In Kanti Rawal’s footsteps

Remy S. Pasquet (rpasquet@icipe.org), Dominique Dumet (d.dumet@cgiar.org), and Sunday E. Aladele (sundayaladele@yahoo.com)

Cowpea is a rich source of dietary protein for millions in West Africa. Photo by IITA.
Cowpea is a rich source of dietary protein for millions in West Africa. Photo by IITA.

Cowpea, Vigna unguiculata (L.) Walp. is the major legume crop in the African lowlands. It is the main protein supply of half of the population in sub-Saharan Africa.

Nigeria is the most populous country in West Africa, and also produces the largest amount of cowpea. Its urban population is growing in leaps and bounds, and thus, it is also importing a lot of cowpea from all its neighbors

Cowpea is considered by several authors as having been domesticated in Nigeria or within a larger area including Nigeria (i.e., Vaillancourt and Weeden 1992). In addition, the first wild cowpea accession was collected in northern Nigeria by J.M. Dalziel, a British botanist, and this led Piper (1913) to propose the African origin of cowpea1.

To some extent, this partly explains why Nigeria was the first country surveyed for cowpea accessions by IITA’s then Genetic Resources Unit. Between 1970 and 1973, Kanti Rawal traveled 38,000 km around Nigeria and Niger. He collected wild cowpea accessions as well as numerous accessions of domesticated cowpea.

According to his map, he collected wild cowpea in 68 places (Rawal 1975). Unfortunately, over the years, the passport data of these accessions were lost and, today, the place of collection is known for only four out of the 40 accessions still maintained at IITA.

Regarding Nigeria, Rawal (1975) wrote in the abstract of his paper: “As in the case with many cultivated species, Vigna unguiculata (L.) Walp. has a wild form growing in secondary forests and derived savannahs and a companion weed form adapted to disturbed habitats such as roadside ditches and fields. Evidence of introgressive hybridization between weedy and cultivated forms has been presented. The zone of extensive natural hybridization corresponds to the cultivation area of northern Nigeria and Niger and may well extend to Upper Volta (now Burkina Faso) and Senegal.”

Rawal gave very good descriptions of what he called the wild and weed forms. His wild forms were samples of subsp. baoulensis (A.Chev.) Pasquet; the weed forms were samples of subsp. unguiculata var. spontanea (Schweinf.) Pasquet. We (Pasquet and Padulosi in press) believe that the first subspecies belongs to the secondary gene pool of cowpea and the second to the primary gene pool. However, since Rawal’s material is mostly lost2, the assessment of the diversity of wild cowpea from Nigeria is impossible in the absence of new collection missions in the country.

In addition, factors such as climate change, increased incidence of pests and diseases, cultural change, or the adoption of improved lines are also likely to affect the diversity of cowpea and wild Vigna in the near future. To avoid the irreversible loss of Vigna and to secure highly viable Vigna diversity, the Global Crop Diversity Trust in association with IITA and Nigeria’s National Centre for Genetic Resources and Biotechnology (NACGRAB) organized a collecting mission for wild Vigna germplasm in 2010. The mission covered 27,000 km in Nigeria between 14 October and 7 December and collected 260 accessions (242 of var. spontanea and 18 of subsp. baoulensis . In addition, 13 populations were sampled for further population genetic analysis.

In comparison with the Rawal missions that took place in 1971–73, we surveyed more localities within a shorter time. Unlike Rawal, we focused on wild cowpea only and benefited from a much better road network, especially in northern Nigeria where we were driving more than 600 km/day. In the end, there is a general agreement between the results of Rawal’s survey and our own in terms of geographical distribution of both subspecies.

In the northern ranges, we often encountered wild cowpea in fields or at roadsides. Wild cowpea plants are easy to spot in the field, as they twine 2–3 m above soil level on sorghum or pearl millet stems. Domesticated cowpea are prostrate or short and erect but usually not twining.

Based on the ecological definition of a weed, which is ”an uncultivated plant taxon that benefits from human impacts or ’disturbance’,” var. spontanea is a weed mainly encountered in disturbed places, such as in fields and gardens, at roadsides, and sometimes within towns (sewage ditches, grassy places); it was not observed within Yankari National Park. However, to some extent, var. spontanea is also a weed in the economic sense of the word since it is usually pulled out from the fields by farmers. It usually appears as isolated plants or isolated patches of fewer than 20 plants or as a few plants forgotten by the farmer while weeding.

In some places, we found fields with as many wild cowpea as domesticated cowpea (SP 815, Katsina State, for example). We suspect that, in these places, farmers were primarily interested in fodder. Var. spontanea is obviously a good fodder plant and farmers primarily cultivating cowpea for fodder would not choose to lose time weeding wild cowpea.

Domesticated cowpea close to var. spontanea (white arrow), SP 949, Borno State, Nigeria. Source: R. Pasquet, i<em/>cipe.” title=”domesticated-cowpea-close-to-var-spontanea” width=”300″ height=”252″ class=”size-medium wp-image-2510″ /></a><figcaption class=Domesticated cowpea close to var. spontanea (white arrow), SP 949, Borno State, Nigeria. Source: R. Pasquet, icipe.

Since experiments have proved pollen flow between wild and domesticated cowpea at over 30 m distances (Fatokun and Ng 2007), we checked if domesticated cowpea was grown within 30 m of the collecting sites for wild cowpea. This occurred frequently (70%) in the northern part of the range which is also the main cowpea production area. Our survey confirms Rawal’s (1975) conclusion. There are numerous situations in Nigeria in which domesticated cowpea and wild cowpea exchange genes. Therefore, its diversity may not be much higher than that of the domesticated gene pool. An evaluation of diversity among the collected material would help confirm or disprove this assumption.

The potential hybridization between wild and cultivated forms has implications for the transgenic Bt cowpea which are presently under confined field trials in Nigeria (www.aatf-africa.org/userfiles/Cowpea-Project-brief.pdf). If the Bt gene could move through the pollen from transformed to wild plants, further careful studies need to evaluate the advantage given by the Bt gene to a wild cowpea plant and whether Bt cowpea poses any risk to biodiversity.

References
Fatokun CA and Ng Q. 2007. Outcrossing in cowpea. J Food Agric Environ 5:334–338.

Pasquet and Padulosi. In press. Genus Vigna and cowpea (V. unguiculata (L.) Walp.) taxonomy: current status and prospects. Presented at the 5th World Cowpea Research Conference, Saly, Senegal, September 2010.

Piper CV. 1913. The wild prototype of the cowpea. US Dept. Agric. Bureau Plant Ind. Circular 124: 29–32.

Rawal KM. 1975. Natural hybridization among wild, weedy and cultivated Vigna unguiculata (L.) Walp. Euphytica 24(3):699–707.

Vaillancourt RE and Weeden NF. 1992. Chloroplast DNA polymorphism suggests Nigerian center of domestication for the cowpea, Vigna unguiculata (Leguminosae). Am. J. Bot. 79-10:1194–1199.

Why conserve germfree-germplasm?

Dominique Dumet, d.dumet@cgiar.org and Lava Kumar, l.kumar@cgiar.org

Seeds of important grain legumes are conserved in IITA's Genetic Resources Center. Photo by IITA.
Seeds of important grain legumes are conserved in IITA's Genetic Resources Center. Photo by IITA.

Plant genetic resources (germplasm) are the foundation for sustainable agriculture and global food security. They possess genes that offer resistance to pests and diseases and resilience to abiotic stresses, such as drought tolerance, soil erosion, and other constraints.

However, genetic resources are eroding at unprecedented rates as a result of the loss of habitat, outbreaks of pests and diseases, and abiotic stresses. Therefore, it has become imperative to conserve genetic resources for agricultural sustainability and the preservation of global biodiversity.

In the mid-1970s, IITA has initiated an ex situ conservation of germplasm of important African food crops which are held in trust on behalf of humanity under the auspices of the United Nations. To date, IITA’s Genetic Resources Center (GRC) conserves over 27,000 accessions of six main collections of African staple crops, namely, cowpea and other Vigna, soybean, maize, cassava, banana, and yam. Germplasm is distributed worldwide for use in research for food and agriculture. Depending on the species’ reproductive biology and mode of dissemination, collections are stored in field, seed, or in vitro genebanks.

Conservation of virus-free germplasm. Source: L. Kumar, IITA.
Conservation of virus-free germplasm. Source: L. Kumar, IITA.

However, germplasm (seeds or vegetative propagules) infested with pathogens such as, viruses, fungi, bacteria, and nematodes, insects, mites and even weeds (hereafter all referred to as pests) can spread along with the planting materials. Because of this risk, planting materials are traditionally sourced from healthy-looking plants and as an additional safety measure they are treated with chemicals to eliminate bacteria, fungi, nematodes, insects and other pests. However, viral pathogens are difficult to detect and pose challenges to “clean” (pest-free) planting material production procedures. IITA’s collections were sourced over 35 years from several countries in Africa and other parts of the world.

Knowledge on viruses infecting crops conserved in the IITA genebank and the means for their detection and production of clean planting material have dramatically improved over the past two decades. To ensure that germplasm conserved is free of pests, particularly viruses, a systematic approach was taken to assess the health status of every accession in the genebank and produce clean planting materials for conservation.

For seed-propagated crops (maize and legumes), clean seed production requires planting accessions in contained screenhouses. Emerging plants are monitored for symptoms and each plant is tested using diagnostic tools for all known seed-transmitted viruses occurring in the territory where they were last grown. Plants that test positive for virus and/or showing virus-like symptoms are destroyed. Seeds are harvested from the virus-negative, healthy-looking plants. Clean seeds are then deposited in the germplasm collections. This work started in 2008, and so far over 4000 accessions of legumes have been evaluated and clean seed material produced have been conserved in the genebank.

Researcher in genebank. Photo by IITA.
Researcher in genebank. Photo by IITA.

For clonally propagated crops (cassava, yam and banana), production of clean planting material involves in vitro procedures using meristem culture. In cassava, source plants are subjected to thermotherapy (exposing plants to 27-30 °C) from 1 to 3 weeks prior to meristem excision and in vitro propagation. In vitro plants are indexed for viruses and plants that test positive are discarded while virus-negative plants are further propagated for conservation in the in vitro genebank. So far, over 2000 accessions of clonal crops have been subjected to this process to derive virus-free plants.

Production and conservation of “clean” planting material is expensive; however it improves the turn-around time for processing germplasm for exchange and dramatically improves its use. In addition, clean germplasm improves the viability of the material conserved in the genebank and prevents the risk of the accidental spread of pests from one region to another through the planting materials.

To conserve or not to conserve?

IITA maintains more than 15,000 accessions of cowpea in its genebank. Photo by IITA.
IITA maintains more than 15,000 accessions of cowpea in its genebank. Photo by IITA.

Crop improvement through breeding and biotechnology is one way of tackling the challenges of feeding the world. Conservation of genetic resources is an important component of crop improvement, providing a pool of materials for the researchers to draw from.

IITA’s Genetic Resources Center (GRC) created in 1975, maintains over 28,000 accessions of six main staple crop collections that are available to food and agriculture researchers worldwide working on crop improvement. They are cowpea or “black-eyed pea” (Vigna unguiculata L.), maize (Zea mays L.), soybean (Glycine max (L.) Merr.), cassava (Manihot esculenta Crantz), yam (Dioscorea spp.), and banana (Musa spp.).

Over 50% of the collection is made of cowpea collected from 89 countries, mainly in Africa, and other Vigna spp. It is also the most shared, with 54 of all the germplasm materials being distributed.

Ex situ conservation in IITA genebank: medium-term storage, 5 °C. Photo by IITA.
Ex situ conservation in IITA genebank: medium-term storage, 5 °C. Photo by IITA.

Since 1985, IITA has distributed germplasm of cowpea and its wild Vigna relatives for genetic improvement research to institutions in sub-Saharan Africa, Asia, USA, and South America. This has contributed to the development of new cultivars or varieties currently adopted by rural farmers in the regions.

The effectiveness of the distribution system from the genebank, the use of the distributed germplasm, and conservation costs were assessed in a study conducted by Victor Manyong, Dominique Dumet, and A.T. Ogundapo from IITA and D. Horna from the International Food Policy Research Institute. Likewise, the impact of the conservation of germplasm of cowpea and wild relatives was examined to justify the conservation efforts.

Methodology
Questionnaires were e-mailed to partners who had collected germplasm from GRC between 1975 and 2009 to determine the ease of accessing material and their use. To estimate the cost of conserving a unit of the two crops, the Decision Support Tool (DST) developed by IFPRI was used.

Ex situ conservation in IITA genebank: medium-term storage, in vitro. Photo by IITA.
Ex situ conservation in IITA genebank: medium-term storage, in vitro. Photo by IITA.

Only about 13% of the beneficiaries responded but they accounted for about 84% of the accessions distributed to beneficiaries in West Africa, Asia, East Africa, Europe, and North America.

No responses were received from beneficiaries in Australia, the Caribbean, Central Africa, the Middle East, North Africa, South Africa, and South America. This may partly have been due to lack of updated contact details in the genebank’s electronic database. This needs to be improved for future feedback surveys.

Use of cowpea and wild Vigna germplasm
The study findings show that most of the distributed cowpea and wild Vigna accessions were used for breeding followed by activities in agronomy and biotechnology research. However, in many cases, they had multiple uses, such as breeding, biotechnology, and agronomy.

Between 2001 and 2005, about 76% of the accessions were used for various agricultural research activities and were found adaptable to different agroecological zones, from forest to the savanna in the tropics and subtropics. Derived, Sudan, and Sahel savannas were recognized as the adaptable agroecological zones for the cultivation of cowpea and wild Vigna.

Ex situ conservation in IITA genebank: long-term storage, −196 °C. Photo by IITA.
Ex situ conservation in IITA genebank: long-term storage, −196 °C. Photo by IITA.

The majority of the users of the germplasm found it easy (32%) to very easy (68%) to get the material from the genebank. Only a few experienced difficulties. These included the inability of the genebank to supply the required quantities (3% of accessions), poor collaboration with NARS and universities (3%), long bureaucratic procedures to acquire germplasm (2%), and improper documentation of the passport database of accessions (1%).

Desired traits
High yield and pest resistance were the two traits desired by the majority of agricultural researchers who made requests, irrespective of their specialization. Other desired traits included compatibility to cross with other accessions, seed color and size, nutritive value, palatability and attractiveness, drought tolerance, nematode resistance, early flowering, and storability.

Moreover, many were satisfied with the accessions they received. Findings show that 68% of the accessions received by agronomists met their desired traits, 76% for food technologists, but only 3% for breeders where the main issue was the low level of resistance to pests and diseases. However, the breeders recorded 100% satisfaction in the exploitation of accessions for seed color, seed size (good), and compatibility with crossing. Likewise, 95% satisfaction was achieved on high seed yield and 74% on the combination of high yield and pest resistance by some of the breeders.

Cost of conservation
The structure cost of the genebank in the DST has four categories: capital, quasi-fixed, variable labor input, and variable nonlabor input. Capital inputs include infrastructure, such as germplasm storage and genebank facilities, and equipment for field operations and offices.

Ex situ conservation: field genebank, IITA. Photo by IITA.
Ex situ conservation: field genebank, IITA. Photo by IITA.

Using 2008 as a reference year, US$358,143 and $28,217 was spent annually on the conservation and management of cowpea and wild Vigna. The capital cost took the major share of the costs, followed by quasi-fixed costs for scientific staff, nontechnical labor, and nonlabor supplies and consumables. Each accession cost about $72 for cowpea and only about half of that for wild Vigna. A large share of the expenditure, $28,537, went into the regeneration of 2,228 accessions of cowpea, at an average cost of approximately $12.81 per accession.

Cowpea germplasm is regenerated in the screenhouse to produce high quality germplasm, with considerations of purity and sanitation, hence the relatively high cost per accession. Seed health testing ($13.94/accession) and distribution ($22.63/accession) were the other high costs.

One way to reduce these costs is by increasing the number of accessions, thus lowering the unit cost. Also, upgrading and expanding the current infrastructure to improve the efficiency of the genebank were recommended.

A classical approach to saving life’s variety

iita-forest-img_0485

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.

wharf1

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.

The butterflies of IITA

Robert Warren, robertdavidwarren@yahoo.co.uk

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, ladipoolajide@yahoo.com

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, L.kumar@cgiar.org and Kamal Sharma, k.sharma@cgiar.org

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.

Scott Miller: Guardian of life

Scott Miller, Undersecretary for Science, Smithsonian Institution and Chair, Executive Committee, Consortium for the Barcode of Life. photo courtesy of S. Miller.
Scott Miller, Undersecretary for Science, Smithsonian Institution and Chair, Executive Committee, Consortium for the Barcode of Life. photo courtesy of S. Miller.

As Deputy Undersecretary for Science at the Smithsonian Institution (SI), Scott Miller helps oversee the work of SI’s science units, including the National Museum of Natural History, National Zoological Park, Smithsonian Tropical Research Institute, and others. He is also Chair of the Executive Committee of the Consortium for the Barcode of Life (CBOL), and Co-Chair of the US Government Inter-Agency Working Group on Scientific Collections, where he works on science capacity building activities on national and international scales. He maintains an active research program in the systematics and ecology of moths, and the application of that information to conservation and agricultural issues in New Guinea and Africa.

How did you become interested in biodiversity?
I grew up fascinated by nature as a child, and was able to get involved early in insect research projects at a local natural history museum, leading to a career in biodiversity. As I gained a broader perspective, I became especially concerned about helping developing countries to develop the capacity to manage their biodiversity wisely. They lead to my work in Africa.

What will the International Year of Biodiversity achieve?
This is an important opportunity to raise the profile of biodiversity issues. But we have to remember that our reliance on biodiversity is constant, and so must be our attention to understanding and wise management.

Most ecological studies show that biodiversity is declining at an alarming rate worldwide. Could you comment on this?
I agree that biodiversity is being degraded at an alarming rate. While the exact rate can be debated, it is clearly not sustainable.

What is the value of lost biodiversity?
We need much better economic models and data for biodiversity and ecosystem services, but some studies give an idea of the economic importance [Costanza et al. 1997, Pimentel et al. 2000]. One-third of global crop production relies on insect pollinators, valued at some US$ 117 billion. Natural biological control is valued at some $400 billion. Soil arthropods that maintain soil fertility provide trillions of dollars in value to agriculture.

How can Africa reduce the loss of biodiversity?
Action is needed at all levels, from wise government policies, enlightened management of industries that use natural resources, through the empowerment of local people to conserve and benefit from their own natural resources. Wise management requires understanding biodiversity, and valuing conservation to maintain the benefits to society over the long term. The economies of most African countries are based on natural resources, and sustainable development requires wise management. I have always been impressed by the “Working for Water” program in South Africa as a model for integrating landscape scale conservation, invasive species management, economic development and job creation, but there are many other success stories across Africa.

You worked in the International Center for Insect Physiology and Ecology (icipe) in Kenya some time ago. Tell us about your experiences in conservation and sustainable development.
My time in Kenya was a tremendous learning experience for me, and I hope I was able to help build programs that will have lasting impact. I am still involved in Kenya through collaborations with icipe, Mpala Research Centre, and the National Museum. We tried to help local people understand the value of their biodiversity, how to restore degraded landscapes, and how to benefit from the biodiversity resources. Among other things, I was involved in an integrated conservation development project at Kakamega Forest in western Kenya that involved many synergetic components. These included strengthening forest management, replanting degraded lands, reducing the use of wood as fuel (through promoting efficient cooking stoves), developing sustainable income sources (especially “low tech” uses of natural products, and ecotourism), providing microfinance facilities, and enhancing the accessibility of health care and family planning.

What do you think of IITA’s efforts in agrobiodiversity conservation/sustainable agriculture?
Historically, IITA has played a very important role in agrobiodiversity conservation efforts. While some of those efforts remain strong, I am concerned that financial pressures threaten some of them, such as the collections that support biological control research and application in insects and fungi. The institutional infrastructure for understanding biodiversity is very weak in West and Central Africa, and as an international organization, IITA can play a vital role in filling the gap, and building national capacity. I am pleased to see IITA’s leadership in the CGIAR study of biomaterial collections beyond plant germplasm, which recognizes these collections as Global Public Goods.

Do you see the investment in conservation well spent?
IITA’s investment has been critical in the past, and needs to be enhanced to support future agricultural development and pest management. Climate change will bring new challenges to agriculture in Africa, and crop germplasm will be crucial, as well as knowledge of crop relatives, pest organisms, and beneficial organisms. The native forest on IITA’s Ibadan campus is an important biodiversity resource, and the protection that IITA has provided it for many years has been an important service.

What is the contribution of insect diversity to agriculture?
Insects provide vital ecosystem services to agriculture, including pollination, biological control of pests, and the maintenance of soil fertility. A recent study on the impact of CGIAR research in Africa (Maredia and Raitzer 2006) found that 80% of the impact (valued at $17 billion) resulted from four biocontrol programs using insects and mites. All those programs had to solve significant taxonomic problems (e.g., understanding the biodiversity) before they became successful, underscoring the importance of research and documentation.

How does the Consortium for the Barcode of Life contribute to the conservation and protection of biodiversity?
DNA barcoding is a species diagnostic system using short sequences of DNA (www.barcoding.si.edu), and the Consortium is an international organization promoting the development of standards and the building of the reference library of sequences. Understanding species, being able to identify them, and being able to communicate about them are basic to managing and using biodiversity. Thus, CBOL contributes through allowing fast and accurate identifications in difficult situations such as the immature stages of plant pests, the wood or roots from medicinal plants, or parts of butchered wildlife or fish in the illegal trade.

CBOL works closely with organizations with similar interests, such as BioNET INTERNATIONAL and the Global Taxonomy Initiative of the Convention on Biological Diversity. We are communicating with organizations such as the International Plant Protection Convention to help establish formal protocols for the DNA-based identification of agricultural pests.

Biodiversity conservation is key

Dominique Dumet, d.dumet@cgiar.org

Researcher sorting bambara groundnut seeds, IITA genebank. Photo by J. Oliver.
Researcher sorting bambara groundnut seeds, IITA genebank. Photo by J. Oliver.

Biodiversity or biological diversity is the variety of life on earth; it includes all living forms, animal, plant, or microbial. It is accessible at three levels: ecosystems, species within the ecosystem, and genes within the species. Today, 65 million years after the fifth and largest notable extinction of species (that wiped away the dinosaurs), alarming reports state an unprecedented rate of biodiversity loss—maybe the sixth extinction (Eldregde 1999).

The loss of spectacular trees in the rainforests or of polar bears at the North Pole is well-publicized and of great concern. However, equally worrying but so much less acknowledged is the loss of agricultural biodiversity. Agrobiodiversity refers to the part of biodiversity that feeds and nurtures people—whether derived from the genetic resources of plants, animals, fish, or forests. The diversity of these genetic resources is the foundation for sustainable agriculture and global food security. It enables plants to adapt to new pests and diseases as well as to climatic and environmental changes.

There are two complementary methods to conserve plant genetic resources: ex situ (in an artificial environment) and in situ (in a natural environment). Both approaches have pros and cons. In situ conservation allows further evolution of germplasm in natural conditions, but ex situ conservation allows ready access to clean germplasm.

Since its establishment in 1967, IITA has devoted considerable resources to ex situ conservation. In 1975, the Genetic Resources Unit was created to collect, conserve, and study food legumes, roots and tubers, and their wild relatives. Today, IITA’s Genetic Resources Center (GRC) maintains over 28,000 accessions of six main staple crop collections: black-eyed pea (cowpea), maize, soybean, cassava, yam, and banana. The biggest collection is of cowpea, with over 15,000 accessions collected or acquired in or from 89 countries, mainly in Africa. This biodiversity is very valuable for further genetic improvement and food security. It is maintained in trust for the international community and is available to all.

Any new sample entering the genebank is given a “passport” and a unique accession number. The passport holds important information related to the background of the accession. Such data, and in particular the georeference, i.e., the exact location where the sample was collected, provide valuable information. Indeed, when searching for drought tolerance traits, breeders may want to give priority to samples collected in dry areas. The analysis of georeferences of accessions also shows any potential ecogeographical gaps in the collection. Finally, the genetic erosion of a crop can be assessed during recollecting missions based on vernacular names and georeferences of already collected accessions. Unfortunately, for most collections, passport data are far from complete; the country of origin may be known, but the georeferences are missing. This lack of information is partly because the importance of passport data was underestimated in the past.

Diversity of crop genetic resources in the IITA genebank. Photo by IITA.
Diversity of crop genetic resources in the IITA genebank. Photo by IITA.

A collection of biodiversity is traditionally measured at the accession level using phenotypic characterization and evaluation descriptors. The former category generally refers to highly heritable, easily seen, measured, and expressed descriptors. The second includes descriptors that are more sensitive to the environment, such as yield or pest and disease resistance. Among the 52 international descriptors used to describe cowpea diversity, some quantitative traits show a high rate of diversity. Cowpea pod length varies from as little as 5.6 cm up to 49.9 cm, depending on the accession.

Vegetative trait diversity can be equally spectacular. Depending on the accession, the number of days required to harvest the first mature pod varies from 49 to 129 days after planting. In the context of global climate change and the shortening of the rainy season, such a descriptor is of high interest to the breeding community. Although it is important to capture diversity for today’s breeding interests, it is equally important to capture “neutral” diversity. Something that has no direct use for improvement today may become valuable in the future.

Since the 1980s, the development of molecular tools has had a substantial impact on biodiversity characterization. This fast-evolving tool provides increasingly efficient, precise, and cost-effective methods of managing collections. Where the combination of passport and phenotypic descriptors fails to identify duplicates, molecular methods provide a new tool for discriminating and identifying. It is also used to detect the potential loss of genetic integrity, whether associated to conservation or regeneration. IITA is presently fingerprinting the international collections of yam and cassava.

The genetic resources of one given crop are classified in three gene pools based on their respective compatibility/incompatibility to produce viable and fertile progeny (Harlan and de Wet 1971). Gene pool I includes the crop species itself and its wild progenitor. Gene pools II and III include other species that are related to yet different from the crop species of interest (Gepts 2006). Gene pool I is generally well represented in ex situ collections but gene pools II and III have often been neglected, although they represent a valuable reservoir of untapped genes as they evolved independently of human preferences.

Africa is a center of diversity for two of the crops maintained at IITA: cowpea (Vigna unguiculata) and yam (Dioscorea spp.) (Padulosi 1993, Orkwor et al 1998). IITA has devoted considerable resources for conserving the wild relatives of Vigna. However, efforts are still needed to further collect more wild relatives and cultivated cowpea. Although generally African biodiversity remains rich, various threats exist. Climate change attracts most attention in this matter but agriculture intensification should not be overlooked. The paradox is that research in agriculture requires diversity to build on existing traits but is one of the main threats to that vital biodiversity.

IITA is planning a collecting mission for cowpea in 2010 in regions of Nigeria where collecting had not been done and will focus on two species: V. unguiculata var. spontanea (gene pool I) and V. unguiculata subsp. baoulensis (gene pool II). Remi Pasquet, a taxonomist expert for cowpea from the International Centre of Insect Physiology and Ecology (icipe), will lead the expedition.

Researcher checks tissue culture-grown cassava. Photo by Jeffrey Oliver, IITA.
Researcher checks tissue culture-grown cassava. Photo by Jeffrey Oliver, IITA.

Over the last 30 years, there has been a profound change in the legal landscape with regard to ownership of biodiversity in general and crop genetic resources in particular (Gepts 2006). In the past, biodiversity was considered a common heritage of humanity, but in 1992, the Convention on Biological Diversity (CBD) assigned sovereignty over biodiversity to national governments. CBD is the first legally binding framework for the conservation of biodiversity that recognizes the “knowledge, innovations, and practices of indigenous and local communities and encourages the equitable sharing of benefits arising for the utilization of such knowledge, practices, innovation, and knowledge” (Shand 1997).

More recently, the International Treaty on Plant Genetic Resource for Food and Agriculture reconsidered the question of sovereignty over plant genetic resources. It promotes the exchange of germplasm for 64 crops in a multilateral agreement (multilateral system, MLS). Within this frame, the conservation of plant genetic resources, i.e., the future of food security, relies on shared initiatives and responsibility and the construction of a global system. Within this system, each stakeholder has a role based on comparative advantage—whether it is access to germplasm, technology, human resources, or capacity development.

The opening of the Svalbard seed vault in Norway, in 2008 is one of the building blocks of the global system. Such an initiative caught the attention of the media and, consequently, directed the attention of the world on the erosion of plant diversity. It is somehow reassuring to know that part (even a little) of plant diversity is now kept in a place that is naturally clean, cool (energy efficient), isolated (as the North Pole), and protected (by polar bears). However, not all plant diversity can be conserved in Svalbard. In fact, many species producing so-called recalcitrant seeds as well as those clonally propagated cannot be maintained at low temperatures for various physiological reasons. These problematic species, which in IITA’s collections include yam, cassava, and banana/plantain, are generally banked in the field or in vitro slow-growth conditions. The latter approach is preferred as it protects germplasm from field biotic and abiotic risks and allows easy access to distribution of clean material.

The ultimate in vitro conservation approach is cryopreservation (conservation at very low temperatures, generally at –196 °C). At such a temperature, all biochemical and biological processes are stopped. Thus, plant tissue can, in theory, be stored forever. IITA has recently developed such a process for cassava (Dumet et al. accepted).

Whatever the ex situ conservation approach, it will never be preferable to in situ conservation. However, whenever biodiversity preservation poses a threat to human livelihoods, comfort, or convenience, the politically expedient choice is usually to “liquidate” the natural capital (Ehrlich and Pringle 2008). It seems unlikely that more natural space will be available to ensure the safety of biodiversity in the future…This is not impossible, however, if the schools are involved in teaching the value of biodiversity to the younger generations.

References
Dumet, D., S. Korie, and A. Adeyemi. (accepted by Acta Horticulturae) Cryobanking cassava germplasm at IITA.

Ehrlich, P.R. and R.M. Pringle. 2008. Where does biodiversity go from here? A grim business-as-usual forecast and a hopeful portfolio of partial solutions. PNAS. Vol. 105, suppl. 1.

Eldregde, N. 1999. An ActionBioscience.org original article.

Gepts, P. 2006. Plant genetic conservation and utilization: the accomplishments and future of a societal insurance policy. Crop Science 46:2278–2292.

Harlan, J.R. and J.M.J. de Wet. 1971. Towards a rational classification of cultivated plants. Taxon. 20:509–517.

Karp, A. 2002. The new genetic era: Will it help us in managing genetic diversity. In: Engels, J.M.M., V. Ramanatha Rao, A.H.D. Brown, and M.T. Jackson, eds. Managing Plant Genetic Diversity. Wallingford and Rome, CAB International and IPGRI, pp. 43–56.

Orkwor, G.C., R. Asiedu, and I.J. Ekanayake. 1998. Food yams: Advances in research, IITA and NRCRI, Nigeria.

Padulosi, S. 1993. Genetic diversity, taxonomy and ecogeographic survey of the wild relatives of cowpea (V. unguiculata). Ph.D. thesis, University of Louvain la Neuve, Belgium.

Shand, H. 1997. http://www.ukabc.org/ukabc3.htm