Molecular diagnostic tools for plant health protection

Lava Kumar (
Head of IITA’s Germplasm Health Unit and Virologist, Ibadan, Nigeria

Molecular tools in disease diagnosis
Rapid advancements in biotechnologies have led to the development of a myriad of molecular diagnostic tools in the past decade1. These tools, either based on the properties of nucleic acid (DNA or RNA) or proteins of the target agents, have improved the efficacy, accuracy, and speed of detection and identification of disease-causing agents and characterization of the diversity of pathogens and pests.

Researcher observing mouse hybridoma cell lines under microscope in the Virology and Molecular Diagnostics Unit, IITA, Ibadan, Nigeria. Photo by IITA.
Researcher observing mouse hybridoma cell lines under microscope in the Virology and Molecular Diagnostics Unit, IITA, Ibadan, Nigeria. Photo by IITA.
Most popular protein detection methods depend on antigen-antibody interactions. Polyclonal or monoclonal antibodies produced against the proteins of interest are used as probes to detect the target proteins by techniques such as enzyme-linked immunosorbent assay (ELISA), Western immunoblotting, dot immunobinding assay, and a number of variants of these techniques, Meanwhile, nucleic acid-based diagnostic tools are based on the hybridization of homologous nucleotides, size of the DNA fragments generated by restriction enzyme treatment, order of nucleotide arrangement, or a combination of more than one of these approaches. Polymerase chain reaction (PCR), developed in the mid-1980s, has led to the development of several new and simplified techniques, fast established as a mainstay of applied molecular biology and molecular diagnostics.

Platform for development of molecular diagnostics
The objective of the molecular diagnostics research in IITA is to develop tools and technologies for better understanding, diagnosis, and monitoring of biological systems. This program emphasizes the development of simple and accurate tools and procedures for rapid identification of pathogens and pests affecting the food and horticultural crops in sub-Saharan Africa (SSA). Both protein and nucleic-acid based diagnostic tools have been developed against target agents (viruses, fungi, bacteria, phytoplasma, insect pests, and mycotoxins). These tools are critical to several programs on crop improvement and crop protection, including evaluation of germplasm for host resistance, breeding for pest and disease resistance, surveillance surveys, and monitoring programs.

ELISA-based diagnostics are preferred for the identification of plant viruses. It is simple, reliable, cost-effective, and easy to adopt in minimally-equipped labs. Backed with facilities for purifying proteins, and production of polyclonal and monoclonal antibodies, ELISA-based diagnostics were established for about 20 economically important viruses affecting IITA’s mandate crops in SSA (e.g., Maize streak virus, cassava mosaic begomoviruses, Cowpea mottle virus, Southern bean mosaic virus, and more). Antibodies were also produced against nonviral targets such as mycotoxins. Polyclonal antibodies produced against aflatoxin B1 were used to develop the ‘Afla-ELISA’ test for quantitative estimation of aflatoxins in maize and other commodities (see companion article on Afla-ELISA). Monoclonal antibodies are usually produced for discriminating closely related virus species or strains (e.g., African cassava mosaic virus and East African cassava mosaic virus). The production of monoclonal antibodies is expensive and tedious, but it offers the advantage of perpetual production of antibodies from mouse hybridoma cell lines. Because of this, IITA has placed increasing emphasis on producing monoclonals for all important pathogens.

PCR-based diagnostics are developed as an alternative tool or to overcome the limitations of ELISA in detecting viroids, viral satellites, and to discriminate strains and closely related species. Oligonucleotide primers have been developed based on the genomic data generated from our research programs and those available in the public database for the specific detection of targets in PCR assays. Procedures were also established to simplify PCR application. For instance, a procedure established for direct detection of viruses in leaf sap bypasses the need for nucleic extraction2. Emphasis is placed on the development of multiplex PCR assays for the simultaneous detection of more than one virus in a single reaction. A multiplex PCR method has been developed for the simultaneous detection of African cassava mosaic virus and East African cassava mosaic like-viruses responsible for cassava mosaic disease in SSA2. This test was further improved to detect cassava brown streak viruses that have emerged as a major threat to cassava in East Africa, thereby making it a one-stop test for detecting all the major viruses infecting cassava in SSA.

Similar efforts are being devised to detect all viruses infecting yam. Real-time PCR using TaqmanTM probes are being developed to quantify virus concentrations within the plants to characterize host response to virus inoculation. Presently, specific and generic diagnostic tools for the detection of almost all the pathogens that affect major food staples in SSA have been established at IITA.

Pathogen diversity and DNA barcodes
Detailed knowledge of pathogen diversity is a prerequisite to developing unambiguous diagnostic tools. Pathogen populations are characterized by sequencing the specific genes and the data generated is used to interpret origin and spread of the pathogen, taxonomy, and phylogeny. For diversity assessment, gene targets are selected based on the pathogen that comprise, ribosomal Internal Transcribed Sequence (ITS), mitochondrial cytochrome oxidase-I (COI), histone, virus coat protein, etc. This approach has been used for assessing the diversity of Colletotrichum gloeosporioides responsible for anthracnose of yam, Cercospora spp. causing gray leaf spot of maize, cassava brown streak virus, banana bunchy top virus, and several others agents. Information generated from these studies have provided valuable clues to understand the origin and drivers of spread, identification of previously uncharacterized pathogens3,4 and identification of unique markers known as “DNA barcodes” for use as genetic markers for identifying pathogens and pests5.

Workflow in development of protein biomarkers. Source M. Cilia, Cornell University.
Workflow in development of protein biomarkers. Source M. Cilia, Cornell University.
Biomarkers for insect vectors
Recently a new initiative was started in collaboration with Cornell University to identify protein biomarkers to rapidly identify variation in vectoring potential of aphid and whitefly vector populations. Diagnostic tools developed in this program will aid in better understanding the virus-vector interactions, disease epidemiology, and improved management of insect vector-borne virus diseases.

Training in application of molecular diagnostics
In addition to technology development, efforts are made to transfer technology, products, and skills to stakeholders in national research and extension services. This is done through collaborative activities and organization of training courses at regular intervals in collaboration with national organizations such as the Nigerian Institute of Science Laboratory Technology (NISLT). During the training courses, specific emphasis is placed on the application of diagnostics in monitoring and surveillance programs. Standard diagnostic protocols are compiled into a cook-book style laboratory manual6 and distributed during the training courses.

End note
Molecular diagnostics development programs in IITA consider the latest knowledge and state-of-the-art technologies in establishing simple and robust tools that are relevant to end-users, are low-cost, and conducive for adoption in minimally equipped labs. We are adding new tools, such as, loop-mediated isothermal amplification reaction (LAMP) assay and deep sequencing approaches to broaden the knowledge on pathogens occurring in our mandate crops to increase the repertoire of available tools.

Molecular diagnostic tools are routinely used in germplasm indexing, phenotypic evaluation of germplasm, disease surveillance, and monitoring programs in SSA. They are also used in collecting baseline information and monitoring shifts in pathogen and pest dynamics due to changes in agriculture systems and climate change effect. These tools are already proving useful in rapid detection and identification of new and emerging pathogens and pests [e.g., Paracoccus marginatus (papaya mealybug) in Nigeria; Phytophthora colocasiae causing taro leaf blight in Nigeria and Ghana; 16srII group phytoplasma responsible for witches’ broom disease of soybean in Southern Africa; and Banana bunchy top virus in Benin].

1 Benali, S., et al. 2011. Eur. J. Sci. Res. 50:110–123.
2 Alabi, O.J., et al. 2008. J. Virol. Methods 154:111–120.
3 Alabi, O.J., et al. 2010. Arch. Virol. 155:643–656.
4 Sharma, K., et al., 2010. Phytopathology 100 (6): S117.
5 Kumar, P.L. and K. Sharma. 2010. DNA barcodes for pathogens of African food crops. R4D Review 4: 51–53.
6 Kumar, P.L. (ed.). 2009. Methods for diagnosis of plant virus diseases: a laboratory manual. IITA, Ibadan, Nigeria. 90 pp.

Climate change & plant health

Irmgard Hoeschle-Zeledon*, or
*Coordinator of the CGIAR Systemwide Program on Integrated Pest Management (SP-IPM) convened by IITA

Diverse crop production system. Photo by IITA.
Diverse crop production system. Photo by IITA.

The discussion on the impact of climate change (CC) on agriculture has often focused on how changes in temperature, rainfall, and CO2 concentrations will affect the suitability of temperate regions for crop production and how crops will react in terms of yields. The effects of climate change on biotic factors in the tropics, such as weeds, pests, and pathogens (hereafter referred to as pests), have not received much attention.

Empirical data exist, however, to show that these biotic factors have major effects in determining productivity in the tropics. For instance, during the 1997 El Niño phenomenon, the mean temperature on the Peruvian coast increased by about 5 °C above the annual average, causing a decrease in potato infestation by the leafminer fly Liriomyza hydobrensis, which otherwise was a major pest. However, the abundance and infestation severity of all other pests increased in all crops, including potato (Kroschel et al. 2010). The complex consequences of CC particularly on pests and pathogens are still only imperfectly understood (Gregory et al. 2009).

CGIAR’s work on climate change
What are IITA and the other centers of the Consultative Group on International Agricultural Research (CGIAR) doing to mitigate the impacts and adapt to the effects of CC on pests? Historically, CGIAR centers have a broad R4D focus; centers have been developing knowledge (e.g., pest profiles), products (e.g., new crop varieties, biocontrol agents against invasive pests), and technologies (e.g., predictive models, diagnostic tools) that are suitable for diverse agroecologies including the tropics, wet, humid, semiarid, and dry, and to some extent the temperate zones as well. The broad knowledge and experience of centers provide an unprecedented advantage to assess the products and technologies in different agroecologies and weather settings and to determine their resilience and ability to cope in altered climatic situations.

Several programs directly focus on managing pests. For instance, the breeding of crop varieties for resistance to pests and pathogens has always been a focus of the CGIAR. With the uncertainties of CC, this work has become more relevant. Breeding for resistance to drought and waterlogging, although not the primary objectives, also aim at making varieties better able to tolerate biotic threats, since drought and excess water in the soil both increase the plants’ vulnerability to these factors.

A good example is the effort to develop drought-resistant maize cultivars by CIMMYT and IITA. These will not only allow the expansion of maize production into areas with less reliable rainfalls but also ensure the continued production in regions that are prone to future water scarcity. Drought- tolerant cultivars also reduce the risk of aflatoxin contamination in the field. Additional characters are incorporated into the drought-tolerant maize, such as resistance to maize streak disease which is endemic in Africa. Similar programs are ongoing to develop drought-resilient cassava and cowpea, and yam with tolerance for major pests.

The CGIAR centers are also working towards the development of cropping systems with greater intra- and interspecific diversity to increase resilience to CC-induced threats from biotic factors. For example, IITA is promoting maize–cowpea intercropping to reduce the pest pressure on cowpea.

Bioversity International is exploring how intra-specific crop genetic diversity on-farm not only reduces current crop losses to pests and pathogens, but also decreases the risk of genetic vulnerability and the potential of future crop damage, thus enhancing the impact of other IPM strategies and providing farmers with increased adaptive capacity to buffer against climatic changes.

CIP developed a temperature-driven phenology model for the potato tuber moth, Phthorimaea operculella that provides good predictions for the population in areas where the pest exists at present (Kroschel et al. 2010). Linked with geographic information systems (GIS) and atmospheric temperature, the model allows the simulation of risk indices on a worldwide scale to predict future changes in the distribution of the species due to increasing temperatures. The approach can also be used for other insect species. Hence, CIP created the Insect Life Cycle Modeling software (ILCYM) to facilitate the development of other insect phenology models. With its support, the phenology model can be implemented and allows for spatial simulation of insect activities.

Many centers support the collection and conservation of plant genetic diversity that can be built into new cultivars to enhance their resistance to biotic stresses. Diagnostics capacity is continuously augmented for the accurate and timely recognition of endemic pests, new variants, and invasive pests. Crop biodiversity—landraces and wild relatives that are the reservoirs of genes for abiotic and biotic factors—is conserved ex situ to protect the species from erosion by CC-induced changes.

In a collaborative effort, CIP, IITA, icipe, and partners in Germany and Africa are implementing a project to understand the effects of rising temperatures on the distribution and severity of major insect pests on main food crops. ILCYM will be further improved and adapted to cover a wide range of insect species. The results will contribute to filling the knowledge gap about CC effects on economically important insect herbivores and their natural enemies.

IITA is planning to research the effect of changes in temperature on the invasion potential of major biotic threats in the Great Lakes region of East Africa and elsewhere: Banana bunchy top virus (BBTV), Banana Xanthomonas Wilt (BXW), and Panama Disease–Tropical Race 4, cassava brown streak virus disease, cassava mosaic disease, maize streak, soybean rust, and pod borer pests, among others.

As whiteflies and aphids are considered to become more problematic with increased temperatures, IITA is also preparing research on the biocontrol of different whitefly and aphid species in vegetables and staple crops.

A project has been proposed on the bio-enhancement of seeds and seedlings of cereals and vegetables for East Africa to stimulate the plants’ defense mechanisms against pests and pathogens expected to increase in number, frequency, and severity. This project also addresses the registration of biopesticides and the availability of endophytes to the tissue culture industry.

CGIAR research programs
Under the new CGIAR Research Programs (CRPs), centers are addressing CC-induced crop health issues in various ways. Breeding for resistance to predicted biotic stresses continues to be a major focus in CRP3 (roots, tubers, banana) and its subcomponents. This component, coordinated by CIP, specifically recognizes CC and agricultural intensification as drivers for higher pressure from pests. Hence, this program aims at developing management strategies for priority biotic threats to these crops. These include the development of improved detection and monitoring tools, and surveillance methods for detecting and mapping existing, emerging, and resurgent molecular pests and pathogens. It will look into increasing general plant and root health through the enhancement of the natural disease suppressing potential of soils, and the antagonistic pest and disease potential of the aboveground agroecosystems.

The CRP on Integrated Systems for the Humid Tropics, led by IITA, will have a substantial focus on CC, its impact on pests, and plans for mitigation. For example, research will establish the relationship between CC and key cassava pests to develop integrated pest management (IPM) strategies including those for whitefly, African root and tuber scale, termite, green mite, aphid, and mealybug.

Phenology models for insect and mite pests and their antagonists on several crops will be developed and validated and their potential for changes in warming will be determined.

In collaboration with CABI, community surveillance for pests and diseases will take place through the expansion of the mobile plant clinic network.

Larva of the noctuid moth feeding on the pistil of cowpea. Photo by S. Muranaka, IITA.
Larva of the noctuid moth feeding on the pistil of cowpea. Photo by S. Muranaka, IITA.

Knowledge and decision support tools for the management of potato and sweetpotato pests (diseases and insects) will be developed and assessed in relation to the expected intensification of the agroecosystems in the humid and subhumid tropics.

Sustainable management of cassava virus disease in the cassava-based system will also be studied, and the vulnerabilities of these systems to CC- induced pest and disease problems will be determined.

The CIAT-coordinated CRP on CC, Agriculture, and Food Security began operations this year. It will continue the activities initiated by the CGIAR Challenge Program on CC. This CRP aims at mainstreaming strategies that address the management of CC- induced pest and disease threats among international and national agencies. It will identify and test innovations that enable communities to better manage and adapt to climate-related risks from biotic factors.

A lot of surprise shifts in ecosystems could come. It is therefore important that research capacity and knowledge bases are maintained to understand and rapidly react to mitigate any debilitating impacts (Shaw and Osborne 2011).

To accomplish this, it is necessary to establish good baseline data on current pest status in agroecosystems. This knowledge base will serve as a reference point to measure the fluctuations and the effectiveness of interventions.

It is important to determine the key weather variables that could change as a consequence of CC and their influence on agroecosystems and pests, and establish preemptive coping strategies. Available CC models could be handy for predicting CC factors.

A diverse scientific base including specialists in pathology, entomology, ecology, taxonomy, and epidemiology is required. They should work together to ensure that the outcomes of their research are linked to existing knowledge, economic forces, and common understanding (Shaw and Osborne 2011).

As it generally takes more than 10 years to breed a new resistant cultivar of a crop, breeding programs must start well in advance of the serious risk of a biotic threat Breeders need to be informed on the problems which might become important in the future (Chakraborty et al. 1998 in Juroszek and Tiedemann 2011).

Crops being bred for abiotic threats such as drought, waterlogging, and salinity should be prepared for the pests that could flourish under these conditions and select varieties that can tolerate pests as well.

Changes in occurrence, prevalence, and severity of infections and infestations will also affect crop health management (CHM) practices. There is a need to effectively disseminate and use those techniques that are currently underused (Juroszek and Tiedemann 2011).

Significant contributions could be made in improved field monitoring of pests and diseases, and better delivery systems for pest control products (Strand 2000 in Juroszek and Tiedemann 2011). Preventive crop protection measures may become more relevant under CC to reduce the risks (Juroszek and Tiedemann 2011).

CC is a global problem that affects all countries. Hence, global cooperation is required. However, given the nature of plant pests and pathogens, more local or regional strategies need to be put in place that define potential risks and measures to tackle expected threats. Investments in early detection systems, including border controls to monitor the migration of pests through plants, plant products, and other goods, will be the key to avoid the spread of invasive pests and reduce high management and eradication costs (FAO).

New farming practices, different crops, and IPM technologies must be developed to control the established pests and prevent the spread of new ones (FAO).
Governments should consider developing country-specific strategies to cope with CC-induced changes and put in place favorable policies for the introduction and promotion of new technologies for CHM.

It is also crucial to create and augment awareness about the effects of CC among policymakers and other officials involved in developing agricultural strategies.

Chakraborty S and Newton AC. 2011. Plant Pathology 60: 2-14.

FAO. unknown.

Govindasamy B et al. 2003. Climate Dynamics 21: 391-404.

Gregory PJ et al. 2009. Journal of Experimental Botany 60: 2827-2838.

Juroszek P and von Tiedemann A. 2011. Plant Pathology 60: 100-112.

Kroschel J et al. 2010.

Shaw MW and Osborne TM. 2011. Plant Pathology 60: 31-43.

IAPSC: Protecting Africa’s plant health

Jean-Gerard Mezui M'ella, IAPSC
Jean-Gerard Mezui M'ella, IAPSC

Jean-Gerard Mezui M’ella is the Director of the Inter-African Phytosanitary Council (IAPSC), the African Plant Protection Organization with headquarters in Nlongkak, Yaounde, Cameroon. IAPSC is an intergovernmental organization with 53 members under the umbrella of the African Union. It coordinates plant protection procedures in Africa.

The IAPSC Director coordinates the activities of its four sections (Phytopathology; Entomology; Documentation, Information and Communication; Administration and Finance). He represents the African region in the Commission for Phytosanitary Measures of the International Plant Protection Convention (IPPC/FAO), promotes compliance with International Standards for Phytosanitary Measures (ISPMs), and represents the African Union Commission on diplomatic matters in Central Africa. In this interview, he talks about the important work of IAPSC.

Why is IAPSC important?
IAPSC is a technical office of the African Union/Directorate of Rural Economy and Agriculture. It is one of the 10 Regional Plant Protection Organizations of the IPPC. As the regional organization for Africa, it works in collaboration with the national plant protection organizations of the 53 countries of the AU.

IAPSC mostly implements its activities through the eight African Regional Economic Communities (RECs) and sub-RECs. It addresses phytosanitary issues in Africa including the following:
– The vulnerability of African crop production systems to the impact of diseases, insect pests, and noxious weeds;
– Economic losses incurred through spoilage;
– Noncompliance with ISPMs, trade regulations, and equivalents;
– Dearth of phytosanitary data (Pests Risk Analysis, diagnostics, surveillance, etc.)

AU-IAPSC safeguards agriculture and natural resources from the risks associated with the entry and establishment or spread of pests of plants and plant products to ensure food safety and quality supply to intra-African and international markets.

How would you assess the state of plant protection in Africa?
Africa still has a lot of problems with plant protection. In fact, most African countries inherited an administration put in place before independence, which to a certain extent, has safeguarded the plant health of the different countries. There were departments of Agriculture and Divisions such as plant pathology, entomology, agricultural chemistry, and also plant quarantine. After independence, with the coming into force of the IPPC, adopted by the FAO Conference of 1951, the global approach and harmonization of phytosanitary measures started to take shape. For example, a common format for phytosanitary certificates was set up, common action was secured to prevent the spread of pests of plants and plant products, guidelines were provided regarding phytosanitary matters and the relevant actions to be taken by national governments in the implementation of plant quarantine.

IAPSC promotes cooperation among countries to prevent the movement of serious pests. It provides a forum for African countries to promote their views on plant health. In addition, quarantine structures in Africa differ from one region to another. In fact, some countries have operational quarantine stations but others do not. We at IAPSC encourage the creation of regional and subregional quarantine stations, although even those in existence find it difficult to comply with IPPC standards. It is our hope to have quarantine stations in each country.

Quarantine inspector reading about banana bunchy top. Photo by L. Kumar, IITA.
Quarantine inspector reading about banana bunchy top. Photo by L. Kumar, IITA.

Harmonizing phytosanitary regulations and policies in Africa must be quite challenging. How are you doing this?
Nontariff barriers such as SPS measures are often used as a disguised way to restrict trade. It is becoming essential, following the World Trade Organization‘s agreement on SPSMs for member countries of the WTO to ensure that the SPS measures they apply are in line with this agreement. To do so, the technical and organizational capacity of the various organizations at national, regional, or international levels have to be given the necessary tools to deal with the new challenges.

The 1995 WTO agreement was set up to remove unnecessary, unjustified, and arbitrary pressure on international trade in plants and plant products. This was a new situation for the various stakeholders, e.g., new themes such as transparency, scientific justification, notifications, inquiry points, risk analysis, and standards are now the guiding principles.

It is thus of the utmost importance for African countries, where phytosanitary capacity deficits are most severe, to begin a process of developing a strategy for capacity building to meet their obligations under the WTO rules.

In 2003, the RECs became the implementation arm of IAPSC whose technical programs are assessed by the RECs during the annual meetings of the Steering Committee and General Assembly.

IAPSC, much like AU, encourages regional common markets.

What are your major challenges?
Besides funding, the major challenges IAPSC faces on a daily basis include the entry of new pests on the African continent that annihilate the efforts of member countries; the proliferation of invasive pests; climate change that brings about new plant heath challenges; and a lack of scientists specialized in plant protection.

How do you ensure that regulations or policies are strictly implemented?
We endeavor to strengthen the capacities of countries so that they can prevent and control the introduction of plant pests in Africa. We encourage the setting up of Centers of Phytosanitary Excellence, the creation of phytosanitary networks, and the regular updating of pest lists in Africa.

IITA researchers conduct plant health tests in lab. Photo by L. Kumar, IITA.
IITA researchers conduct plant health tests in lab. Photo by L. Kumar, IITA.

What are you doing to improve the links and working relationships among NPPOs and networks in Africa?
We organize workshops and seminars on plant matters; we publish a quarterly phytosanitary news bulletin; and we enrich on a regular basis the phytosanitary information in the International Plant Protection Portal of FAO.

IAPSC provides information on quarantine pests on plants as well as for the protection of plant products for the AU member countries through both the paper and electronic media. Paper-based information systems include a scientific analysis, a phytosanitary situation in Africa, reports of service activities, and a collection of phytosanitary regulations and standards. Electronic information on compact discs covers a database of the meetings and phytosanitary regulations of member States. The Phytosanitary News bulletin of IAPSC is issued four times a year. It welcomes contributions and articles from National Plant Protection Organizations.

There is a web site for the worldwide dissemination of information (, and a library that hosts scientific books.

Our workshops and seminars aim at sharing information on the phytosanitary situation and on the findings in crop protection research.

We frequently conduct monitoring and evaluation exercises (country visits, exchange and information sharing among countries). All these activities help in networking among the partners in Africa.

What support do you need from the member countries? From partners? From clients?
To improve the prevailing situation concerning quarantine standards, regional cooperation and compliance with international regulations, the following priorities have been identified:
1. Ensuring that all African countries are parties to the IPPC;
2. Ensuring the harmonization of plant protection policies across RECs through capacity building;
3. Regularly updating pest lists and quarantine pests;
4. Harmonizing phytosanitary inspection systems; surveillance, emergency responses, risk analysis: procedures to analyze and reduce the risk of new pests entering a country;
5. Setting up a harmonized pesticide management system.

Describe your collaboration with IITA.
IAPSC-IITA cooperation is in the following key areas: Cassava pests’ diagnostics and control technique methods, Cassava germplasm and planting material exchange, Banana pests’ diagnostics and control technique methods, Banana germplasm and planting material exchange, and Harmonization of African countries’ phytosanitary systems.

What could international bodies such as IITA do to ensure that Africa’s agriculture is safeguarded?
IITA, like other bodies, should work with country structures through IAPSC, and collaborate with recognized subregional and regional structures of the public and private sectors in plant protection.

Towards a healthy banana TC industry

Thomas Dubois,

Tissue culture banana
Banana in smallholder farmer systems is traditionally propagated by means of suckers. These contain soil-borne pests and diseases, and by using them, farmers unknowingly distribute and perpetuate pest and disease problems.

Plants produced by tissue culture (TC), because they are produced axenically in the laboratory, are material that is free from pests and diseases with the exception of fastidious bacteria and viruses.

Young tissue culture plantation in Nairobi, Kenya. Photo by T. Dubois, IITA.
Young tissue culture plantation in Nairobi, Kenya. Photo by T. Dubois, IITA.

There are many added benefits to using TC plants: (1) they are more vigorous, allowing for faster and superior yields; (2) more uniform, allowing for better marketing; and (3) can be produced in huge quantities in short periods of time, allowing for faster and better distribution of existing and new cultivars, including genetically modified banana. In other words, the TC technology can help banana farmers to make the transition from subsistence to income generation.

However, TC plantlets are relatively fragile and require appropriate management practices to fully harness their potential, especially during the initial growth stages shortly after being transplanted to the field. In East Africa, TC plantlets are often planted in fields burdened with biotic pest pressures and abiotic constraints.

A SWOT analysis
The importance of the private sector
The adoption of TC technology is still relatively low in East Africa. In Kenya, coverage of TC banana is estimated at 5–7% of the total banana acreage; adoption rates are significantly lower in countries such as Uganda, Burundi, and Tanzania, although reliable data do not exist.

Cumulative yield (t/ha/cycle) of a plantation derived from tissue culture (orange bars) compared to one derived from conventional planting material (blue bars), over 5 cropping cycles under two management regimes (low input and high input). Every little block represents one crop cycle. Data based on 1,600 plants total.
Cumulative yield (t/ha/cycle) of a plantation derived from tissue culture (orange bars) compared to one derived from conventional planting material (blue bars), over 5 cropping cycles under two management regimes (low input and high input). Every little block represents one crop cycle. Data based on 1,600 plants total.

In East Africa, the technology is booming under the impetus from the private sector. At least 10 commercial private laboratories have sprung up in the last decade in Burundi, Kenya, Uganda, and Tanzania. Collectively, they produce at least 2 million plants/year, although exact numbers seem to fluctuate widely and are hard to come by. Most of these companies manage the entire production chain, from sourcing the mother plants to weaning the TC plantlets. Despite the steep entry barrier, the TC business is very lucrative for the entrepreneur who engages in plantlet production. In some countries, universities and research organizations are also involved in the commercial production of TC banana.

Lack of quality standards and virus indexing
One of the biggest dangers for sustainable commercial production of TC plants is the lack of several essentials: (1) standards for quality management during the production process, (2) plant health certification, and (3) regulatory procedures. Such conditions are especially important to avoid spread of viruses, which are easily transmitted through TC plantlets.

For instance, Banana bunchy top virus (BBTV) is on the list of the 100 most dangerous invasive species worldwide. It is widely distributed in Central Africa and also in Burundi and Rwanda in East Africa, yet implementation of virus indexing schemes is largely absent in East Africa. It is important to put in place standard procedures for ensuring the production and distribution of high-quality, virus-free planting material, and to establish independent agencies that set and implement standards and improve the skills of personnel. In East Africa, certification schemes need to be regionally harmonized, especially with the transnational movement of plants between the countries, so that there is no weak link in the region.

Unregulation—a potential danger to the spread of diseases
At present, the commercial production of TC banana plantlets is largely unregulated. Not only are TC banana plantlets being moved in very large quantities across borders; uncertified mother material is also crossing borders. This practice is potentially risky, and could perpetuate infected sources and cause new outbreaks of disease.

In the ideal situation, there need to be certification standards for the quality and health of TC plants and the monitoring of TC producer operations. These are largely ignored because of poor awareness, and the lack of capacity and regulations required for the implementation of such standards. To transform the system, governments and/or the TC industry could consider common facilities to implement certification schemes. For instance, an accredited governmental or independent virus indexing laboratory, established as a commercial service for TC operators, would leverage costs and improve TC standards.

Another important requirement for TC producers is sustainable access to virus-free and true-to-type mother plants and this is currently lacking. The establishment of certified mother plant gardens as a common resource, either by governmental agencies or a consortium of commercial TC producers, would provide this essential requirement.


Contrary to a general perception, especially among donors, it is not merely the standards themselves that are a constraint, but also a lack of knowledge on how procedures are actually implemented along the value chain, through certification schemes. The equipment for virus indexing has become relatively cheap and technical skills are quite easily acquired. Their costs can be offset, e.g., through a service-based fee to private sector stakeholders.

Also, emphasis could equally be placed on certifying general operational procedures in a private TC laboratory. Currently, the quality of TC plantlets varies significantly, and several producers are struggling with off-types and accidental mixtures of varieties that become apparent only after being planted in the field, resulting in negative perceptions about TC.

Certification schemes need to be implemented in such a way that they do not become burdensome to producers or create bureaucratic barriers. Several quality certification schemes used for clonal crops, including banana, from other regions can be considered to develop an appropriate scheme for East Africa. Ultimately, it is not only the commercial sector that should self-regulate; governmental bodies need to take responsibility.

Nurseries for TC plants are essential, as they act as a distribution hub connecting producers to the farmers. They also act as focus centers for farmers and farmers’ groups, and are therefore an easily approachable venue for training and other interventions. The survey by IITA and University of Hohenheim of all TC nurseries in Burundi, Kenya, and Uganda, found that nurseries in East Africa face an array of problems. Relationships between producers and nurseries, especially those related to timing, quality, and quantity of plantlet supply, are often suboptimal.

At the nursery level, there are three main operational issues: access to water, credit, and the transport of plantlets. The location of the nurseries is also crucial. Nurseries need to be close to the producer and to the market, otherwise they might fail. Clear drivers for the success of a nursery are good agricultural practices and, interestingly, a diversification into crops outside banana.

Plantain for sale in market. Photo by IITA.
Plantain for sale in market. Photo by IITA.

In TC banana value chains, nurseries have different roles across countries in East Africa. In Uganda, nurseries are run as businesses independent of the TC operators and of the farmers. In Burundi, the nurseries are owned and managed by the producers. In Kenya, nurseries are run as entities separate from the producers, and most of them are owned by farmers’ groups that act as the customers for these nurseries. The business model in Kenya seems to hold the secret for a sustainable and vigorous link between producers and farmers.

Distorted value chains
One danger for a healthy commercial TC sector is the lack of sustainable market pathways to deliver the plants to the farmers. Especially in Burundi and Uganda, outlet markets for TC plantlets are mainly governmental and nongovernmental organizations, a situation which seems unsustainable in the long term.

The sustainability of the banana TC industry is especially worrisome in Burundi, where the entire value chain is subsidized. Virtually all TC plantlets are being bought by developmental agencies, which then pass on these plantlets to often untrained farmers, free of charge, and without embedding this transfer in an encompassing training program or input package (e.g., fertilizers).

Empowerment of farmers in the value chain through farmers’ groups
Organizing banana farmers into groups has long been considered advantageous, because of increased buying and selling power, reduced economic and social risk, increased economies of scale, and improved access to credit and inputs by formally certified groups.

The study by IITA and the University of Hohenheim of the farmer-to-market linkage in Uganda demonstrated that farmers in marketing groups obtain higher prices than their ungrouped colleagues. The certification of farmers’ groups implemented by IITA’s national partners, ISABU (L’Institut des Sciences Agronomiques du Burundi) in Burundi and VEDCO (Volunteer Efforts and Development Concerns) in Uganda, has made them eligible for savings and credit schemes. Some have even engaged in other commercial activities, such as the start-up of a catering service.

The importance of a training package
In East Africa, the distribution of superior planting material alone will not ensure a good crop. Commercial farmers are skilled in juggling the inputs and effort needed to produce crops and make a profit but smallholder farmers are constrained by factors such as a lack of land and capital, access to technology, and a good marketing infrastructure. Therefore, efficient distribution systems will be needed to deliver the TC plants as part of a package, including training and access to microcredit.

Training of farmers' group on business skills in Uganda. Photo by M. Lule.
Training of farmers' group on business skills in Uganda. Photo by M. Lule.

IITA and its national partners, ISABU, JKUAT (Jomo Kenyatta University of Agriculture and Technology), and VEDCO, have been implementing hands-on, comprehensive training schemes for farmers as well as the operators of TC banana nurseries. Training schemes encompass modules in agronomy, marketing, business and financing, and for farmers, group formation and group dynamics. Participants were followed for over a year, and their ability to implement the skills learned during the training program was monitored. So far, a total of 851 separate training events have been implemented in Burundi, Kenya, and Uganda, and through the partnership, 10 new farmers’ groups and 5 new nurseries have been established.

Location, location, location
TC banana plantlets come at a cost, and might not be economically beneficial throughout all banana-producing areas in East Africa. Location is everything.

IITA, in collaboration with Makerere University, conducted a cost-benefit analysis of the technology based on a comprehensive quantitative questionnaire with 240 farmers across four districts in Uganda, and compared it with the use of conventional planting material.

Gross margins (in Ugandan shillings)/ha/year of banana plantations derived from tissue culture (yellow bars) compared to conventional planting material (orange bars) in Uganda, the further away from the main banana market.
Gross margins (in Ugandan shillings)/ha/year of banana plantations derived from tissue culture (yellow bars) compared to conventional planting material (orange bars) in Uganda, the further away from the main banana market.

Both production costs and revenues were consistently higher for TC-derived material than for suckers. However, banana prices varied greatly with district and declined significantly with increasing distance from the main market (see graph). Also, production costs decreased significantly the further away the farms were from Kampala due to better agroecological conditions and the much reduced pressure from pests and diseases. As a result, although both TC plantlets and suckers were profitable to the farmer, TC material was more profitable than suckers closer to the main banana market.

In districts with low banana prices and at a greater distance from the main banana market, farmers could receive similar gains by planting suckers rather than TC plants. For a farmer in Uganda, it makes economical sense to grow TC banana close to the main urban market.

An objective ex-post assessment
Despite a booming commercial sector, there is only anecdotal evidence that farmers who have adopted TC banana benefit tremendously in terms of higher yields and household incomes. Sound socioeconomic analyses are crucial to guide policy strategies, learn from successes already achieved, and identify important constraints for a wider dissemination of TC banana in the region.

Earlier studies on the impacts of TC banana in the region have either employed ex ante methods before any meaningful adoption was actually observable, or they have used relatively simple and ad hoc qualitative methodological tools, which do not allow robust and representative statements. The large body of subjective ‘gray’ literature, sometimes unconditionally and unilaterally promoting the benefits of TC banana, without considering the quality of the plant material, input package, and market access, risks having an adverse effect on the adoption of the technology in the long term.

Banana market in Ikire, Nigeria. Photo by O. Adebayo, IITA.
Banana market in Ikire, Nigeria. Photo by O. Adebayo, IITA.

The University of Göttingen, in collaboration with IITA, is currently answering the following main research questions: (1) What are the determinants of TC banana adoption among farmers? (2) What are the impacts of this technology on on-farm productivity, household income and income distribution, and poverty and food security? (3) How do institutional factors in technology delivery and product marketing influence adoption and impact?

Some of these research questions have been answered. In Kenya, a substantial share of the population has heard about TC banana and is, therefore, generally aware of the technology’s existence, although only a few have had a chance to fully understand its performance and requirements. This study finds that farmers’ education, access to agricultural information, knowledge of the location of a TC nursery within a reasonable distance, and affiliation to social groups significantly increase the likelihood of the TC technology being adopted.

This study also highlights the positive role of access to credit and of gender in the adoption of TC material. Farmers with access to credit and female-headed households are more likely to adopt TC plants. The latter finding is particularly interesting from a policy perspective, because it shows that, when there is an equal chance for both men and women to acquire sufficient knowledge about an innovation, women are more likely to adopt it.

GHU: Gateway for the safe exchange of germplasm

Lava Kumar,

Seed testing. Photo by L. Kumar, IITA.
Seed testing. Photo by L. Kumar, IITA.

International exchange of germplasm: an essential step for sharing international public goods
Since its inception in 1967, IITA has been actively involved in the collection, conservation, and use of the plant genetic resources of important crops, such as banana and plantain, cassava, cowpea, maize, soybean, and yam, and their wild relatives from Africa and other parts of the world. Using this germplasm, IITA’s crop improvement programs, based in several locations in sub-Saharan Africa, have been developing high-yielding, nutritionally superior crop varieties resistant to pests, diseases, and drought.

These are regularly exchanged with national and international programs for crop improvement and agriculture development.

Germplasm safety matters
As part of the measures to prevent the inadvertent spread of pests through exchange activities, IITA has established a Germplasm Health Unit (GHU). The GHU is responsible for the production, maintenance, and exchange of healthy (pest-free) germplasm in accordance with the international requirements on plant protection. These are covered by the International Plant Protection Convention (IPPC) under the auspices of FAO, and those set up by the Inter-African Phytosanitary Council (IAPSC) and National Plant Protection Organizations (NPPOs) to safeguard agriculture and natural resources from the risks associated with the entry, establishment, or spread of plant pests.

Scheme for phytosanitary management of germplasm.
Scheme for phytosanitary management of germplasm.

GHU (a) facilitates germplasm exchange in support of IITA’s international crop improvement programs; (b) inspects for pests and certifies the health status of germplasm; (c) ensures compliance with the national regulations on plant introductions and exports; (d) guards against the introduction of exotic pests into countries where they do not occur; (e) ensures phytosanitary management of plant genetic resources conserved in the IITA genebank; and (f) provides capacity building and awareness creation on phytosanitary measures.

GHU operates within the framework of the procedures for the introduction and export of germplasm established by the government of the host country in which IITA’s operations are based. For instance, all the exchange operations of IITA’s activities in Nigeria are organized in accordance with the legislation of the Nigerian Agriculture Quarantine Service (NAQS) of the Federal Department of Agriculture, Nigeria.


Ensuring exchange of clean germplasm
Crops researched at IITA comprise those propagated through botanical seeds or true seeds (maize, soybean, cowpea, and other legumes of importance to African farming) and crops that are propagated through vegetative propagules, including stems (e.g., cassava), tubers (e.g., yam), and in vitro plants (e.g., banana and plantain, cassava, and yam).

Each type of germplasm demands a unique set of procedures for assessing the health status of the material. At IITA, this work goes on from production to postharvest to the point when the material is dispatched.

Plant material generated for international exchange is inspected with the technical officers of NPPO during the active growth stage in the field or screenhouse to ensure the selection of pest-free material. The sorted materials (seeds or vegetative propagules) are then brought to the GHU laboratories for critical inspection for the presence of pests. Detection methods used for this purpose include visual inspection of dry seeds, seed washing, agar and blotter tests, seed soaking, and seedling symptom tests which aid in identifying any pest-infested material. Additional techniques are used for pest identification including culturing techniques, microscopy, and biochemical analyses of samples by enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and genomic sequencing. Only materials that are free of the regulated and unregulated quarantine pests are released for international exchange.

GHU also monitors for genetically modified organisms (GMO) to comply with the Cartagena biosafety protocol, also under the regulation of NPPOs. This is done mainly by seeking an additional declaration from the exporting parties on the GMO status of the planting material as stipulated in the conditions of the import permit issued by the NPPO. Diagnostic capacity exists to monitor germplasm for traces of GMOs by PCR assays, targeting constitutive elements of transgene constructs, such as promoters of Agrobacterium tumefaciens or Cauliflower mosaic virus 35S gene, that are widely used for generating transgenic plants.


Complying with regulations
Germplasm exchange activity commences with the application of a permit from a host country for germplasm import (for use in IITA’s R4D programs) or germplasm export (to partners, collaborators and other stakeholders, including IITA’s missions in other countries). This is an essential process under the Convention of Biological Diversity (CBD) treaty that regards biodiversity as a national treasure, and requires authorization from the respective governments for free exchanges. Every country has a nodal agency tasked with issuing permits for the movement of germplasm.

In addition, GHU applies for phytosanitary certificates (PC) for the export of material. The PC is issued by NPPO after the condition has been satisfied that the material being exported meets the phytosanitary standards of the IPPC and the importing country. GHU invariably complies with national regulations in obtaining these two documents for all seeds or plant materials sent or received. Similarly, when material is imported it is subjected to post-entry inspection to ensure its compliance with the conditions specified in the import permit. Depending on the need, material is held in the post-entry isolation facility until the necessary clearances are obtained. Material that satisfies all the conditions is released for IITA’s use.

Germplasm export and import events facilitated by GHU to various countries around the world. Source: L. Kumar, IITA.
Germplasm export and import events facilitated by GHU to various countries around the world. Source: L. Kumar, IITA.

From 2005 to 2010, GHU, from IITA‘s Ibadan Station in Nigeria in liaison with NAQS, has facilitated about 492 exchanges, 157 imports, and 335 exports of crop and other plant material to 69 countries, 34 of which are in Africa (Fig. 1). USA, India, Colombia, Mexico, and Japan are among the top 5 non-African countries. Within Africa, the top 5 countries with which IITA has exchanged germplasm are Bénin, Ghana, Cameroon, Kenya, and South Africa. Each of these countries has specific legislation. However, procedures for health monitoring have the same underlying principle, i.e., the exclusion of pests and the prevention of pests from spreading.


Phytosanitary protection of genetic resources
GHU ensures the phytosanitary management of the germplasm of food crops (about 27,000 accessions) conserved in the IITA genebank and also in the in situ germplasm collections of breeding programs. Germplasm conserved in the genebank is systematically evaluated for its health status and clean germplasm is conserved for distribution by IITA’s Genetic Resources Center (GRC).

Contributing to phytosanitary capacity development in SSA
Together with the Virology and Molecular Diagnostic Unit and GRC at IITA, Ibadan, GHU augments diagnostic procedures for monitoring pests in germplasm; develops a reference pest collection and DNA bank to use as controls; establishes DNA barcode databases of the pests of African food crops; and augments procedures for salvaging clean germplasm.

Information dissemination through exhibits and hands-on demos, IITA Open Day. Photo by IITA.
Information dissemination through exhibits and hands-on demos, IITA Open Day. Photo by IITA.

GHU plays an active role in developing the skills of NPPOs in the testing for germplasm health and the production of pest-free germplasm via training courses and short-term assignments. It also creates awareness on quarantine pests, quality standards for planting material, and the sanitary and phytosanitary (SPS) measures.

Knowledge and technologies developed are disseminated through training programs, the publication of protocol manuals, information flyers and a website. The unit also collaborates with NPPOs and IAPSC as a technical partner to develop phytosanitary capacity in Africa.


NAQS: IITA contributes to our effectiveness

Olufunke Awosusi is a Senior Plant Quarantine Officer with the Nigeria Agricultural Quarantine Service (NAQS) in the Federal Ministry of Agriculture and Rural Development. NAQS is charged with the responsibility of protecting the Nigerian agricultural economy from the attacks of pests, especially “foreign” pests, and also enhancing agricultural trade through export inspection and certification. Below are excerpts from an interview with Godwin Atser on the role of the NAQS and the collaboration with IITA.

Olufunke Awosusi, NAQS
Olufunke Awosusi, NAQS

What is the role of NAQS?
The NAQS evolved from the former Plant Quarantine Service. It was established in recognition of the fact that agricultural quarantine is the control of the introduction and spread of pests and diseases by means of legislation and as a result of the country’s problems within a decade before independence with the introduction of cocoa and maize pests. The cocoa industry almost collapsed; plantations were destroyed; and disease-resistant cocoa varieties were handed to farmers for replanting. This cost the Government a colossal amount. For maize, it took the concerted efforts of several West African nations coming together to revive production in the region.

NAQS was created to harmonize the quarantine of plant, veterinary, and aquatic (fisheries) resources in Nigeria to promote and regulate sanitary (animal and fisheries health) and phytosanitary (plant health) measures in connection with the import and export of agricultural products with a view to minimizing the risk to the agricultural economy, food safety, and the environment.

The main objective of NAQS is to prevent the introduction, establishment, and spread of animal and zoonotic diseases and pests of plants and fisheries including their products. NAQS also undertakes emergency protocol to control or manage new pest incursion or diseases outbreak in collaboration with key stakeholders.

What is the situation with NAQS today?
The standards have improved drastically. Today NAQS has improved personnel who are more skillful and trained in pest diagnosis stationed in the entry and exit points in the country. We have had improvements in diagnostic facilities and this is perhaps one of the reasons why some of the exotic pests have been kept outside our borders.

What is your assessment of quarantine in Africa?
Africa has witnessed improvement in the quarantine system. The Inter-Africa Phytosanitary Council (IAPSC) has been playing a tremendous role in harmonizing phytosanitary regulations within the continent, training phytosanitary inspectors, and coming up with pest lists to guide nations, revision of phytosanitary legislation and regulation, and implementation of phytosanitary standards, among others.

Any challenges in carrying out your task?
The problem faced by NAQS is the lack of political will concerning the quarantine system itself. Again, the role of the quarantine service is not very much appreciated, especially in food security. A lot of attention has been focused on how to improve production. The attention placed on plant protection is not as much as that given to plant improvement. But, however successful the improvement program, once you allow pests to come in, they would destroy the crops/gains. This understanding hasn’t been appreciated and it is partly why the sector is given low funding.
Also, the public is not properly being informed about what plant quarantine stands for. Therefore, having voluntary compliance with the regulations is a bit difficult. Another problem is the lack of emergency funds and preparedness to contain the immediate outbreak of pests.

Keeping pests out of borders is a key function of NAQS. Photo by S. Muranaka, IITA.
Keeping pests out of borders is a key function of NAQS. Photo by S. Muranaka, IITA.

In recent times, what are some of the pests you find challenging?
Recently, we have noticed the introduction of fruitflies that are fast devastating fruits in our country. But we need a regional approach to tackle this problem, because the insect involved is a strong flier. We are also faced with the threats of more pests. On cassava, we have Cassava mosaic virus (Ugandan strain) which is ravaging crops in East Africa. Another is the Cassava brown streak virus, which affects cassava leaves and roots. We also have threats of banana bunchy top and banana bacterial wilt. We need to inform people so that they don’t bring planting materials into the country from East Africa. There is the need to put preemptive action in place so that new diseases don’t get to Nigeria and West Africa.

What measures are being put in place to contain the spread of these pests?
For fruitflies, we held a sensitization workshop in 2009 where different stakeholders participated. The FAO is coming up with a regional control measure for the West African bloc to harmonize and adopt. Again, scientists are looking for ways to control these pests. For cassava brown streak disease or CBSD, we have stepped up quarantine efforts aimed at curtailing/scrutinizing the entrance of planting materials from those endemic regions. In the future, we are thinking of training our officers on new tools that aid the inspection of imported planting materials.

Why is the response to crop pests especially slow when compared with the response to animal pests?
When new crop pests come in, the impact for the first few years is not so obvious. This is not the case with the invasion of animal pests when you see the deaths of animals. Perhaps this is the reason why crop pests don’t catch the attention of the Government immediately. We could be talking about fruitflies but people are saying, “Mangoes and oranges are still on the streets.” When the devastation arising from pest establishment, spread, and destruction becomes much serious and farmers start crying, that is the time we get an official response, especially in terms of funding for control measures.

What kind of support would you ask for specifically?
Capacity building to enhance pest interception and diagnosis is very important for us. If you don’t have knowledge about the biology of the pests, you may have problems. The quarantine inspectors/officers need to be trained and the training needs to be continuous. Secondly, a country like Nigeria has a very diverse culture and the climatic conditions to grow crops all year round, so there is a need for us to conduct pest surveillance so that we know the pest status in the country.

There is an ongoing pest survey and this is being done on a crop by crop basis. Scientists from universities, national agricultural research institutes, and international organizations are involved and we hope it will be on a continuous basis with support from the government and stakeholders.

How good an option is biocontrol?
Biocontrol is a good strategy. Everybody wants to deemphasize the use of pesticides because of the effect of chemical residues and there is a lot of emphasis now on food safety. Also there is concern about preserving biodiversity. Now the emphasis is on integrated pest management. The more often you can eliminate the use of pesticides, the better.

How is the collaboration with IITA?
We have a very good and strong relationship with IITA. IITA is our major stakeholder when it comes to germplasm exchange.

IITA has been assisting us in the training of our officers—upgrading their skills—especially in the area of pest diagnosis.

Sometimes when we are handicapped by inadequate facilities IITA steps in. Also IITA is good in the area of information dissemination which had been beneficial to us.
The collaboration with IITA is quite strong and mutually beneficial. Sometimes IITA assists us to attend international workshops and seminars that are relevant for job improvement.

The institute has contributed to our effectiveness in the country.

COMESA: Ensuring sanitary and phytosanitary standards in the region

Martha Byanyima, COMESA
Martha Byanyima, COMESA

Martha Byanyima is a food science and trade expert from Uganda. She has worked in the region on sanitary and phytosanitary (SPS) and agricultural trade programs, supporting countries to carry out the necessary policy and legal reforms and strengthening private sector/industry systems.

Currently, she is the Regional Process and Partnerships Facilitator of the Comprehensive Africa Agriculture Development Program (CAADP) at the COMESA Secretariat. CAADP is the Africa Union Commission and the NEPAD Coordinating Agency (AUC/NPCA) continental program aimed at increasing agricultural productivity in Africa.

She supports development of the regional CAADP process and establishes partnerships for regional investments in key areas prioritized to address the challenges of food security and poverty in the Common Market for East and Southern Africa (COMESA) region. She also leads COMESA’s SPS work program.

What is COMESA all about?
COMESA is a regional economic community (REC) of 19 countries. Our mandate is to create a vibrant and dynamic common market in which business will thrive and expand regionally. We improve the competitiveness of the farmers, entrepreneurs, and traders. In this regard, compliance with international standards, particularly SPS measures, which are a prerequisite for agriculture and agro-industry competitiveness and access to regional and global markets, becomes very important to us.

Why are SPS measures important?
SPS measures are mandatory requirements instituted by governments to protect human, animal, and plant health. These commonly take the form of legislation, inspection, and testing requirements and border controls. Measures similar to SPS had been in place for several decades; however, they became more important under the World Trade Organization (WTO) Agreement in 1995, which recognized the right to protect the agricultural sector and biodiversity. These measures ensure that products produced domestically or imported conform with the regulations and standards of the territory.

The SPS agreement of WTO encourages countries to use common standards, guidelines, and recommendations as developed by the International Plant Protection Convention for plant protection, the Codex Alimentarius Commission for food safety, and the World Organization for Animal Health for pests and animal diseases and zoonoses.

How can compliance with SPS standards facilitate trading and marketing of agricultural goods?
Compliance with SPS standards promotes economic development and trade. SPS is a very important area as we deepen regional integration to reduce barriers to transacting business and to free the movement of agricultural and food products among member countries. COMESA has slowly progressed from a Preferential Trade Area with lower duties charged on goods originating from member countries to a Free Trade Area (FTA) in 2000 where no duty is charged on goods from member countries as long as they comply with the rules of origin and to a full Customs Union in 2009 where a common external tariff is applied to goods imported from outside the region.

How do you promote these standards?
While such a progression is based on tariff reduction and/or elimination to reduce the cost of transacting business, SPS barriers constitute an added cost to business that is not easily quantified, requiring scientific and technical capacity that is often lacking. In this regard, strengthening SPS infrastructure, such as laboratories, and the harmonization of SPS laws, regulations, procedures, and standards are essential for intra-regional trade and successful regional integration.

What is the Green Pass system?
It is the harmonization of SPS measures across COMESA countries and the establishment of equivalence through common certification schemes. The Green Pass system is intended to restore confidence among trade partners and remove SPS barriers to facilitate trade and the marketing of food and agricultural products within the region.

How can Green Pass help trade and markets in East and Southern Africa?
Since SPS is an important area for effective markets in the context of regional integration, COMESA has a regional work program aimed at mobilizing resources to address the critical gaps in the SPS systems of regional member countries. The work program has four result areas: (a) common certification schemes (standards), (b) monitoring, surveillance, and preparedness for emergencies, (c) improved exchange of SPS information between the public and private sectors, and (d) improved regional leadership and coordination.

Our activities include encouraging the adoption of regional standards, establishing regional SPS databases and information systems, establishing modalities and piloting mutually agreed certification schemes such as the Green Pass, awareness and training workshops, and strengthening SPS infrastructure, such as laboratories.

How are you implementing the Green Pass system?
The first step in creating awareness and motivating countries to step up harmonization efforts is the establishment of the SPS legal framework to guide countries on the necessary policy and legal reforms. At the heart of the legal framework is the Green Pass system.

Enforcing phytosanitary policies and regulations in the region would benefit  trade and commerce, and ultimately the farmers and consumers. Photo by IITA.
Enforcing phytosanitary policies and regulations in the region would benefit trade and commerce, and ultimately the farmers and consumers. Photo by IITA.

What can international organizations or networks do to help promote standards and the Green Pass system?
Currently we are developing proposals to pilot commercially driven Green Pass certification schemes. For example, we will support the member countries to develop common protocols to address the problem of fruitflies in banana, passion fruit, and avocado, or aflatoxins in maize. Such protocols, developed and piloted by the private sector and governments, with support from COMESA, will constitute the science to inform the Green Pass certification scheme. The protocols and related infrastructure, such as reference laboratories, are regional public goods that serve both the private and public sectors.

Who are your partners in implementing the system?
In piloting the Green Pass certification scheme, we envisage partnerships with the private sector, regional institutions with relevant expertise, such as IITA and governments. The decision to implement the Green Pass was endorsed by ministers of agriculture in July 2010, and thus all countries will be involved to the extent that the Green Pass is the viable option to resolve the existing SPS problem.

What are some of your challenges?
The greatest challenge is to create a common understanding of the Green Pass concept; there are variations in the way it is understood by experts, governments, the private sector, and other stakeholders.

Another challenge is traditional certification schemes that are based on international standards but may not respond to intraregional trade challenges. For example, South Africa (SA) demands a certificate of origin from Zambia honey exporters in addition to the animal health certificate issued by the Government. The Zambia market, however, has lots of food imports from China which treats bees with antibiotics. SA regulations restrict antibiotic residues in honey. Therefore, SA demands full proof that the honey originates from Zambia and not China, where the honey is not organic. In this case the Green Pass would come in handy to establish a certification scheme that includes traceability protocols and a certificate of origin in addition to the animal health certificate from the Government.

Of course, there are also constraints in both human and financial resources.

Food supplies being loaded on trucks for transportation to urban centers. Photo by IITA.
Food supplies being loaded on trucks for transportation to urban centers. Photo by IITA.

Why a common market for East and Southern African?
On 22 October 2008, heads of States and Governments of the 26 countries in Eastern and Southern Africa that have membership in COMESA, EAC, and SADC, made a landmark decision that the three RECs should immediately start working towards a merger into a single FTA to deepen regional integration. The three have a combined population of 565 million, and a gross domestic product of US$875 billion. These are 57% of Africa’s population and 59% of the GDP. The total land mass of the COMESA-EAC-SADC region is 14.8 million km² or 49% of Africa’s total land mass.

The decisions of the Tripartite Summit have far-reaching implications on the operations of the three RECs with regard to joint planning, programming, and implementation of the common agenda. In addition, there will be a need for development partners to rationalize and harmonize their support in the tripartite framework.

Since then, the Agreement to establish the Tripartite FTA has been developed and will be signed in mid-2011. The purpose of the Agreement is to enhance collaboration (through joint investments) and avoid the duplication of effort that has characterized the COMESA region as a result of multiple membership of the regional communities.

Annex 14 of the Agreement to establish the Tripartite FTA specifically addresses SPS, requiring Tripartite member countries to harmonize SPS measures and, where necessary, to implement joint programs.

What role do you envisage for IITA in COMESA?
IITA and other regional specialized scientific institutions have a huge role to play They can ensure that the best science informs agricultural planning and development, using the CAADP framework that has proved to be an effective instrument in harnessing knowledge and bringing it to sector planning processes at the national and regional levels. However, governments are responding slowly to the all-inclusive principle of CAADP; non-State actors such as IITA, farmers, and the private sector have not been engaged to the extent necessary to achieve the effective transfer of scientific knowledge and expertise.

What support do you need?
At this stage, it is important for all players to recognize the transformation taking place in the agricultural sector on this continent—the bumper harvests and the increased investments. This is largely driven by RECs through support to country CAADP processes and regional integration programs. Policy reforms and technical support are important elements of the transformation process that cannot be achieved by RECs acting alone; specialized institutions such as IITA and other nonstate actors need to fill this gap. It is, thus, important that development partners, donors, and other actors respond positively to the call by the African Union to align with regional priorities embedded in the RECs’ regional integration programs and in so doing support the transformation process currently taking place on this continent.

What is your vision for African agriculture, trade, and economy?
I look forward to deeper regional integration among the African countries. The Tripartite framework provides the best means to achieve this. By strengthening infrastructure on key trade corridors and facilitating the transport of goods while strengthening the countries’ SPS systems through the best science available, agricultural value chains will expand beyond the COMESA region. New opportunities will be opened for the private sector. At the same time, it is my hope that the Tripartite framework will encourage collaboration in scientific research and innovations to further strengthen value addition and trade in value-added food products.

A hot bath for the suckers!

An effective treatment against nematode and weevil pests of banana and plantain

Plantain plant with three sword suckers, field trial on IITA campus, Ibadan, Nigeria. Photo by A. zumFelde, IITA.
Plantain plant with three sword suckers, field trial on IITA campus, Ibadan, Nigeria. Photo by A. zumFelde, IITA.

Banana and plantain (Musa spp.) are important food crops for millions of people all over the world. The banana is the most popular fruit in the world and number one in international trade. The FAO estimates that over 100 million t of banana and plantain were produced worldwide in 2007. In sub-Saharan Africa (SSA), over 70 million smallholder farmers depend on the two crops for their food and income.

Banana and plantain production is greatly constrained by pests and diseases that lead to annual losses of millions of US dollars. The most important pests are nematodes (several species) and weevils (Cosmopolites sordidus) that are found in the soil and roots.

Nematodes attack the roots, hampering the uptake of nutrients from the soil and drastically reducing yield. In severe cases, they topple the whole plant. Weevils, on the other hand, attack the plant’s underground corm, weakening the plant and causing stem breakage. Average production losses from nematodes are estimated at 30% of the harvests of highland banana in East Africa and can exceed 60% for plantain in West Africa.

These two pests are spread from one farm to another through the planting of infested suckers. Farmers can avoid infesting their farms by ensuring that they plant disease- and pest-free suckers, such as those derived from tissue culture. These are, however, out of reach for the millions of small-scale farmers in sub-Saharan Africa.

Farmers dipping peeled suckers in boiling water. Source: D. Coyne, IITA.
Farmers dipping peeled suckers in boiling water. Source: D. Coyne, IITA.

Research has shown that peeling and treating the suckers in hot water, at 50 °C, can effectively remove both nematodes and weevils and their eggs. This method has worked successfully for commercial farms and organized cooperatives but not for small-scale farmers. This is because a thermometer must be used to ensure precision and the right temperature and this is not readily accessible to the farmers in SSA.

IITA’s scientists Danny Coyne and Stefan Hauser have developed an easier method that is just as effective by simply immersing the peeled or unpeeled suckers in boiling water for 20–30 seconds.

The counting
The duration of 20–30 seconds can be achieved by simply counting from 1 to 30. Farmers can also use small objects, such as pebbles, to mark the time: picking the pebbles one by one and placing them in a small container. The counting takes about 1 second/item but farmers can check the time for more accuracy.

This technique has proven to be friendly to small-scale farmers and is better than the hot water treatment at 50 °C as the time taken to treat a sucker is reduced and the measurement of the temperature and timing is simplified. It effectively disinfects suckers of various sizes without affecting their germination

Plantain field planted with suckers treated in boiling water. Photo by A. zumFelde, IITA.
Plantain field planted with suckers treated in boiling water. Photo by A. zumFelde, IITA.

The method is radical and requires skill and care when it is promoted to farmers who may be sceptical at first. The scientists recommend the use of a demonstration plot to introduce the technology and convince farmers to adopt it. They must keep within 30 seconds as otherwise they risk damaging the suckers, especially those that are small-sized.

Although the technology requires a fuel/energy source and the process has to be followed precisely, it is definitely a much easier method to use than the hot water treatment.

Using boiling water to treat the suckers has the potential to improve banana and plantain productivity by eliminating the two pests.

Investing in aflasafeâ„¢

aflasafeâ„¢ is a cost-effective, safe, and natural method for preventing the formation of aflatoxin in maize and other susceptible commodities in the field and also in postharvest storage and processing. It is providing hope for African farmers and opening doors for entrepreneurs looking to invest on a winning formula in the agricultural sector.

Maize farmers receive aflasafeâ„¢ from IITA. Photo by IITA.
Maize farmers receive aflasafeâ„¢ from IITA. Photo by IITA.

Scientific studies suggest that investment in aflasafeâ„¢ in Africa is viable, not only for profit but also to improve people’s health. For instance, the study of Wu and Khlangwiset (2010) estimated that the cost-effectiveness ratio (CER; gross domestic product multiplied by disability-adjusted life years saved per unit cost) for aflatoxin biocontrol in Nigerian maize ranged from 5.10 to 24.8. According to the guidelines from the World Health Organization (WHO 2001), any intervention with a CER >1 is considered to be “very cost-effective”.

About aflatoxins
Produced by the fungi Aspergillus spp., aflatoxins are highly toxic fungal substances that suppress the immune system, and cause growth retardation, liver cancer, and even death in humans and domestic animals.

Aflatoxins also affect the rate of recovery from protein malnutrition and Kwashiorkor, and exert severe nutritional interference, including in protein synthesis, the modification of micronutrients, and the uptake of vitamins A and D.

Exposure in animals reduces milk and egg yields. The contamination of milk and meat is passed on to humans after consumption of these products. Aflatoxins affect cereals, oilseeds, spices, tree nuts, milk, meat, and dried fruits. Maize and groundnut are major sources of human exposure because of their higher susceptibility to contamination and frequent consumption.

The toxins are most prevalent within developing countries in tropical regions and the problem is expected to be further exacerbated by climate change.

The high incidence of aflatoxin throughout sub-Saharan Africa aggravates an already food-insecure situation. Agricultural productivity is hampered by contamination, compromising food availability, access, and utilization. Unless aflatoxins in crops and livestock are effectively managed, marketable production and food safety cannot improve. Thus, the economic benefits of increased trade cannot be achieved.
Aflatoxins cost farmers and countries hundreds of millions of dollars annually. These losses have caused crops to be moved out of regions, companies to go bankrupt, and entire agricultural communities to lose stability.

IITA staff producing aflasafeâ„¢ in the lab. Source: R. Bandyophadyay, IITA.
IITA staff producing aflasafeâ„¢ in the lab. Source: R. Bandyophadyay, IITA.

aflasafeâ„¢ to the rescue
An innovative scientific solution in the form of biocontrol has been developed by the US Department of Agriculture’s Agricultural Research Service (USDA-ARS). This breakthrough technology,already widely used in the United States, reduces aflatoxins during both crop development and postharvest storage, and throughout the value chain.

IITA and USDA-ARS have been collaborating since 2003 to adapt the biocontrol for Africa. They achieved significant breakthroughs that resulted in the development of an indigenous aflatoxin technology in Nigeria, now called aflasafeâ„¢. aflasafeâ„¢ contains four native atoxigenic strains of Aspergillus flavus that outcompetes and replaces the toxin-producing strains, thus reducing aflatoxin accumulation.

IITA and partners conducted trials in Nigeria. Native atoxigenic strains reduced contamination by up to 99%. The National Agency for Food and Drugs Administration and Control (NAFDAC) gave IITA provisional registration to begin testing of the inoculum of a mixture of four strains under the trade name aflasafeâ„¢. In 2009 and 2010, maize farmers who applied aflasafeâ„¢ achieved, on average, a reduction of >80% in aflatoxin contamination at harvest and 90% after storage.

Groundnut farmers also achieved more than 90% reduction in Nigeria and Senegal using a version of aflasafeâ„¢ with native atoxigenic strains from Senegal.

In the future
The success recorded so far in the control of aflatoxin comes from aflasafeâ„¢ produced in the lab. Consequently, to meet the demands of farmers in sub-Saharan Africa, large-scale production is needed.

In Nigeria, for instance, nearly 30% of harvested maize has high levels of aflatoxins and is prone to being rejected by the feed industry. In Kenya, last year because of aflatoxin contamination, more than two million bags of maize were declared unfit for human consumption in the Eastern and the Coast provinces. Some countries, such as Senegal, have lost groundnut export market to the European Union due to aflatoxin contamination.

Commercial production of aflasafeâ„¢ would allow easy and widespread availability of a simple solution to the most recalcitrant problem affecting farmers and consumers. The monetized value of lives saved, quality of life gained, and improved trade by reducing aflatoxin far exceeds the cost of aflasafeâ„¢ production.

Wu F and Khlangwiset P. 2010. Health economic impacts and cost-effectiveness of aflatoxin-reduction strategies in Africa: case studies in biocontrol and post-harvest Interventions. Food Additives & Contaminants. Part A, 27: 4, 496—509, First published on: 05 January 2010 (iFirst).

Related website

Aflatoxin management website –

Sustainable production and distribution of clean banana

Bi Irie Vroh,

Banana (Musa spp.) including the plantain type are among Africa’s most important staple food and cash crops. Nearly 30 million t of banana are produced yearly in Africa, mostly by smallholders and consumed locally.

The major edible types are parthenocarpic (produces fruit without fertilization) and seedless. They are propagated traditionally by planting corms and suckers (daughter plants that grow from the rhizomes at the base of mother plants).

However, propagation material derived from the infected mother stocks results in perpetuation of diseases (e.g., viruses such as banana bunchy top, banana streak) and pests (e.g., nematodes and weevils) leading to low yields and poor quality fruits.
Due to the unavailability of disease- and pest-free or clean planting materials, farmers in sub-Saharan Africa traditionally plant suckers derived from their own plantations, most of which are affected with pests and diseases.

IITA has been using three approaches to generate clean planting material of farmer-favored banana cultivars:

Boiling water treatment of suckers: Suckers are submerged in boiling water for 30 seconds to kill nematodes and weevils. This method is efficient and easy for farmers, but it has low output and is laborious.

IITA’s Emmanuel Njukwe, Paula Bramel, and Bi Irie Vroh visit the Fritz Jakob Foundation. Source: B. Vroh, IITA.
IITA’s Emmanuel Njukwe, Paula Bramel, and Bi Irie Vroh visit the Fritz Jakob Foundation. Source: B. Vroh, IITA.

Macropropagation using the PIF technique: Through the technique known as PIF (plantes Issues de Fragments de tige) tens of good quality plantlets are produced within two months at relatively low costs. In this approach, the primary buds of entire suckers or fragments of corms are destroyed and axillary buds are exposed to high humidity to induce sprouts which are then harvested, hardened, and distributed.

This approach can be implemented in remote rural areas near farmers’ fields or by NGOs in direct contact with farmers for training and the distribution of good planting materials. This procedure is simple to replicate using locally made humidity chambers.

Micropropagation: Also known as in vitro production of tissue culture (TC) material this is the most efficient approach to the production of clean planting material in terms of throughput and germplasm exchanges across international borders. In vitro plantlets are micropropagated in the TC laboratory of IITA in Ibadan, Nigeria, and hardened first in the acclimatizing rooms, then in screenhouses before being distributed to farmers. Planting materials from preferred landraces and improved hybrids are propagated through TC, and hardened for use or maintained in a conservation cold room where each genotype is replicated several times from the initial meristem for future use.

IITA’s Delphine Amah holding racks of TC plants in a growth room. Source: B. Vroh, IITA.
IITA’s Delphine Amah holding racks of TC plants in a growth room. Source: B. Vroh, IITA.

Combining the TC pipeline with the macropropagation through PIF, IITA regularly distributes thousands of seedlings to NARS, NGOs, and farmers in West and Central Africa. Besides the preferred local varieties, the most distributed improved materials include the plantain hybrids PITA 14, PITA 21, and PITA 23 and the cooking banana hybrid BITA 3. These hybrids express a higher level of tolerance for black Sigatoka diseases compared with local varieties.

IITA trains farmers in applying boiling water treatment of suckers and macropropagation by PIF to produce clean planting material. However, IITA primarily uses micropropagation as the method of choice for conservation, propagation, and distribution of germplasm, and also to support its breeding programs. IITA also provides training programs on TC operations for NARS. For IITA’s projects in West Africa, clean planting materials are produced by TC or by PIF, hardened and raised in screenhouses, and then transferred to specific project sites.

Hardening of clean planting materials produced by TC and PIF methods. Source: B. Vroh, IITA.
Hardening of clean planting materials produced by TC and PIF methods. Source: B. Vroh, IITA.

In rural communities, IITA emphasizes training for farmers and rural entrepreneurs so they can produce clean planting materials in their own communities. These various efforts enhance the farmers’ access to clean planting materials and also encourage involvement of commercial operators in distribution of planting materials. The improvement of the capacity of NARS and the involvement of the private sector are needed to scale up the technologies for the sustainable production of clean planting materials of banana and plantain.