
related to germplasm in ESC Africa. This article defines the vision for the future that was articulated at
the workshop, and outlines the necessary steps that need to be taken to reach that goal.
Vision for Germplasm Management in ESC Africa:
The workshop participants defined the vision for the conservation and use of cassava landraces in ESC
Africa as: a comprehensive collection of landraces, accompanied by complete passport data and farmer
knowledge, safely conserved pathogen-free for the long-term in duplicated genebanks, and fully
evaluated for use in breeding programs.
It was recognized that although this was the ‘core’ traditional responsibility of a genebank, there were
two important additional roles that should to taken up due to a void in these services in the region, with
the genebank vision being extended to a ‘germplasm centre’ with (1) responsibilities of conserving, and
providing access to, important breeding lines and (2) feeding virus free germplasm (whether landrace or
improved varieties) into a seed system. Breeders frequently complain of losing breeding material in the
field, and not being able to access virus-free stocks of preferred varieties that they can move around the
region. This seriously hampers progress in breeding. Quick access to correctly identified and tracked,
virus-free plantlets of preferred varieties or landraces is a major limitation in both breeding and seed
systems in ESA Africa. Similar skill sets, facilities and technologies are required by a traditional genebank
and by virus-free pre-basic seed suppliers. Both need access to virus elimination procedures including
thermotherapy, meristem tip culture and tissue culture. Tissue culture is also required for storage of
virus-free foundation plantlets. In addition, access to genotyping for varietal identification, virus
diagnostics to certify virus-free status and germplasm multiplication facilities are required. In addition,
both disciplines require interaction with phytosanitary regulatory agencies within countries. A
germplasm centre could produce pre-basic seed to be fed into basic seed production which would
eventually be distributed to farmers and enter both formal and informal seed systems. This would make
germplasm diversity more accessible to both farmers or their organization, NGOs (Adam et al. 2018;
Westengen et al. 2018) and breeders, thus enhancing sustained utilization of diversity at the farm level.
In addition, the centres would both be a safe entry point of novel genetic variation into the region from
West Africa or South America, and operate under strict quarantine regulations. The potential pivotal
role of such a germplasm centre is illustrated in Figure 1.
The vision is based on the development of two in vitro germplasm centres, one at the National Crop
Resources Research Institute (NaCRRI), Uganda, which is also designated as the East African Agricultural
Productivity Project (EAAPP) Centre of Excellence for Cassava, and the other at IITA-Tanzania, based in
Dar-es-Salaam using common, state of the art methodologies for collection, identification,
documentation, multiplication, distribution and use of germplasm together with farmers’ knowledge. A

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unified and coherent approach across these two facilities will greatly facilitate increased range and
scope of the collection, responding to the urgent need throughout the region. The ‘standard operating
procedures‘ (SOPs) developed for this are likely to be seen as templates for other such activities not only
in cassava but (at least) in clonal crops in general, e.g. they will be very relevant to collection and
conservation of yams (Dioscorea spp.), bananas/plantains, taro and sweet potato. In the longer term,
the virus-free germplasm will be duplicated at the Genetic Resources Centre (GRC) in IITA, Ibadan,
Nigeria.
In vitro conservation, as opposed to field genebanks, would be prioritized, however if resources allowed
field genebanks would be considered. Field genebanks would have to be located in low disease-pressure
areas, as susceptible genotypes could be lost in high disease-pressure environments. In such
environments, field genebanks could provide ready access to characterization and evaluation and are
‘low tech’ so could be implemented relatively easily at reasonable cost. They can be a backup to a more
secure in vitro system. Field genebanks could not be used as a source of material for international
germplasm transfer.
There are a number of activities, studies and milestones that need to be completed for the strategy
outlined above to become a reality. These activities are outlined in Action Themes below and in Table 1,
and illustrated in Figure 2:
Action Theme 1: Documentation for germplasm acquisition and exchange
 Collection proposals must be developed with host-country collaborators, describing the
collection activities, including the taxa and information to be collected, foreign and host-country
participants, dates, locations to be visited, collecting protocols, possible benefits to the host
country, intended use of the germplasm and budget. Based on this document, prior informed
consent will be sought from the host country authorities (See Moore and William (2011) for
more information).
 The IITA-GRC cassava collection is held ‘in trust’ for the international community under Article
15 of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). In
general the ITPGRFA supports the multilateral system (MLS) for germplasm exchange.
Distribution of cassava accessions is carried out using the Standard Material Transfer Agreement
(SMTA). This incorporates arrangements under the ‘access and benefit sharing (ABS) regime’ by
which commercialization of products arising from germplasm received under an SMTA triggers
payment into an ABS fund. All potential participating countries in this initiative, including
Democratic Republic of Congo, Uganda, Kenya, Tanzania, Rwanda, Burundi, Mozambique,
Madagascar, Angola and Zambia, are contracting parties of the International Treaty on Plant
Genetic Resources for Food and Agriculture (ITPGRFA). Therefore, as an Annex 1 crop (part of
the multilateral system), cassava germplasm will be collected and exchanged within ESC African
countries following the regulation of the ITPGRFA.
 Discussions must be held with appropriate authorities to determine whether additional
conditions are required beyond the SMTA, and if necessary develop a customized MTA within
the framework of ‘Nagoya Protocol’ (Buck and Hamilton 2011; Kamau et al. 2010) that details
conditions for use of germplasm through specific agreements.
 Support must be gained from relevant quarantine authorities to obtain necessary permits for
exchange of material.

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 A realistic plan must be developed for the long-term conservation of these new collections,
which clearly includes commitments from IITA and NaCRRI, as well as integration into other
ongoing global genetic resources initiatives.
Action Theme 2: Germplasm and Indigenous Knowledge Collection
As a result of the workshop in Dar-es-Salaam, and the urgency placed on the need for collections by
NaCRRI, a standardized collection form was developed for both cassava germplasm and farmer
knowledge (See Annex 1). The germplasm collection form takes into account known ontologies, such as
those developed by CIAT and Bioversity International.
The germplasm collection methodology takes into consideration recent evidence for the existence of
genetic variation within cassava landraces of the same name. This is commonly recognized in other
crops, but has not until recently been appreciated in the clonally propagated crop, such as cassava. This
variation is addressed through collection of stakes from among various plants of a single farmer-named
variety, and subsequent genetic fingerprinting.
Steps that need to be taken to implement this Action Theme include:
 An understanding of the genetic variation within landraces should be obtained to validate the
collection strategy recommended in Annex 1. This will require a separate pilot study.
 Personnel need to be trained in the use of the collection forms and on how to conduct semi-
structured interviews with farmers. This could be achieved through a series of training
workshops within country for participating NARS. These workshops could also serve to field test
the collection SOPs in each country to determine their appropriateness to the prevalent social
and agronomic environment.
 Germplasm collection missions need to be carried out by NARS and IITA and should be preceded
by a careful analysis of proposed collection sites based on existing knowledge of genetic
diversity, use and farmers’ knowledge and level of threat from disease, climate change or other
elements.
 One copy of germplasm should be retained in-country by NARS and maintained if possible in a
field or in vitro genebank. Another copy should be transferred to one of the germplasm centres
in Dar-es-Salaam or NaCRRI for virus cleaning and in vitro conservation and if possible safety
duplicated at the other germplasm centre. This is in line with the ‘two germplasm centre’ vision
outlined earlier.
Action Theme 3: Phytosanitation
Germplasm collected must be virus tested and virus-free germplasm stocks should be generated for
conservation and exchange. Production of virus-free stock however is a time consuming and sometimes
challenging procedure, due to genotype-specific requirements for in-vitro establishment. Different
methods including thermotherapy, chemotherapy and meristem culture are being used for this purpose
(Kumar et al. 2012; Wasswa 2010; Maruthi et al. 2014)(Figure 3). Therefore, the following actions are
needed to implement this Action Theme:
 Although standard protocols are available at CIAT and IITA and elsewhere for the establishment
of cassava varieties in vitro, some landraces do not respond well to these protocols
(Tumwegamire et al. 2018, Acedo and Corazon 2018). Alternative protocols must be
documented and a pipeline developed for the ultimate robust growth of all varieties in vitro.

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 Establish a laboratory for phytosanitation at the germplasm centres and evaluate in the
laboratory different protocols for virus elimination.
 Document sensitive, cost-effective and reliable detection procedures for indexing of the
causative viruses of CMD and CBSD, including use of deep sequencing methods (Zheng et al.
2017). Although several procedures have been established, no consensus exists within the
community as to the most appropriate methods for virus indexing. Therefore there is a need to
develop SOP for virus indexing and certification of plantlets for freedom from known viruses.
Laboratory facilities are already available to implement diagnostics in the ESC Africa region.
Action Theme 4: DNA Fingerprinting
With the advent of next-generation sequencing (NGS) technologies, the cost of sequencing has
plummeted, and fingerprinting methodologies that utilize NGS have developed rapidly (Metzker 2010).
One of these approaches utilizes a simplified reduced-representation library (Altshuler et al. 2000)
sequencing method to simultaneously discover and genotype a high density of single nucleotide
polymorphism (SNP) markers. Several SNP fingerprinting technologies exist, including genotyping-by-
sequencing (GBS) (Elshire et al. 2011), Restriction-Associated DNA (RAD) tag sequencing and DaRTSeq
(Diversity Arrays Technology Pty. Ltd.). These methodologies are now well established for cassava.
A standardized genotyping technology should be adopted for all cassava clones coming into the
germplasm centre. This will enable the immediate identification of duplicate genotypes, and assess
levels of variation within landraces. This will enable decisions to be made as to whether a variety should
be maintained as a new accession or discarded as a duplicate. The aim should be to maintain accessions
as a single genotype with no or limited within-accession variation. The cut-off to determine what level of
variation constitutes a new genotype will have to be defined once more data on existing levels of
variation within landraces is accumulated, or known duplicates are genotyped (Rabbi et al. 2015).
Once a new accession is designated, a ‘type-specimen’ genotype will be assigned, against which other
genotypes can be compared. In the case where several genotypes exist with the same name eg. ‘Albert’,
if variants are sufficiently different, they will be distinguished by appropriate suffixes eg. Albert-1,
Albert-2. If different names exist for the same genotype, alternative names will be documented.
To genotype a larger number of samples, for confirmation of identity, a sub-sample of SNPs distributed
across the genome will be selected and be made available for cheaper array-based or single SNP
genotyping. One such panel of 36 SNPs specifically designed from ESC Africa landraces is already
available (Ferguson, 2018, Oyesigye et al. 2018) and is available for use through LGC Ltd. and High-
throughput Genotyping Service (HTPG) (http://cegsb.icrisat.org/high-throughput-genotyping-project-
htpg/). This situation may well change as sequencing costs are driven down and bioinformatics pipelines
for distilling sequence data into a simple fingerprint format improve. It is envisaged that DNA extractions
will outsourced in conjunction with genotyping service providers through companies such as Intertek
Group plc.
For implementation of this Action Theme, the following steps need to be taken:
 Decisions need to be made on how much variation defines a new genetic resource, to be
maintained as a new accession. This limit would also define which incoming germplasm is
discarded as not being distinct enough. This requires prior information on the genetic diversity
within cassava landraces as outlined as a required Pilot study under Action Theme 1. Rabbi et al.
(2015) used Ward’s distance of 0.05 to define the threshold below which two clones
represented the same variety. This was based on the genotyping of known duplicates.
Action Theme 5: In vitro conservation and cryopreservation

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NaCRRI has already secured funding to equip a germplasm centre, including in vitro, for a range of crops
including cassava. The new facility at IITA-Tanzania is yet to be equipped. A modest in vitro facility is
envisaged with two laminar flow hoods, autoclaving equipment and short-term and longer-term growth
rooms. Cryopreservation is becoming an increasingly viable option and the appropriateness of this form
of conservation in East Africa will be assessed.
For implementation of this action theme, the following needs to be accomplished:
 Equipment needs to be sourced and purchased for equipping the in vitro facility at IITA-Tanzania
 Further research to optimize cryopreservation for cassava is required
Action Theme 6: Evaluation and Characterization
Accessions within the genebanks should, within time, be characterized and evaluated to enhance
utilization. Standard germplasm characterization and evaluation procedures are available through IITA
and CIAT, although appropriate methodologies and scales for scoring traits that are important for
consumer preferences including ‘mealiness’ and ‘cookability’ must be developed and agreed upon.
Action Theme 7: Documentation and knowledge sharing
Documentation of collected germplasm will include geo-referenced passport data and farmer
knowledge (the latter using methodologies as described under Action Theme 2). Accession level data will
be compatible with the current IITA germplasm database and also for migration to the web based portal
Genesys2 being developed by all CG Centre genebanks and the Crop Trust. Information on Genesys can
be found at http://www.genesys-pgr.org/.
For this Action Theme to be implemented, the following is required:
 The IITA germplasm database must be mirrored at the germplasm centre at IITA - Tanzania
 Structures for documentation of farmer-knowledge and SNP fingerprint data must be
incorporated into the IITA germplasm database
 Analytical tools for comparing and identifying variation and quantifying the extent of variation
among genotypes must also be made available
Action Theme 8: Germplasm Exchange
Germplasm exchange within the region and availability of collected germplasm to cassava breeders and
all other users is a crucial component of the proposed germplasm centre, including the supply of pre-
basic seed (plantlets). Two aspects are important for this to happen:
 The ITPGRFA provides the overarching framework for germplasm conservation, exchange and
use
 National plant protection agencies must be well integrated into the entire germplasm exchange
procedure by awareness creating and training.
 Knowledge and experience related to the policy framework, phytosanitary and quarantine
aspects and the biological and physical aspects of preparing and transporting germplasm (tissue
culture plantlets, stem cuttings and botanical seed) must be transferred to staff at the proposed
germplasm cnetres at NaCRRI and IITA-Tanzania and associated national plant health regulatory
agencies. It is likely that much of this knowledge could be transferred from the IITA Genetic
Resources Centre in Ibadan, Nigeria.

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Action Theme 9: Analysis of Indigenous Knowledge (IK) and incorporation into a more farmer-centric
approach to cassava breeding
Adoption of modern varieties has been considerably lower in orphan crops (such as cassava), compared
to the cereal staples and particularly low in Africa as opposed to Asia and Latin America (Evenson 2003,
Renkow and Byerlee, 2010). Rabbi et al. (2015) were able to match approximately 30% of 917 plants
sampled to improved varieties in an adoption survey in Ghana. Several factors contribute towards this
variable uptake of highly performing varieties (HPVs), including lack of access to seeds, agricultural
inputs and credit. The suitability of new varieties to meet end-user demand has been little researched,
but may be a factor, particularly as demands change for new market opportunities.
In ESC Africa over 90% of cassava is consumed on-farm, or sold at local markets for local consumption. It
is envisaged that this ‘market’ will not change dramatically in the near future, although supply to local
markets may increase as cities grow. Demand for pro-vitamin A enhanced cassava may also increase. It
is important to firstly understand these markets and their dynamics, and secondly breed cassava
varieties with suitable characteristics to meet market requirements if adoption of new varieties is to be
improved. To assist this process, the following activities should be undertaken:
 Design questionnaires to capture ‘market research’ at the time of germplasm collection to drive
a more design-led approach to breeding. Decisions on determining the preferred traits for which
to breed new varieties are paramount for success. Experience in collection of ‘market data’ can
be drawn from both the public and private sectors which have considerable experience
worldwide in developing crop varieties that address the needs of customers.
 Collect information relating to the most frequent constraints limiting adoption (for example
what factors accelerate or limit new variety uptake; what is the relative importance of varietal
traits, in comparison with other factors limiting uptake).
 Farmer knowledge and market information collected at the time of germplasm collection must
be analyzed and summarized to inform breeders on farmer preferences and guide appropriate
breeding objectives. Information should be considered both from the home processing and
consumption perspective, influencing food security, as well as an income generation
perspective, taking particularly female and youth preferences into consideration.
 Workshops must be conducted to explore how farmer-knowledge and market information can
be analyzed to inform plant breeding for better adoption of improved varieties and yield gains. It
is anticipated that the collection of this information, in the longer term, will lead to increased
levels of adoption by small scale farmers of new crop varieties that meet market needs.
Conclusions and the way forward
In ESC Africa the vast majority of cassava is grown by smallholder farmers for local consumption, yet
there is a dearth of information on farmer preferences and farmer knowledge, in addition to a lack of
access of farmer varieties by cassava breeders. This lack of ‘farmer-centric’ information and germplasm
means that breeders may not fully understand the subtleties of farmer preferences with implications for
varietal adoption of improved germplasm. In addition, cassava landraces are gradually displaced
especially in areas where pests and diseases, especially CMD and CBSD, pressure is high, possibly leading
to narrow genetic diversity and erosion of landraces.
This ‘Road Map’ outlines a strategy for the collection, establishment of pest and disease-free stocks and
documentation of traditional knowledge of cassava germplasm from SEC Africa for the benefit of
millions of cassava farmers and conservation of natural diversity. The state-of-the-art SOPs described
are compliant with standard international procedures for conservation, use and exchange of germplasm.

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Funding must be secured if the majority of the activities outlined in this ‘Road Map’ are to be
implemented. It is anticipated that scientists in the ESC Africa region together with the relevant global
stakeholders will work together to raise resources for the implementation of this vision and strategy.
References

Acedo, Z. V., & Corazon, U. L. (2008). Rapid propagation of released Philippine cassava varieties through
tissue culture. Journal of Root Crops, 34(2), 108–114.
Adam, R. I., Badstue, L., & Sindi, K. (2018). The dynamics of smallholder farmers’ acquisition and
distribution of sweetpotato vines in the Lake Victoria Zone Region, Tanzania. Food Security, 10(2),
339-350, doi:10.1007/s12571-018-0776-5.
Alicai, T., Omongo, C., Maruthi, M., Hillocks, R., Baguma, Y., Kawuki, R., et al. (2007). Re-emergence of
cassava brown streak disease in Uganda. Plant Disease, 91, 24-29.
Altshuler, D., Pollara, V. J., Cowles, C. R., Van Etten, W. J., Baldwin, J., Linton, L., et al. (2000). An SNP
map of the human genome generated by reduced representation shotgun sequencing. Nature , 407,
513-516. DOI:10.1038/35035083
Bigirimana, S., Barumbanze, P., Ndayihanzamaso, P., Shirima, R., & Legg, J. (2011). First report of cassava
brown streak disease and associated Ugandan cassava brown streak virus in Burundi. New Disease
Reports, 24, 26,DOI: 10.5197/j.2044-0588.2011.024.026
Buck, M., & Hamilton, C. (2011). The Nagoya Protocol on Access to Genetic Resources and the Fair and
Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity.
Review of European Community & International Environmental Law, 20, 47-61. DOI:
/10.1111/j.1467-9388.2011.00703.x.
Carter, S., Fresco, L., Jones, P., & Fairbairn, J. (1995). Introduction and diffusion of cassava in Africa. (Vol.
Guide No. 49, pp. 32): International Institute of Tropical Agriculture.
Cours, G., Fargette, D., Otim-Nape, G., & Thresh, J. (1997). The epidemic of cassava mosaic virus disease
in Madagascar in the 1930s-1940s: lessons for the current situation in Uganda. Tropical Science
(United Kingdom).
DeVries, J., & Toenniessen, G. (2001). Securing the Harvest: biotechnology, breeding, and seed systems
for African crops. Wallingford, Oxon, UK: CABI Publishing.
Dubern, J. (1979). Quelques propriétés de la Mosaïque Africaine du Manioc. I : La transmission.
Phytopathologische Zeitschrift, 96, 25-39.
Dubern, J. (1994). Transmission of African cassava mosaic geminiviruses by the whitefly (Bemisia tabaci).
Tropical Science, 34, 82-91.
Elshire, R., Glaubitz, J., Sun, Q., Poland, J., Kawamoto, K., & al., (2011). A robust simple genotyping-by-
sequencing (GBS) approach for high diversity species. PLoS ONE, 6, DOI:
10.1371/journal.pone.0019379.
Evenson, R. E. (2003). Crop Variety Improvement and it's Effect on Productivity. Wallingford, UK: CABI
Publishing.
FAO, & IFAD (2001). The Global Cassava Development Strategy and Implementation Plan. Vol. 1. In
Proceedings of the validation forum in the global cassava development strategy, Rome, 26-28 April
2000.
FAOSTAT (2018). FAOSTAT. http://faostat.fao.org.
Ferguson, M. (2018). A Panel of 36 SNPs for Quality Control in Cassava Research and Breeding. SP02-06
poster presentation. GCP21 IV International Cassava Conference, Cotonou, Benin, June 11-15, 2018.
Hillocks, R. J. (2003). Cassava brown streak virus disease: Summary of present knowledge on
distribution, spread, effect on yield and methods of control. In J. Legg, & R. Hillocks (Eds.),

11
 Road Map for Cassava Landraces in ESC Africa – Page 12

Proceedings of International Workshop, Mombasa, Kenya, 27-30 October 2002, (pp. 23-27): Natural
Resources International Limited, Aylesford, UK
Hoornweg, D. and Pope, K. (2017). Population predictions for the world’s largest cities in the 21st
century. Environment and Urbanization 29: 195-216.
IITA (2012). Map database for GLCI project cassava pest and disease surveys conducted in six countries
of East and Central Africa. Accessed, November 3rd, 2014.
Kamau, E. C., Fedder, B., & Winter, G. (2010). The Nagoya Protocol on Access to Genetic Resources and
Benefit Sharing: What is new and what are the Implications for Provider and User Countries and the
Scientific Community? Law, Environment and Development Journal, 6, 246.
Kawuki, R. S., Herselman, L., Labuschagne, M. T., Nzuki, I., Ralimanana, I., Bidiaka, M., et al. (2013).
Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern
and central Africa. Plant Genetic Resources, 11, 170-181. DOI: 10.1017/S1479262113000014.
Kumar, L., Oguntade, O., & Gueye, B (2012). Safe exchange of cassava and yam germplasm. In The Roots
and Tubers of Development and Climate Change: Proceedings of the 16th Triennial Symposium of
the International Society for Tropical Root Crops (ISTRC), Federal University of Agriculture,
Abeokuta, 23-28 September, 2012. p.77.
Legg, J., Owor, B., Sseruwagi, P., & Ndunguru, J. (2006). Cassava Mosaic Virus Disease in East and Central
Africa: Epidemiology and Management of a Regional Pandemic. Advances in Virus Research, 67, 355-
418.
Legg, J. P., Jeremiah, S. C., Obiero, H. M., Maruthi, M. N., Ndyetabula, I., Okao-Okuja, G., et al. (2011).
Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus
pandemics in Africa. Virus Research, 159, 161-170. DOI: 10.1016/j.virusres.2011.04.018.
Legg, J. P., & Thresh, J. M. (2003). Cassava virus diseases in Africa. In Proceedings of the First
International Conference in Plant Virology in Sub-Saharan Africa. 4th -8th June, Ibadan, Nigeria,
2003 (pp.517-552)
Maruthi, M. N., Whitfield, C. W., & Legg, J. P. (2014). A Laboratory Manual in Virus - indexing, chemo-
and thermo-therapies, and micro propagation for generating virus-free cassava plants. Natural
Resources Institute, University of Greenwich.
Metzker, M. L. (2010). Sequencing technologies [mdash] the next generation. Nature Reviews Genetics
11, 31-46. DOI: 10.1038/nrg2841
Moore, G. and Williams, K.A. (2011). Chapter 2: Legal issues in plant germplasm collecting. In: Collecting
Plant Genetic Diversity: Technical Guidelines – 2011 Update. Guarino L, Ramanatha Rao V, Goldberg
E, editors. Bioversity International, Rome, Italy. ISBN 978- 92-9043- 922- 6.
Mulimbi, W., Phemba, X., Assumani, B., Kasereka, P., Muyisa, S., Ugentho, H., et al. (2012). First report of
Ugandan cassava brown streak virus on cassava in Democratic Republic of Congo. New Disease
Reports, 26, DOI: 10.5197/j.2044-0588.2012.026.011.
Nichols, R. F. J. (1950). The brown streak disase of cassava: distribution, climatic effects and diagnostic
symptoms. East African Agricultural Journal, 15, 154-160.
Oyesigye E., Zacarias A., Mondjana A., Magaia H. and Ferguson M. (2018). Single nucleotide
polymorphism (SNP) diversity of cassava genotypes in relation to cassava brown streak disease in
Mozambique. Plant Genetic Resources doi:10.1017/S1479262118000126
Patil, B. L., Legg, J.P., Kanju, E., & Fauquet, C. M. (2014). Cassava brown streak disease: A threat to food
security in Africa. Journal of General Virology. DOI: 10.1099/jgv.0.000014
Pita, J., Fondong, V., Sangare, A., Otim-Nape, G., Ogwal, S., & Fauquet, C. M. (2001). Recombination,
pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of
severe cassava mosaic disease in Uganda. Journal of General Virology, 82, 655-665.

12
 Road Map for Cassava Landraces in ESC Africa – Page 13

Rabbi, I., Hamblin, M., Gedil, M., Kulakow, P., Ferguson, M., & Ikpan, A. (2014). Genetic mapping using
genotyping-by-sequencing in the clonally propagated cassava. Crop Sci, 54(4), 1384 - 1396.
Rabbi, I., Kulakow, P., Manu-Aduening, J., Dankyi, A., Asibuo, J., Parkes, E., et al. (2015). Tracking crop
varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta
Crantz). BMC Genetics, 16(1), 115.
Renkow, M., & Byerlee, D. (2010). The impacts of CGIAR research: A review of recent evidence. Food
Policy, 35, 391-402. DOI: 10.1016/j.foodpol.2010.04.006.
Storey, H. (1936). Virus diseases on East African plants. VI. A progress report on the studies of the
diseases of cassava. East African Agricultural Journal, 2, 24-39.
Tomlinson, J., Ostoja-Starzewska, S., Adams, I., Miano, D., Abidrabo, P., Kinyua, Z., et al. (2013). Loop-
mediated isothermal amplification for rapid detection of the causal agents of cassava brown streak
disease. Journal of Virological Methods, 191, 148-154.
Tumwegamire, S., Kanju, E., Legg, J., Shirima, R., Kombo, S., Mkamilo, G., et al. (2018). Exchanging and
managing in-vitro elite germplasm to combat Cassava Brown Streak Disease (CBSD) and Cassava
Mosaic Disease (CMD) in Eastern and Southern Africa. Food Security 10: 351-368
United Nations, Department of Economic and Social Affairs, Population Division (2017). World
Population Prospects: The 2017 Revision, Key Findings and Advance Tables. Working Paper No.
ESA/P/WP/248.
Wasswa, P. (2010). Optimisation of in vitro techniques for cassava brown streak virus elimination from
infected cassava clones. African Crop Science Journal, 18, 235-241.
Westengen, O. T., Skarbø, K., Mulesa, T. H., & Berg, T. (2018). Access to genes: linkages between
genebanks and farmers’ seed systems. Food Security, 10(1), 9-25, doi:10.1007/s12571-017-0751-6.
Zheng, Y., Gao, S., Padmanabhan, C., Li, R., Galvez, M., Gutierrez, D., et al. (2017). VirusDetect: An
automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology, 500,
130-138, doi:https://doi.org/10.1016/j.virol.2016.10.017

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Table 1: Themes and Actions for ‘A Road Map for the Collection, Documentation, Evaluation and
Preservation of Cassava Landraces in South, East and Central Africa’

Action Theme 1: Documentation for germplasm acquisition and exchange

 Collection proposals must be developed with host-country collaborators.
 Based on collection proposals, prior informed consent must be sought from host-country authorities
 Discussions must be held with authorities in all collaborating countries regarding the appropriateness of
the Standard Material Transfer Agreement (SMTA) and if necessary develop a customized MTA.
 Support must be gained from relevant quarantine authorities to obtain necessary permits for exchange of
material.
 A realistic plan must be developed for the long term maintenance of these new collections.

Action Theme 2: Germplasm and Indigenous Knowledge Collection

 An understanding of the genetic variation within landraces must be obtained to validate the
recommended collection strategy outlined in Annex 1.
 Prioritization of countries and regions for germplasm collection based on perceived importance of
diversity and on threat from CBSD and CMD.
 A germplasm collection form that has been prepared by IITA and NaCRRI must be field tested in all target
countries and approved by collaborating parties.
 Collection teams must be established and trained in collection methodologies.
 One copy of germplasm should be retained in-country by NARS and maintained if possible in a field or in
vitro genebank.
 Another copy should be transferred to the germplasm centre at IITA – Tanzania for virus cleaning and in
vitro conservation and if feasible safety duplicated at the NaCRRI germplasm centre.

Action Theme 3: Phytosanitation

 Germplasm collected must be virus tested and virus-free germplasm stocks generated if necessary.
 Documented protocols to establish cassava landraces in vitro must be validated and alternative protocols
developed for the ultimate robust growth of all varieties in vitro
 Different procedures for virus-elimination should be validated and shared with all parties involved
 Virus indexing SOPs must be documented for sensitive, cost-effective and reliable detection of the
causative viruses of CMD and CBSD.

Action Theme 4: DNA Fingerprinting

 A set of highly polymorphic SNP markers evenly distributed across the genome needs to be selected for
array-based genotyping.
 Decisions need to be made on how much variation defines a new landrace, to be maintained as a new
accession.

Action Theme 5: In vitro conservation and cryopreservation

 Equipment needs to be sourced and purchased for equipping the in vitro facility at IITA-Tanzania.
 Further research to optimize cryopreservation for cassava landraces is required.

Action Theme 6: Evaluation and Characterization

 Accessions housed in the genebank should be characterized and evaluated
 Appropriate methodologies need to be developed for specific consumer traits including ‘mealiness’ and
‘cookability’

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Action Theme 7: Documentation and knowledge sharing

 The IITA germplasm database must be mirrored in IITA-Tanzania.
 A structure for documentation of farmer-knowledge and SNP fingerprinting must be incorporated.
 Analytical tools for comparing and identifying variation and quantifying the extent of variation among
genotypes must be made available.

Action Theme 8: Germplasm Exchange

 National plant health regulatory agencies must be well integrated into the entire germplasm exchange
procedure.
 Training staff in knowledge and experience related to the policy framework, phytosanitary and quarantine
aspects and the biological and physical aspects of preparing and transporting germplasm (tissue culture
plantlets, stem cuttings and botanical seed).

Action Theme 9: Analysis of Indigenous Knowledge (IK) and incorporation into a more farmer-centric
approach to cassava breeding
 Questionnaires must be designed to incorporate ‘market research’ at the time of germplasm collection to
drive a more design-led approach to breeding.
 Decisions on determining the preferred traits for which to breed new varieties are paramount for success.
 Information relating to most frequent constraints limiting adoption, will be collected.
 Farmer-knowledge collected at the time of germplasm collection must be analyzed and summarized to
inform breeders on farmer preferences and guide appropriate breeding objectives.
 Workshops must be conducted to explore how farmer-knowledge and market information can be
analyzed to inform plant breeding for better adoption of improved varieties and yield gains.

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