Cassava improvement in the era of “agrigenomics”

Ismail Yusuf Rabbi (, Melaku Gedil, Morag Ferguson, and Peter Kulakow
I. Rabbi, Postdoctoral Fellow (Molecular Genetics); M. Gedil, Head, Bioscience Center, IITA, Ibadan, Nigeria; M. Ferguson, Molecular Geneticist, IITA, Nairobi, Kenya; and P. Kulakow, Cassava Breeder, IITA, Ibadan, Nigeria

Pro-vitamin A 'yellow root' cassava developed by the IITA cassava breeding program. Photo by IITA.
Pro-vitamin A 'yellow root' cassava developed by the IITA cassava breeding program. Photo by IITA.

In the last 45 years, IITA has played a pivotal role in the genetic improvement of cassava for resource-poor farmers in sub-Saharan Africa (SSA). More than 400 cassava varieties have been developed that are not only high yielding but also resistant to diseases and pests. Many of these improved varieties have been extensively deployed in SSA and have helped to avert humanitarian crises caused by the viral disease pandemics that devastated local landraces in East and Central Africa. The cassava breeding program in Ibadan has a collection of more than 750 elite cassava clones representing current and historical materials accumulated over the last 45 years. These materials, referred to as the genetic gain collection (GGC), are accompanied by extensive field evaluation (phenotypic) data. In addition, the active breeding collection contains over 1000 African landraces and more than 400 new advanced breeding clones that are also accompanied by phenotypic data, including observations of disease and pest resistance, plant architecture, flowering ability, and performance in storage root yield. The most recent success of the conventional cassava breeding program culminated in the release of three vitamin A cassava varieties by the Government of Nigeria. These varieties (IITA TMS I011368, IITA TMS I011371, and IITA TMS I011412) were first cloned from seedlings in Ibadan in 2001 and have been subjected to extensive field testing throughout Nigeria. While almost all cassava in Nigeria are currently white fleshed, vitamin A cassava produces yellow-fleshed roots with nutritionally significant concentrations of carotenoids that produce vitamin A in the human body when consumed as yellow gari or fufu. In cooperation with HarvestPlus, IITA and partners will distribute vitamin A cassava planting materials to more than 25,000 farmers in 2013. New yellow-fleshed genotypes in the pipeline promise continued improvement in pro-vitamin A content, yield, and dry matter in the coming years.

Preparation of cassava DNA for genotyping by sequencing. Photo by IITA.
Preparation of cassava DNA for genotyping by sequencing. Photo by IITA.

As the vitamin A cassava illustrates, the genetic improvement of cassava has mostly been achieved through conventional breeding methods based on phenotypic selection. The only known direct application of molecular markers in cassava breeding is selection for resistance to cassava mosaic disease and cassava green mite. Recent advances and a reduction in the cost of the next-generation sequencing technologies now promise to usher in a new era for cassava breeding that will combine the success of conventional hybridization, selection, and multilocational yield trials with the latest advances in genomic resources.

Setting the stage for “next-generation cassava breeding”
Cognizant of the potential of marker technologies to improve the efficiency and effectiveness of cassava breeding, IITA, in collaboration with partners, embarked on the development and deployment of molecular markers1. With the recent accumulation of genomic resources in cassava research, including the first full cassava genome sequence2, our emphasis at IITA has shifted towards the application of these resources in molecular breeding3. One recent achievement is the identification and validation of nearly 1500 single nucleotide polymorphism (SNP) markers through an international collaboration led by IITA’s geneticist, Morag Ferguson4. These SNPs have been converted to a highly parallel hybridization-based genotyping system that has been shared with the international cassava research community through partnership with the Generation Challenge Program (GCP).

An example of an SNP genotyping data plotted with KBioscience’s SNPviewer software. Inset: raw SNP genotyping data from Illumina’s GoldenGate®assay.
An example of an SNP genotyping data plotted with KBioscience’s SNPviewer software. Inset: raw SNP genotyping data from Illumina’s GoldenGate®assay.

In addition, the first SNP-based genetic linkage map of cassava has been developed by IITA in collaboration with Heneriko Kulembeka of the Agricultural Research Institute (ARI), Ukiriguru, Tanzania. A linkage map is analogous to landmarks (SNP markers in this case) placed along chromosomes that guide researchers to genes or genomic regions controlling traits of interest. Such a linkage map is an indispensable tool for marker-assisted selection (MAS). SNP and SSR markers have also been applied to uncover quantitative trait loci (QTL) associated with resistance to cassava brown streak disease (CBSD)―which is ravaging cassava production in Eastern and Southern Africa―in a collaboration between IITA, CIAT, and ARI-Tanzania. Another dramatic development in cassava genomics is the recently completed sequencing of the cassava genome through the partnership of the US Department of Energy’s Joint Genome Institute and 454 Life Sciences2.

The progress in next- generation technologies has drastically reduced the costs of DNA sequencing so that genotyping-by-sequencing (GBS) is now feasible for species such as cassava, ushering in a new era of agricultural genomics5. This will revolutionize the application of genomic tools for cassava improvement. GBS involves the cutting of genomic DNA into short pieces at specific locations using a restriction enzyme. The ends of these pieces are sequenced using techniques that allow sequencing of many samples at the same time. The beauty of this method is the use of adaptors containing barcodes (unique tags) that are enzymatically joined to the digested DNA fragments, enabling simultaneous sequencing or multiplexing of up to 384 samples in one sequencing reaction. This economy of scale greatly reduces the cost of processing each individual DNA to less than $10/sample. Approximately 200,000 markers can be identified and mapped in a very short time. With this powerful tool, breeders may conduct genomics-based research that was inconceivable a couple of years ago. Some of the exciting new research applications include polymorphism discovery, high-density genotyping for QTL detection and fine mapping, genome-wide association studies, genomic selection, improving reference genome assembly, and kinship estimation.

High-density QTL mapping and fine mapping
In the past, a limitation for QTL mapping was the number of markers on a genetic linkage map. With new SNP-based technologies this is no longer a limitation. This allows for fine mapping of QTLs so long as a sufficient number of individuals in the mapping population can be developed. IITA, in collaboration with national partners [ARI-Tanzania and National Crops Resources Research Institute (NaCRRI), Uganda], is using SNPs to discover QTLs associated with sources of tolerance for CBSD.

Preparation of gari, the most popular food product from cassava. Photo by IITA.
Preparation of gari, the most popular food product from cassava. Photo by IITA.

The next frontier for cassava genomics
Using the genotyping by sequencing approach, scientists from IITA and Cornell University, USA, are currently genotyping more than 2000 accessions of cassava, including released varieties, advanced breeding lines, and landraces from Africa. This is a pilot study of genomic selection funded by the Bill & Melinda Gates Foundation to explore the potential for using the IITA breeding collection, including genetic gain, local germplasm, and current advanced breeding lines, as the base population to begin genomic selection for West Africa. The IITA breeding collection has been extensively characterized in many locations and over many years. The convergence of high-density SNP data and extensive phenotypic data in IITA’s cassava collection sets the stage for the implementation of genome-wide association studies (GWAS) and genomic selection (GS) in breeding. The aim of GWAS is to pinpoint the genetic polymorphisms underlying agriculturally important traits. In GWAS, the whole genome is scanned for significant marker-trait associations, using a sample of individuals from the germplasm collections, such as a breeder’s collection. This approach of “allele mining” overcomes the limitations of traditional gene mapping by (a) providing higher resolution, (b) uncovering more genetic variants from broad germplasm, and most importantly, (c) creating the possibility of exploiting historical phenotypic data for future advances in breeding cassava.

A schema of genomic selection (GS) processes, starting from phenotyping and genotyping of the training population and selection of parental candidates via genomic estimated breeding value (GEBV)–based selection. Note that selection model improvement can be performed iteratively as new penotype and marker data accumulate.
A schema of genomic selection (GS) processes, starting from phenotyping and genotyping of the training population and selection of parental candidates via genomic estimated breeding value (GEBV)–based selection. Note that selection model improvement can be performed iteratively as new penotype and marker data accumulate.

GS is a breeding strategy that seeks to predict phenotypes from high-density genotypic data alone, using a statistical model based on both phenotypic and genotypic information from a “training population”. For cassava, phenotyping is the slowest and most expensive phase of the crop’s breeding cycle because of the crop’s low multiplication ratio of between 5 and 10 cuttings/plant. Thus, it takes several cycles of propagation (up to 6 years) to carry out a proper multilocational field trial evaluation. The implementation of GS at the seedling stage should: (a) dramatically reduce the length of the breeding cycle, (b) increase the number/unit time of crosses and selections, and (c) increase the number of seedlings that could be accurately evaluated. The reduced breeding cycle means that the ”engine of evolution,” i.e., recombination and selection, can proceed at a rate that is three times as fast as phenotypic-based selection, while saving resources. In conclusion, cassava breeding in IITA is being redefined, thanks to the increasing availability and deployment of genomic resources. Combining these resources with IITA’s long-standing conventional breeding pipeline means that the best days of cassava improvement lie ahead. These efforts will ultimately satisfy the increasing need for more healthy and nutritious food produced in environmentally sustainable ways.

1 Lokko et al. 2007. Cassava. In: Kole et al (ed). Genome mapping and molecular breeding in plants, Vol. 3. Pulses, Sugar and Tuber Crops. Springer-Verlag Berlin Heidelberg.
2 Prochnik S., P.R. Marri,B. Desany, P.D. Rabinowicz, et al. 2011. Tropical Plant Biol. doi:10.1007/s12042-011-9088-z. 3 Ferguson M., I.Y. Rabbi, D-J.Kim, M. Gedil, L.A.B. Lopez-Lavalle, and E. Okogbenin. 2011a. Tropical Plant Biol. DOI 10.1007/s12042-011-9087-0.
4 Ferguson M.E., S.J. Hearne, T.J. Close, S. Wanamaker, W.A. Moskal, C.D. Town, J. de Young, P.R. Marri, I.Y. Rabbi, and E.P. de Villiers. 2011b. Theor Appl Genet. DOI: 10.1007/s00122-011-1739-9.
5 Elshire R., J. Glaubitz, Q. Sun, J. Poland, and K. Kawamoto. 2011. PLoS ONE 6:e19379.

A classical approach to saving life’s variety


The beginning of the tragedy to come wasn’t so clearly understood, but it became more visible as scientists studied the demise of the dinosaurs and came to consider, over the centuries, the reduction of species. The destructive trend is clear and fast encroaching on domesticated plants and wild animals alike, putting some species such as the whales and panda bears on the endangered list and threatening food security.

Consequently the world is losing biodiversity at rates not seen before.

In Nigeria, for instance, the country has lost some 6.1 million hectares or 35.7% of its forest cover since 1990. Worse, Nigeria’s most biodiverse ecosystems—its old-growth forests—are disappearing at an even faster rate. Since 2000, Nigeria has been losing an average of 11% of its primary forests every year, twice as fast as in the 1990s.

Adeniyi Jayeola, a Senior Lecturer in plant systematics, Department of Botany and Microbiology, University of Ibadan, says, “The deterioration we find worldwide today is unprecedented. Unless we act together, and quickly too, we may sooner than later induce a global ecological crisis far beyond the control of any technology. It is a multi-faceted challenge requiring all hands to be on deck.”

Areas visited in Nigeria in particular and the world in general have shown that man has demonstrably failed to accord the environment the respect it deserves, whether this is the air, sea, or land.

Consequently, out of more than 10,000 species in the past people today depend on only 12 species for 80% of all their food.

To stem the loss of biodiversity, in 2002, 10 years after the Convention on Biological Diversity (CBD), 193 nations participating in the treaty had agreed to “achieve by 2010 a significant reduction of the current rate of biodiversity loss at the global, regional, and national level as a contribution to poverty alleviation and to the benefit of all life on earth.”

This year, parties are converging to take stock of the journey so far but the general assumption is that more action needs to be taken.


What is biodiversity worth?
As the world prepares to take a retrospect on set targets, we can, however, no longer expect nature to provide us with a free lunch. Efforts to protect natural resources could depend on our putting a price tag on the goods and services they provide us. The United Nations Environment Programme’s 2007 Global Environment Outlook 4 report states that the pollination of crops by honeybees alone is worth US$2−8 billion, and the global herbal medicine market was worth US$43 billion back in 2001.

In addition, the tropical forests provide a whole variety of leaves, fruits, barks, roots, and nuts which form the mainstay of the modern pharmaceutical industry. We depend totally on the variety of life for our food security. The loss of biodiversity therefore presents us with one of the toughest puzzles, and concrete steps are needed to slow down the tide.

Innovative approaches to contain biodiversity loss
Despite the decline in species, which are currently disappearing at 50–100 times the natural rate, a regenerated forest on IITA’s campus in Ibadan has proved that indeed we can restore nature if we so desire. The forest, located on the west bank in IITA, sits on 350 ha of land and was initiated from abandoned farmland.

Forty three years after its establishment, this swathe of securely protected trees stands out as one of the least disturbed patch of forest in Nigeria with floristic characteristics ranking almost at par with a natural forest. The regeneration of the forest has brought appeal from the scientific community as researchers are seeking to uncover and understand the variation in plant species, composition, and structure of a forest regrowing from abandoned farmland and the causes of the variation.

David Okali, Chair, Nigerian Environmental Study/Action Team, who plans to do the study on the IITA forest with other colleagues, says such long-term studies are rare. The results on the rate of growth will be used in calculating directly the rate of carbon storage in the forest.
As the world marks the International Year of Biodiversity, Okali says deliberate efforts to conserve nature are important to stem biodiversity loss, stressing that the reestablishment of the IITA forest presented a good scenario for conservation.

Apart from forest regeneration, Okali says local communities could adopt other initiatives to curtail the loss of biodiversity. These include a return to traditional practices that made it a taboo for people to cut some species of trees or kill sacred animals. Also traditionally regulating hunting practices, and planting and protecting shade-providing fruit trees that adorn the village squares will help.

The success of the regenerated forest at IITA has reinforced the possibility that the opportunity is still within our reach.

Based on this experience, it is clear that the plan by parties to the CBD to create a global network of terrestrial and of marine protected areas can be done if there is the will and the means. How this will happen and funded is a question that all Governments must answer.

Yam festival

The Yam Festival is a popular holiday in Ghana and Nigeria, two countries in the yam belt in West Africa. It is usually held in the beginning of August at the end of the rainy season. The festival is named after yam, which are the first crops of the season to be harvested. It marks the end of one farming season and the beginning of another, a season of plenty.

Man with huge yam tuber. Photo by IITA.
Man with huge yam tuber. Photo by IITA.

In West Africa, yam cultivation is associated with a wide variety of beliefs and taboos which govern planting, harvesting, and consumption. Sacrifices are offered to the gods at various stages of growth from planting to harvest. These are also performed in various yam-growing areas of the Pacific.

Sometimes cocoyam substitutes for yam in offering food sacrifices to earth deities. Raw yam is also used for forecasting harvest prospects.

The New Yam Festival is a 2-day cultural festival in southern Nigeria. Dancers wear masks that reflect the seasons or other aspects of nature. It is chiefly celebrated by two large cultural groups: the Ibo or Igbo of the southeast, and the Yoruba of the southwest. The Ibo call the festival Iri Ji; ji means yam. The Yoruba call it Eje.

Various communities celebrate Iriji in different ways. But all have a parade, songs, dancing, and drumming. Because a good yam harvest is important for survival, the people give thanks to the spirits of the earth and sky. The New Yam Festival is celebrated by gathering, blessing, and then feasting on the new yams.

The Yam Festival is called the Homowo or “To Hoot at Hunger” Festival. The people hope for a good harvest so that no famine will hit in the coming year. This festival takes place in many rural communities. Women dig up the yam and carry them home in baskets on their heads. Villagers gather together as the women and young girls prepare the feast, with the yam as prized food. They choose a young boy to carry the best yam to the festival dinner, and another boy follows him beating a drum. Other young people from the village march to the beat of the drum and the sound of a woodwind instrument, and sometimes musket fire. Chiefs, under umbrellas and wearing robes made from the famous, brightly colored Ghanaian Kente cloth, follow the yam, and the young people dance. Other activities include singing, wearing animal masks, and displaying fetishes.

Outside Africa
In Indonesia, the traditional yam festival occurs once every 4 years. A big seed yam weighing 2-3 kg is planted near a tree which is stripped of its bark to provide the yam vine with sturdy support. The yam is watered during the dry season and harvested after 4 years for the festival. Similar festivals are celebrated in the Pacific Islands, especially in Papua New Guinea.

History and legend
The New Yam Festival in Nigeria also has religious meaning for those who still practice the native tribal religions. Although most Nigerians are either Muslim or Christian, many still honor the spirits of the land and the souls of their ancestors in their everyday lives and in their ceremonies.

According to Ibo myth, a man named Ibo, or Igbo, gave the tribe its name. A very old legend explains how the yam and the cocoyam, another starchy root vegetable, became such important foods for the Ibo.

During a time of terrible famine, a tribesman named Ibo was told by a powerful spirit that he must sacrifice his son Ahiajoku and daughter Ada to save his other children from starvation. After Ahiajoku and Ada were killed, the spirit told Ibo to cut their bodies into many pieces and to bury the pieces in several different hills of soil.

Ibo did these, and, in a few days, yam leaves sprouted from the hills containing pieces of Ahiajoku’s flesh, and leaves of the cocoyam sprouted from the hills where Ada’s flesh was buried. The spirit told Ibo and his living children to farm these two crops. They did so, and when the yam and cocoyam were harvested, they provided food that kept the family from starvation. Because of this, Ahiajoku is worshiped as the god of yam. He is greatly honored during the New Yam Festival.

Orkwor, G.C., R. Asiedu, and I.J. Ekanayake, editors. 1998. The importance of yams. Chapter 1 in Food yams: Advances in research. p. 10.

The butterflies of IITA

Robert Warren,

Charaxes imperialis. Photo by IITA.
Charaxes imperialis. Photo by IITA.

IITA boasts a wide range of butterflies. Knowledge about the diversity of these species, however, is incomplete. For instance, a preliminary survey conducted from 2002 to 2009 has confirmed the presence of 149 butterfly species. The actual number could fall somewhere in the range of 250 to 400.

A survey carried out in a directly equivalent location (Olokomeji Forest Reserve) in the late 1960s found 267 species, with quite limited collecting inputs (estimated total >450). A more complete survey at Agege, near Lagos in southwestern Nigeria, found more than 380 species. This location is in the moist evergreen forest zone, and is fairly comparable to the secondary nature of the IITA forest.

Completing a survey at IITA would yield information useful for conservation. The fact that the IITA forest is small and now isolated would allow the assessment of pressures on extinction. Despite the enormous destruction of West African forests to date, records show that butterfly extinction has yet to occur when viewed on a regional scale.

While the primary consideration for survival will be the presence of the host plants, there is also a consideration of the range required for survival. Knowledge of the total species population within IITA and specific species present could be likely to provide answers on the cut-off point where the range is too small for survival of certain species groups.

The IITA forest is also an important conservation target itself because of its location. It is quite possibly the westernmost representative of semi-deciduous forest on this scale before the Dahomey gap. Attempts to locate equivalent forests within Nigeria to the west of IITA, guided by satellite imagery, yielded only one small, unprotected patch (5 km west of Tapa). Forest reserves have all but disappeared. Several butterfly species (e.g., Liptena ilaro, Euriphene kiki, Axiocerses callaghani) found near IITA have not been seen elsewhere, pointing to the biogeographical importance of such habitats. If results eventually show that the IITA forest is indeed too small to allow the survival of all the species that should be present in an equivalent forest type, it will nonetheless remain an important refuge.

Display cases of all but a handful of the 149 species observed to date have been donated to IITA to promote further interest.* A specimen of the very rare species Melphina noctula was found at IITA (there are only three in the Natural History Museum), and has been donated to the African Butterfly Research Institute in Nairobi, Kenya.

An in-depth study of the IITA butterflies would be of international interest and importance because very few such surveys have been completed in Africa. Comparison with our knowledge of the fauna of western Nigeria could shed light on the importance of a forest such as IITA’s for the long-term survival of species. It could be one of the localities proposed for studying the survival of the butterflies between now and 2100. Finally, it could show if new species are added as the forest matures from its secondary status over time.

*Specimens were collected, identified, mounted, and donated recently by the author to IITA. These are currently on show at the IITA International School in Ibadan, Nigeria. The author is a buttefly expert who came to Nigeria at the age of 4 months. He has been surveying butterflies all over Nigeria and also at IITA since 2002.

The state of Nigeria’s forests

David Ladipo,

The IITA forest. Photo by K. Lopez, IITA.
The IITA forest. Photo by K. Lopez, IITA.

Nigeria is blessed with a large expanse of land and variable vegetation, but this important resource is not sustainably used or managed. Many rural dwellers in the past have treated our forest resources as inexhaustible.

Today the story is different. The average rural dweller now realizes that the forest is “finished,” but poverty continues to force people to exploit even the relics of remaining forests.

The Federal Government has, over the years, attempted to generate baseline data on the state of our forests including their use. These studies have provided data for a better understanding of the state of forest resources, the rate of environmental degradation, and the rate of forest depletion.

They also emphasize that present-day forest cover is under pressure as a result of human activities such as agricultural development where vast lands are cleared without conservation considerations, large-scale peri-urban housing project development, fuelwood generation, uncontrolled forest harvesting including poaching for logs and poles, and urbanization.

Pterocarpus soyauxii (local name: Silk-cotton) in IITA. Photo by J. Peacock, IITA.
Pterocarpus soyauxii (local name: Silk-cotton) in IITA. Photo by J. Peacock, IITA.

In Nigeria, deforestation or loss of vegetation or the selective exploitation of forests for economic or social reasons is very common. In most areas major losses have been recorded in vegetation, forest complexity (diversity), or in germplasm (quality).

The deforestation rate in the country is about 3.5% per year, translating to a loss of 350,000–400,000 ha of forest land per year. Recent studies show that forests now occupy about 923,767 km2 or about 10 million ha. This is about 10% of Nigeria’s forest land area and well below FAO’s recommended national minimum of 25%. Between 1990 and 2005 alone, the world lost 3.3% of its forests while Nigeria lost 21%.

In addition, some state governments are removing the protected status from forest estates without regard for the environment. The State Forest Departments have been unable to curtail the spate of requests to establish large-scale oil palm plantations in forest estates. The unfortunate impression that has thus been created is that the forest estate exists as a land bank for other sectors as demands continue nationwide.

As the forests are exploited, so too is the biodiversity. Plant and animal genetic resources are also lost with this important genetic resource, vital for breeding in future. Conserving the wild relatives of cultivated crops is also needed.

What factors continue to threaten biodiversity and contribute to poverty? These include deforestation, desertification, habitat alteration, invasive alien species (plants and animals) importation, poor land management (fire and agricultural systems + grazing), climate change, unilateral development decisions, poor political accountability, and poor budget allocation, release, and implementation.

Young Milicia excelsa (Iroko). Photo by J. Peacock.
Young Milicia excelsa (Iroko). Photo by J. Peacock.

We cannot afford not to conserve our forests and thus lose the vital ingredients of rural development. The situation is getting worse every day and the need for forest conservation and restoration is becoming critical.

With the new National Forestry Policy and the National Document on Biodiversity Conservation Action Plan, a new approach is needed now on forestry resources conservation in Nigeria. Enforcement and a community approach will produce positive results.

All stakeholders need to understand that biodiversity is critical to the maintenance of a healthy environment. Its role is enormous in meeting human needs while maintaining the ecological processes upon which our survival depends. Biodiversity not only provides direct benefits such as food, medicine, and energy; it also affords us a “life support system.”

Biodiversity is required for the recycling of essential elements. It is also responsible for mitigating pollution, protecting watersheds, and combating soil erosion. Controlling deforestation will ensure that biodiversity exists and can help reduce the impacts of climate change and thus act as a buffer against excessive variations in weather and climate. It can then protect us from catastrophic events.

Increasing our knowledge about biodiversity can transform our values and beliefs. Knowledge about biodiversity is valuable in stimulating technological innovation and providing the framework for sustainable development. Let us protect our forests as a start.

Edition 4, March 2010

Biodiversity and NRM
Biodiversity conservation is key
Insect biodiversity for NRM
Why manage noncrop biodiversity
A research park for Africa
Unlocking the diversity of yam
Cassava: improver of soils
Participatory yam conservation strategies
Smart NRM approaches
DNA barcodes for pathogens
A new food security crop?

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DNA barcodes for pathogens of African food crops

Lava Kumar, and Kamal Sharma,

Diagnostic tools play an important role in the accurate and timely identification of the pathogens involved in disease etiology, also in disease surveillance, the development of host plant resistance, quarantine monitoring, and support safe conservation and the exchange of germplasm. Detailed knowledge of pathogen population structure and genetic diversity is a prerequisite to developing unambiguous diagnostic tools and is critical in establishing disease management tactics.

Severe anthracnose symptoms on cassava stem. Photo by R. Bandyophadyay, IITA.
Severe anthracnose symptoms on cassava stem. Photo by R. Bandyophadyay, IITA.

Increasingly, modern diagnostic tools are being based on the DNA characteristics of the pathogen as they are neutral to growth stage and environment; offer adequate diversity to distinguish species, strains, substrains, isolates, and even individuals; and offer convenience of detection using modern bio-techniques such as polymerase chain reaction (PCR).

At IITA, we undertook a new initiative to characterize pathogen populations and recognize unique stretches of sequences—known as ”DNA barcodes”—that can be used as genetic markers for the rapid diagnosis of the pathogens and pests affecting the African food crops on which we work. DNA barcodes, otherwise also known as DNA markers or DNA fingerprints, are essentially a short stretch of nucleotide sequences that aid in the specific identification of species strains or substrains. They are used to resolve pathogen taxonomy and phylogeny.

The work focuses on economically important fungal, viral, and bacterial pathogens, insects, and nematodes. The information is used to gain ”barcode” designation in global sequence databases such as BOLD (the barcode of life data system) or NCBI (National Center for Biotechnology Initiative), and to assemble these into a database for public access.

This approach—a combination of conventional biology, biotechnology, and bioinformatics—involves the selection of targets, amplification of target genes using universal or generic primers, sequencing of target genes and identification of unique barcodes, and development of PCR-based diagnostics for specific detection of barcodes. This approach is particularly useful in identifying pathogens that are difficult to distinguish either by morphology or other properties. It offers high accuracy in identifying quarantine pathogens and reduces the risk of spread. In addition to diagnosis, it also contributes to the fundamental understanding of pathogen phylogeography and relationship with host and contributes to the development of management tactics.

Clustering of 25 yam isolates based on rDNA sequences. Courtesy of Lava Kumar, IITA.
Clustering of 25 yam isolates based on rDNA sequences. Courtesy of Lava Kumar, IITA.

We are using this approach to characterize the fungal pathogen(s) causing anthracnose—the most destructive disease of yam and cassava in West Africa. The disease causes severe yield losses in both crops and often kills the plant. The causal fungus, Colletotrichum gloeosporioides Penz., is widespread in West Africa. We identified various isolates of this fungus differing in morphology, growth characters, and pathogenicity, then investigated their genetic relatedness and diversity through molecular analysis of a set of 25 reference isolates (17 from yam and 8 from cassava) using multilocus gene targets. They were grouped into spot (S) and blight (B) isolates based on symptoms they induce. Both types of isolates infect yam, but only B isolates infect cassava. We assessed the genetic diversity in these isolates by nucleotide sequencing and cluster analysis of the ~540 base pair (bp) nuclear ribosomal internal transcribed spacer region (ITS1, ITS2 and the 5.8S gene) and partial gene sequences of actin (~240 bp) and histone (~370 bp).

Phylogenetic cluster analysis grouped the 25 isolates into two major clades (a clade is a group that shares features from a common ancestor) and two subclades within the major clades. Both the S and B isolates were distributed between the two clades (see figure). All the isolates in clade 1 were unique to yam. Seven of these isolates (YA08-1, YA08-2, YA08-3, YA08-4, YA08-7, Y-83, Y-84) formed a genetically distinct lineage, indicating that they could be new strains unique to yam. Isolates in clade 2 infect both cassava and yam, suggesting their capability to infect a wide range of plants. It is plausible that clade 2 isolates could be those most frequently occurring on yam and cassava because of their ability to survive on weeds and other crops. We recognized unique sequence motifs and designed diagnostic PCR primers directly from infected plant tissues for the specific amplification of C. gloeosporioides infecting yam and cassava.

Gray leaf spot lesions in maize. Photo by A. Aregbesola, IITA.
Gray leaf spot lesions in maize. Photo by A. Aregbesola, IITA.

Using a similar approach, we characterized the fungal agent associated with gray leaf spot (GLS), the most destructive disease of maize. We found that GLS in Nigeria is caused by a distinct species of Cercospora, but not C. zeae-maydis, a previous conclusion derived from conventional analysis. This work, in addition to confirming the GLS etiology, allowed us to establish a unique set of primers for the specific identification of the GLS pathogen prevalent in Nigeria.

Through comparative genomics, we identified common genome regions in cassava mosaic begomoviruses occurring in sub-Saharan Africa. We developed a simple multiplex PCR assay that can detect all the major viruses in cassava mosaic disease etiology. This test has been adopted for virus indexing of cassava propagated in vitro.

To aid us in diagnostics research, we developed a simple and cost-effective procedure suitable for extraction of DNA from seeds, leaves, stems, tubers, and even roots. The resultant DNA is suitable for PCR-based diagnoses of fungi, bacteria, and viruses in the infected tissues of a wide range of plant species. It is handy for the quarantine monitoring of germplasm. We are establishing a repository of diagnostic protocols in an approach we call the ”Diagnostic Basket®” and will make it available to users.

Barcodes and diagnostic tools provide a solid base for the understanding of the taxonomy and diversity of pathogens infecting African food crops.

African yam bean: a food security crop?

Daniel Adewale,

Read the Ukranian translation by Martha Ruszkowski

Diversity in color, color pattern, structure, texture, brilliance, etc. of African yam bean seeds. Photo by D. Adewale, IITA.
Diversity in color, color pattern, structure, texture, brilliance, etc. of African yam bean seeds. Photo by D. Adewale, IITA.

Biodiversity assures the evolutionary continuity of species. The collection and conservation of diversity within species are a safeguard against the loss of germplasm. They provide a buffer against environmental threats and assure continual and sustainable productivity. Global food security is becoming shaky with increasing dependence on a few major staple crops. This has resulted in an alarming reduction not only in crop diversity but also in the variability within crops.

The conservation and maintenance of agrobiodiversity of neglected and underutilized plant species such as African yam bean (AYB) in seed banks aim at contributing to food security and preventing a potential food crisis. Increasing the use of underutilized crops is one of the better ways to reduce nutritional, environmental, and financial vulnerability in times of change (Jaenicke and Pasiecznik 2009); their contribution to food security is unquestionably significant (Naylor et al. 2004, Oniang’o et al. 2006). Among other things, the consumption of a broader range of plant species ensures good health and nutrition, income generation, and ecological sustainability.

Potentials of African yam bean
The plant (Sphenostylis stenocarpa) is one of the most important tuberous legumes of tropical Africa. It is usually cultivated as a secondary crop with yam in Ghana and Nigeria. A few farmers who still hold some seed stocks, especially the white with black-eye pattern, plant it at the base of yam mounds in June or July. The crop flourishes and takes over the stakes from senescing yam. It flowers and begins to set fruits from late September and October. The large bright purple flowers result in long linear pods that could house about 20 seeds.

The seed grains and the tubers are the two major organs of immense economic importance as food for Africans. This indigenous crop has huge potential for food security in Africa. However, there are cultural and regional preferences. In West Africa, the seeds are preferred to the tubers but the tubers are relished in East and Central Africa (Potter 1992). The crop replaces cowpea in some parts of southwestern Nigeria (Okpara and Omaliko (1995). Researchers (Uguru and Madukaife 2001) who did a nutritional evaluation of 44 genotypes of AYB reported that the crop is well balanced in essential amino acids and has a higher amino acid content than pigeon pea, cowpea, and bambara groundnut.

Tuber yield per stand of AYB accession TSs96 at Ibadan, 2006. Photo by D. Adewale, IITA.
Tuber yield per stand of AYB accession TSs96 at Ibadan, 2006. Photo by D. Adewale, IITA.

Apart from the use of soybean as an alternative to animal protein, protein from other plant sources is not often exploited. The protein content in AYB grains ranged between 21 and 29% and in the tubers it is about 2 to 3 times the amount in potatoes (Uguru and Madukaife 2001, Okigbo 1973). AYB produces an appreciable yield under diverse environmental conditions (Anochili 1984, Schippers 2000). Another positive contribution of the crop to food security is the identification of the presence of lectin in the seeds, which could be a potent biological control for most leguminous pests.

Although the vast genetic and economic potentials of AYB have been recognized, especially in reducing malnutrition among Africans, the crop has not received adequate research attention. Up to now, it is classified as a neglected underutilized species or NUS (Bioversity 2009). Devos et al. (1980) stressed that the danger of losing essential germplasm hangs over all cultivated food crop species in tropical Africa, especially those not receiving research attention. The quantity and availability of AYB germplasm is decreasing with time. At one time, Klu et al. (2001) had speculated that the crop was nearing extinction; its inherent ability to adapt to diverse environments (Anochili 1984, Schippers 2000) may have been responsible for its continual existence and survival. Nevertheless, scientists think that the genetic resources of AYB may have been undergoing gradual erosion.

IITA keeps some accessions of the crop, but otherwise, its conservation in Nigeria is very poor and access to its genetic resources is severely limited. Seeds of AYB seem to be available in the hands of those who appreciate its value, i.e., the elderly farmers and women in a few rural areas in Nigeria. The ancient landraces in the hands of local farmers are the only form of AYB germplasm; no formal hybrid had been produced as yet.

Improvement of the crop is possible only when the intraspecific variability of the large genetic resources of the species is ascertained. The genetic resources of AYB need to be saved for use in genetic improvement through further exploration in tropical Africa and for conservation.

African yam bean plant showing mature pods ready for harvest. Photo by Daniel Adewale, IITA.
African yam bean plant showing mature pods ready for harvest. Photo by Daniel Adewale, IITA.

Understanding AYB
Eighty accessions (half of the total AYB collection under conservation in the IITA genebank) were assessed for diversity using morphological and molecular methods. Thirty selected accessions were further tested in four ecogeographical zones in Nigeria to understand their productivity and stability. The breeding mode was also studied.

Findings show that each of the 80 accessions of AYB has a unique and unmistakable genetic entity, promising to be an invaluable genotype as a parent for crop improvement. Morphologically, two groups have evolved: the tuber forming and the nontuber forming.

Grain yield differed among individual accessions and across the four agroecologies. The average grain yield across the four diverse environments in Nigeria (Ibadan, Ikenne, Mokwa, and Ubiaja) was ~1.1 t/ha; however, grain yield at Ubiaja was well above 2 t. Most agronomic and yield-determining traits had high broad sense heritability and genetic advances, assuring high and reliable genetic improvement in the species. AYB is both self fertilizing and an outcrosser; the latter trait is exhibited at about 10%.

The good news is improvement through hybridization is possible within the species.

Anochili, B.C. 1984. Tropical Agricultural Handbook. Pages 48–50 in Food Crop Production. Macmillan Publishers, London, UK.

Bioversity International. 2009. [25 February 2010].

Devos, P., G.F. Wilson, and E. Delanghe. 1980. Plantain: Genetic resources and potential in Africa. Pages 150–157 in Genetic Resource of Legumes in Africa edited by Doku, E.V. Proceedings of a workshop jointly organized by the Association for the Advancement of Agricultural Science in Africa and IITA, Ibadan, Nigeria, 4–6 January 1978.

Jaenicke, H. and N. Pasiecznik. 2009. Making most of underutilized crops. LEISA Magazine, 25(1):11–12.

Klu, G.Y.P., H.M. Amoatey, D. Bansa, and F.K. Kumaga. 2001. Cultivation and uses of African yam bean (Sphenostylis stenocarpa) in the Volta Region of Ghana. The Journal of Food Technology in Africa 6:74–77.

Naylor, R.L., W.P. Falcon, R.M. Goodman, M.M. Jahn, T. Sengooba, H. Tefera, and R.J. Nelson. 2004. Biotechnology in the developing world: a case for increased investment in orphan crops. Food Policy 29:15–44.

Okigbo, B.N. 1973. Introducing the yam bean (Sphenostylis stenocarpa) (Hochst ex. A. Rich.) Harms. Proceedings of the first IITA Grain Legume Improvement Workshop, 29 October–2 November 1973, Ibadan. Nigeria. pp. 224–238.

Okpara, D.A. and C.P.E. Omaliko. 1995. Effects of staking, nitrogen and phosphorus fertilizer rates on yield and yield components of African yam bean (Sphenostylis stenocarpa). Ghana Journal of Agricultural Science 28:23–28.

Oniang’o, R.K., K. Shiundu, P. Maundu, and T. Johns. 2006. Diversity, nutrition and food security: the case of African leafy vegetables in Hunger and poverty: the role of biodiversity. Report of an International Consultation on the role of biodiversity in achieving the UN Millennium Development Goal of freedom from hunger and poverty edited by Ravi, S.B., I. Hoeschle-Zeledon, M.S. Swaminathan, and E. Frison. Chennai, India, 18–19 April 2005. M.S. Swaminathan Research Foundation, Chennai, India. pp. 83–100.

Potter, D. 1992. Economic botany of Sphenostylis (Leguminosae). Economic Botany, 46: 262-275.

Schippers, R.R. 2000. African indigenous vegetables: An overview of the cultivated species. Natural Resources Institute/ ACP-EU Technical Centre for Agricultural and Rural Cooperation, Chatham, UK. pp. 89–98.

Uguru, M.I. and S.O. Madukaife. 2001. Studies on the variability in agronomic and nutritive characteristics of African yam bean (Sphenostylis stenocarpa Hochst ex. A. Rich. Harms). Plant Production and Research Journal 6:10-19.

Made to measure: smart natural resources management approaches

Coffee-banana intercropping. Photo by P. van Asten, IITA.
Coffee-banana intercropping. Photo by P. van Asten, IITA.

Coffee and banana yields in the East African highlands are often only 10 to 30% of those achieved in commercial farms in Latin America and Asia. This is the result of a mixture of biotic stresses on the crops such as pests, diseases, and weeds, and abiotic constraints such as poor soil quality and drought.

Poor crop management practices that do not sufficiently address these constraints prevent farmers from reaping maximum benefits from their efforts.

However, the importance of these yield-limiting factors differs from region to region. The natural resources management (NRM) approach therefore starts with identifying the gap between the actual, attainable, and potential yields for each location.

Diagnostic surveys and analytical tools such as the boundary line analysis are used to rank and quantify the causes of low yields. This then guides the development of tailor-made measures and actions for farmers.

Smart use of mineral fertilizer and organic matter
Poor soils are one major cause of low yields in the East African highlands. Much of Africa’s soils are old and poor, situated on very old continental plates. Only a few places have soils that still have substantial nutrient stocks, such as those derived from young volcanic material and metamorphic rocks.

Years and years of soil erosion and poor farming methods that mine minerals have worsened the situation.

IITA is working with farmers to combine organic manure and mineral fertilizer to replenish soil nutrients to meet the needs of banana and coffee.

Piet van Asten, IITA systems agronomist based in Uganda, says the approach stresses the judicious use of mineral fertilizer that is moderate in quantity, applied at the right time and in the right way, and combined with locally available organic matter.

“The combination of fertilizers and organic matter provides much-needed additional nutrients that are efficiently used up by the crops. The organic matter helps to retain mineral fertilizers applied in the topsoil and reduces losses from leaching,” he says. “It also improves the soil physical properties which help to retain soil humidity and control the temperature. Plants thrive in such humid and temperate environments as the roots are better able to take up nutrients.”

Poster on banana fertilizer recommendations for Uganda. Courtesy of P. van Asten, IITA.
Poster on banana fertilizer recommendations for Uganda. Courtesy of P. van Asten, IITA.

Sources of local organic matter are mulch, urine, manure, and compost.

Research has shown that adding mineral fertilizers and mulch to both coffee and banana nearly doubles their yields. However, the fertilizer type and dose have to supply the nutrients that are lacking.

Through mapping soil and plant nutrient status, IITA identified the missing nutrients in each region. Subsequently, it developed region-specific recommendations for using fertilizer and organic mulch in parts of Uganda.

Training materials were also developed to teach farmers how to identify nutrient deficiencies in their own farms by observing plant leaves. This should ultimately help them to localize their fertilizer needs down to the farm level.

Halting and preventing soil erosion by placing contour bunds stabilized by forage/mulch grasses and leguminous plants are also important to conserve and improve soil quality.

Smart intercropping systems
IITA has been working on promoting the intercropping of banana/plantain and coffee as research has clearly shown that intercropping works better than monocropping either crop.

Coffee, a shade-loving plant, performs well when grown under banana/plantain. Research findings showed that creating space for the banana/plantain does not reduce the yield of coffee but instead, the farmer gets bonus income from the banana.

Such intercropping systems, says van Asten, spread the socioeconomic risks of farmers as they become less vulnerable to the price fluctuations of a single crop.

“The two intercrops provide farmers with permanent piecemeal harvests from banana and annual or biannual cash booms from coffee,” he said.

Intercropping has other benefits. It leads to sharing of inputs, such as fertilizers purchased through the cash crop system, such as coffee farmers’ cooperatives. It also improves fertilizer-use efficiency, as fertilizer applied to the cash crop also benefits the food crop.

Coffee plants perform better when grown under the shade of banana plants. Photo by P. van Asten, IITA.
Coffee plants perform better when grown under the shade of banana plants. Photo by P. van Asten, IITA.

Intercropping improves the biophysical efficiency of the systems by providing better and more permanent canopy and soil cover that reduce erosion. It improves soil organic carbon stocks (carbon sequestration) through the biomass produced.

Another benefit, says van Asten, is that intercropping can sometimes increase the quality of some crops. For instance, under suboptimal growing conditions, shade-grown coffee is often of better quality and thus could fetch more money on the market.

Linking to input and output markets
In a study of the factors that limit farmers’ usage of mineral fertilizers for their banana plants, Uganda farmers cited lack of access as one constraint. Moreover, they said it was not available in smaller packaging and more affordable sizes. IITA is working to encourage farmer cooperatives that are organized around postharvest handling, sorting, and bulking to organize the supply of inputs such as fertilizer for their members.

According to van Asten, cooperatives have better access to input/output markets and improved powers of negotiation. They have improved access to market information, bulking and storage facilities, savings and credit schemes through collaboration, and agreements with input/output dealers. They can also facilitate the exploration of niche markets through the certification of products in terms of quality, production, and techniques.

Smart extension services
To meet the information needs of farmers, IITA and partners are exploring options to make location-specific information accessible. This includes the use of extension publications, videos, and mobile phone services.

Farmer detrashing banana intercropped with coffee. Photo by P. van Asten, IITA.
Farmer detrashing banana intercropped with coffee. Photo by P. van Asten, IITA.

Together with the Grameen Foundation, IITA is exploring how information can be tailored to the location of the farmer through a (decision-tree) series of questions. The more information a farmer can provide, the more precise the recommendations will be.

The NRM work on coffee and banana shows that there are practical, readily available measures that farmers can use to increase yield and contribute towards the fight against poverty and hunger. However, they have to be region- and crop-specific for maximum impact.

“For all these measures to be successful, they must start with using clean and resistant planting materials. Investing in fertilizers for use on diseased plants is a futile exercise,” concludes van Asten.

Cassava: improving sustainability of farming systems

Anneke Fermont,

Throughout Africa populations are growing fast and pressure on land is steadily increasing. To maintain productivity, farmers are constantly adapting their management of natural resources. Farming systems are thus changing from ”slash and burn systems” to ”natural fallow” systems into ”continuous cropping” systems without external inputs and ultimately into more ”intensive” systems using agricultural inputs.

Pauline Auma of Busia district, western Kenya, proudly shows her cassava harvest. Photo by  A. Fermont, IITA.
Pauline Auma of Busia district, western Kenya, proudly shows her cassava harvest. Photo by A. Fermont, IITA.

Cassava-maize systems in East Africa
A principal crop in Africa’s farming systems is cassava, with a total production that has quadrupled in the last five decades to about 118 million t/year. Cassava is a major crop in East Africa, where it is often produced together with maize by smallholder farmers. Such cassava–maize-based systems are found around Lake Victoria and in Burundi, Rwanda, and eastern DR Congo. Apart from being dominated by cassava and maize (on average one-third of cropped land is planted with cassava and one-quarter with maize) these systems have a high self-sufficiency in food. Sixty percent of all households sell cassava and maize; each crop generates an average of US$90 per year.

Due to its widely varying levels of land pressure, this region allows an interesting study of natural resource management and opportunities to improve both the productivity and the sustainability of cassava-based farming systems.

Cassava is widely grown in East Africa today, but this is a recent development. Only three decades ago cassava production was limited to the odd corner in farms as enforcement of its production during colonial times had given the crop a very bad image. The remarkable change in the importance of cassava has been driven by sharply increasing land pressure. No longer having the land available to restore soil fertility through natural fallows, farmers replaced fallows with cassava.

Does cassava improve soil fertility?
Jacinta Ouma, a farmer in Teso district, western Kenya, explains: “Cassava drops its leaves on the soil while it grows. This improves the soil, so if I plant maize after cassava it grows better.” Jacinta is not alone in this belief. A similar practice, known as jachère manioc or ‘cassava fallow’, exists in West Africa.

Almost 90% of farmers interviewed in Uganda and Kenya had the same opinion. Farm surveys in Uganda and Kenya showed that farmers plant cassava on all soil types to maintain soil fertility. If land pressure increases and soils consequently become more acidic (pH <5.8) and deficient in phosphorus (P) (available P <4–5 mg/kg), farmers increasingly plant cassava in the poorest fields in their farm. In Siaya district, western Kenya, with nearly 400 people/km2, farmers planted nearly twice as much cassava on infertile soils than on fertile soils.

Women in Teso district, western Kenya, peel cassava for eating. Photo by A. Fermont, IITA.
Women in Teso district, western Kenya, peel cassava for eating. Photo by A. Fermont, IITA.

Modeling to substantiate farmer claims
To understand farmers’ observations, we used a modeling approach. Our results suggest that planting maize on an infertile soil will result in slowly declining levels of soil organic matter, while planting cassava will slowly increase soil organic matter over time. The difference is explained by the fact that cassava grows much better than maize on infertile soils. The large amounts of easily available nitrogen (N) in its crop residues likely give cassava its reputation as a soil improver.

The model estimated that cassava returns about four times more N to the soil than maize. Through its deep rooting system and its association with mycorrhizae, cassava can pump up nutrients from the subsoil and absorb nutrients from less easily accessible pools. Nutrients from its N-rich litterfall are then redistributed to more labile pools in the topsoil.

But all is not sunshine and roses. Continuous cropping systems without external nutrient inputs deplete the soil’s nutrient pool. On the highly weathered soils found in large parts of Africa, this will unavoidably result in nutrient limitation and declining crop yields. In East Africa, N and P limitations for cereal crops are widely documented. A series of field trials with over 100 farmers demonstrated that cassava production is often limited by N and P, and commonly by potassium (K).

Cassava grows better on good soils
Cassava is known for its ability to produce fair yields where other crops fail. This has led many to believe that soil fertility is not important in cassava production. Our field trials show that this is a misconception. On the contrary, using improved varieties but no fertilizer, low soil fertility was the principal constraint to production and caused farmers an average loss of 6.7 t/ ha with respect to an attainable yield of 27 t/ha. Drought caused a loss of 5.4 t/ha and poor weed control 5.0 t/ha, whereas pests and diseases caused an average loss of 3.8 t/ha.

The farm surveys showed that Kenyan and Ugandan farmers harvested on average between 7 and 10 t/ha using farmer practices. This is far below the maximum yield of 35 t/ha that was observed during the two-year on-farm fertilizer trials and clearly shows the potential for improving yields.

The field of Nikirima Arajabu in Iganga district, Uganda, shows a very strong response to NPK fertilizer. Photo by A. Fermont, IITA.
The field of Nikirima Arajabu in Iganga district, Uganda, shows a very strong response to NPK fertilizer. Photo by A. Fermont, IITA.

Using an integrated management package that consisted of an improved genotype, recommended planting practices and NPK fertilizer, average yields in farmers’ fields more than doubled from 8.6 to 20.8 t/ha. About 30% of the yield increase was due to the use of improved genotypes, while a whopping 60% was the result of fertilizer use. These findings reinforce the idea that soil fertility/nutrient availability is a principal production constraint for cassava.

Options to improve system sustainability
Though fertilizer use may be the easiest way to improve cassava productivity and improve system sustainability, high prices limit the adoption of fertilizers, unless strong markets develop. Farmers have, however, other options to improve cassava productivity, increase nutrient availability, and reduce nutrient losses within their farming system. These include: (1) better weed control and drought avoidance strategies; (2) improving cassava’s efficiency as a soil fertility improver; (3) returning cassava stems to the field after harvest to reduce nutrient losses; and (4) planting cassava in rotation/intercrop with (cash) crops that receive manure/fertilizer.

Dealing with the challenges from increasing land pressure and related sustainability issues while substantially improving crop yields requires R4D teams with a strong interdisciplinary character. African farmers have shown great resourcefulness in maintaining system productivity by introducing cassava as a soil fertility improver. Now, IITA and its partners have the challenge to come up with innovative strategies to maintain or further improve system sustainability and crop productivity in increasingly stressed farming systems.