Boosting the productivity of cassava-based systems in DR Congo

Bernard Vanlauwe, b.vanlauwe@cgiar.org, Patrick Mutuo, Nzola Mahungu, and Pieter Pypers

The intensification of African agriculture is an essential response to the increasing demands for more food without endangering important natural resources, including the forests in the Congo basin.

Because of its potential to produce some roots, cassava is often considered a crop that “likes” poor soils but, as all other crops, it responds to and requires a sufficient amount of nutrients to produce attainable yields. The transformation of cassava from a food security to a cash crop in many countries in Africa further stresses the need for nutrient replenishment strategies in cassava-based systems since the transport of cassava roots to processing plants can accelerate the amount of nutrients exported from the farm.

In recent years, integrated soil fertility management (ISFM) (see article by Vanlauwe et al. this publication) has been accepted by many organizations as the underlying technical framework for the sustainable intensification of smallholder systems in Africa. This article highlights the progress of work on the application of ISFM principles in the context of cassava-based systems in DR Congo.

In DR Congo application of 2 bags of NPK fertilizer per hectare results in root yield increases from 30% to 160%.
In DR Congo application of 2 bags of NPK fertilizer per hectare results in root yield increases from 30% to 160%.

Current situation
In the highlands of Sud-Kivu province, cassava and common beans are among the main food crops traditionally cultivated in mixed cropping systems. Cassava monocropping is done only in marginal fields where other crops fail to yield. Farmers generally allocate about 0.2–0.3 ha (30–45% of their farm area) to cassava–legume intercropping and obtain average yields of 400–800 kg/ha of legume grains and 10–15 t/ha of cassava fresh roots. Pressure on land is very heavy due to high population densities and justifies agricultural intensification and investment in soil productivity.

In Bas-Congo province, on the other hand, farmers practice slash-and-burn agriculture. Cassava is grown for 1 or 2 years, followed by fallow periods of 2 to 4 years. In the past two decennia, the population has grown by more than 50% leading to more demands for food, especially from nearby Kinshasa. Improved and sustainable, fire-free production systems are urgently needed. In DR Congo, most farmers have no access to improved varieties and have very limited options to improve soil fertility.

Fertilizer and germplasm
First, the use of improved, pest-and disease-resistant varieties in combination with appropriate rates of NPK fertilizer was observed to result in a 30–160% increase in cassava root yields in eastern DR Congo. A visible increase was observed in yields of the stems, important for the production of planting material (see photo). In western DR Congo, cassava yields doubled from 12 to 25 t/ha with the application of moderate rates of NPK and reached over 40 t/ha with higher rates. Several initiatives are taking place to ensure that large quantities of planting materials reach smallholder farmers with specific attention being given to those varieties resistant to cassava mosaic disease and the brown streak virus.

Figure 1. Cassava storage root yields as affected by application of compound fertilizer (17 nitrogen: 17 phosphorus: 17 potassium) at rates of 0 (F0), 40 (F1), 120 (F2), and 200 (F3) kg K/ha, and green manure (TI = <em/>Tithonia sp.; CH = <i>Chromolaena </i>sp.) at 2.5 t dry matter/ha alone or together with compound fertilizer at 40 kg K/ha in two trial locations in Bas-Congo, DRC. SED: standard error of difference at P<0.05. Source: Adapted from Pypers et al. 2012
Figure 1. Cassava storage root yields as affected by application of compound fertilizer (17 nitrogen: 17 phosphorus: 17 potassium) at rates of 0 (F0), 40 (F1), 120 (F2), and 200 (F3) kg K/ha, and green manure (TI = Tithonia sp.; CH = Chromolaena sp.) at 2.5 t dry matter/ha alone or together with compound fertilizer at 40 kg K/ha in two trial locations in Bas-Congo, DRC. SED: standard error of difference at P<0.05. Source: Adapted from Pypers et al. 2012

Combined application of fertilizer and organic inputs
Fertilizer response and the effect of combining inorganic and organic nutrient resources were also evaluated on cassava systems. The most common fertilizer, NPK 17:17:17, was applied in western DR Congo with or without green manure made from Tithonia sp. or Chromolaena sp., and the effects on storage root yield were evaluated in two locations with a differing soil fertility status (Fig. 1). Both plants are commonly found in fallow vegetation in western DR Congo. Control yields were similar at the two sites (12 t/ha), but the response to fertilizer differed between the sites: storage root yields reached 40 t/ha at Kiduma but only 20 t/ha at Mbuela with the addition of 200 kg K/ha. A much larger response to Tithonia sp. green manure was also observed at Kiduma, which was likely to have been related to the higher quality and nutrient contents of the green manure grown at that site.

Combining organic and inorganic nutrient resources did not result in positive interactions. No significant differences were observed between the yields after the sole application of either fertilizer or green manure to the control and those obtained with the combined application of both nutrient sources (Pypers et al. 2012). In maize-based systems, positive interactions between organic and inorganic fertilizers often arise from better synchrony in N release and N uptake by the crop. In cassava systems, where K is more often the most limiting nutrient, such a mechanism is likely to be less relevant.

In the highlands of eastern DRC alternative spacing of cassava  (2 × 0.5 m instead of 1 × 1 m) allows integration of four lines of legumes during one season and two lines of legumes during the second season without affecting cassava densities and yields.
In the highlands of eastern DRC alternative spacing of cassava (2 × 0.5 m instead of 1 × 1 m) allows integration of four lines of legumes during one season and two lines of legumes during the second season without affecting cassava densities and yields.

In eastern DR Congo, the use of improved germplasm did not result in yield increases without the simultaneous implementation of other ISFM components. Modifying the crop arrangement by planting cassava at 2 m between rows and 0.5 m within the row, intercropped with four legume lines, increased bean yields during the first season and permitted a second bean intercrop. This can also increase the total legume production by up to 1 t/ha and resulted in additional revenues of almost $1000/ha (see photo). The crop arrangement or a second legume intercrop did not affect cassava root yields. Fertilizer application increased both legume and cassava yields, and net revenue by $400–700/ha with a marginal rate of return of 1.6–2.7. Replacing the common bean intercrop by groundnut increased net revenue by $200–400/ha, partly because of the higher market value of the grains, but mostly due to a positive effect on yield of cassava storage roots. Soybean affected cassava yields negatively because of its high biomass production and long maturity period; modifications are needed to integrate a soybean intercrop into the system.

Local adaptation
Due to the high variability in soil fertility status, the varying landscape features, and the variation in access to inputs, local adaptation is required to ensure that the investments made by cassava-producing households  result in the highest returns, in line with the resources (e.g., cash, land, labor) that these households have (see photo). Such adaptation efforts are best led by extension and development partners that have the required skills and capacity to implement such efforts at scale. In eastern DR Congo, erosion is the most urgent issue to be tackled to enhance the sustainability of cassava-based systems. Results from Southeast Asia with the use of live hedges should be explored for these environments.

Cassava land preparation varies widely in DRC partly affected by slope and water status of the land.
Cassava land preparation varies widely in DRC partly affected by slope and water status of the land.

Outlook
These findings demonstrate the large potential of ISFM to increase productivity in cassava–legume systems in DR Congo. This is crucial in view of the fact that cassava is changing from being almost only a food security crop to one for which there is high demand in local and urban markets. The intensification of production is thus a prerequisite for sustaining cassava-producing households and ISFM can assist in achieving such benefits. However, these benefits were not observed in all study sites. In poor soils, productivity increases were variable or absent, and soil amendments are required. Better targeting and local adaptation of the technologies are possible with a better understanding of the conditions under which positive effects occur.

References
Pypers, P., J.M. Sanginga, K. Bishikwabo, M. Walangululu, and B. Vanlauwe. 2011. Increased productivity through integrated soil fertility management in cassava–legume intercropping systems in the highlands of Sud-Kivu, DR Congo. Field Crops Research 120: 76–85.
Pypers, P., W. Bimponda, J.P. Lodi-Lama, B. Lele, R. Mulumba, C. Kachaka, P. Boeckx, R. Merckx, and B. Vanlauwe. 2012. Combining mineral fertilizer and green manure for increased, profitable cassava production. Agronomy Journal, in press.

IITA at 45: 1967 to 2012 and beyond…

This year, IITA marks its 45th year of service to the African farmers and national agricultural research systems.

In 1962, two years after the Ford and Rockefeller Foundations helped launch the International Rice Research Institute (IRRI, Los Baños, the Philippines), both Foundations began discussing the possibility of establishing centers concerned with improving the yield and quality of tropical food crops other than rice. Thus, was the idea of an institute that would conduct research in the tropics of sub-Saharan Africa conceived by IITA’s founders1.

The Institute was established in July 1967, as the first major African link in an integrated network of international agricultural research centers located throughout the developing regions of the world.

IITA is under the umbrella of the CGIAR, a global research partnership that unites 15 organizations engaged in research for sustainable development for a food secure future that carries out research in collaboration with hundreds of partner organizations.

Funding for IITA came initially from the Ford and Rockefeller Foundations, and the land for the headquarters in Ibadan was allotted by the Government of the Federal Republic of Nigeria.

Currently, the Institute is one of the world’s leading research partners in finding solutions for hunger, malnutrition, and poverty. IITA’s award-winning research for development (R4D) addresses the development needs of the poor and vulnerable in the tropics. Together with scores of partners, IITA is contributing to enhance crop quality and productivity, reduce producer and consumer risks, and generate wealth from agriculture.

For the last 45 years, IITA has delivered over 70% of the impact from the CGIAR in sub-Saharan Africa. The Institute has achieved this by focusing on key tropical food crops, such as banana and plantain, cassava, cowpea, maize, soybean, yam, and tree and vegetable crops.

For the next decade, IITA plans to raise over 20 million people out of poverty while simultaneously making available over 25 million hectares of farm lands for agricultural production. This is important as demand for food in the midst of the rising population and limited natural resources will remain as important challenges.

IITA will tackle these challenges by pursuing high quality research that improves food security, increases the profitability of foods and other agricultural products, and helps national entities to expand agricultural growth.

With the help of partners and other stakeholders, IITA endeavors to continue to improve the lives of the poor in the region through R4D.

1 Excerpts taken from Ortiz, R. 2004. IITA: 40 yeas after. Historical account for the Handbook of IITA Board of Trustees. IITA Report. 36 pp.

Issue 8, March 2012

Maize genetic improvement
A success tale in legume work
Breeding superior banana hybrids
Cassava & agrigenomics
Yam breeding at IITA
Genomics for yam breeding
A ‘Green Revolution’ in cocoa belt
Partnerships for development
Estimating aflatoxins
Agrigenomics for improving crops
Transgenics in crop improvement
Molecular diagnostic tools

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Mind the gap…

Excising banana explants. Photo by IITA.
Excising banana explants. Photo by IITA.

IITA was established in 1967 to increase and improve food crop production, and soil and crop management for sustainable agricultural development. The Institute has become integral to the quest by sub-Saharan Africa (SSA) to attain food and income security. Multi-pronged approaches, in partnership with national and international organizations, on natural resource management and the genetic improvement of staple crops in the humid tropics and tropical savannas have led to the development of high-yielding varieties. These have resilience to counter multiple biotic and abiotic threats, and new technologies have been established for crop protection and sustainable natural resource management. Since its establishment, the institute has become a pacesetter in agricultural development in SSA.

This issue commemorates the 45th anniversary of IITA. It focuses on the successes, challenges, and prospects of the genetic improvement programs which have been the cornerstone of IITA’s success in improving food crop production in SSA. These innovations in genetic improvement, together with supportive policies and training, have dramatically improved crop productivity and lifted millions out of poverty.

However, achieving self-sufficiency in food production and reducing poverty still remain as intractable problems in many countries here. There are many reasons for this situation. Inadequate economic and political systems, conflict, adverse weather, lack of crop production support mechanisms, inadequate funds for research and development, inefficient marketing structures, and a limited pool of trained scientists are key factors for the poor performance of the agriculture sector in SSA1.

Many governments are embarking on initiatives to establish agriculture as a commercially viable entity to produce enough food and create opportunities for employment. However, institutional reforms are also required to establish sound technical capacity, infrastructure, and enabling policies for the benefit of technological innovations to be fully realized and to facilitate farmers’ access to inputs and markets.

Governments are urged to show greater commitment to invest in reforms that can foster the establishment of a strong and sustainable agricultural system. This is essential to cater to the demands from economic growth and the rapid rise in population (set to double by 2050 2) and to develop the adaptive capacity needed to cope with risks from climate change. Without these, the current situation can only worsen and increase the levels of hunger and poverty.

1 Joubert, G.D. 2007. Trends in Africa’s crop production and the way forward on research and development. African Crop Science Proceedings 8: 5–7.
2 Eastwood, R. and M. Lipton. 2011. Demographic transition in sub-Saharan Africa: how big will the economic dividend be? Population Studies 65: 9–35.

Countries need strong leadership to introduce changes in implementing agricultural development programs.
— Dr Nteranya Sanginga, Director General, IITA

Maize genetic improvement for enhanced productivity gains

Abebe Menkir (a.menkir@cgiar.org), Baffour Badu-Apraku, and Sam Ajala
Maize Breeders, IITA, Ibadan, Nigeria

Maize streak virus disease causes severe stunting and extreme yield reduction in maize. Creating Maize streak virus-resistant varieties is one of the major successes of IITA's maize breeding program. Source: L. Kumar.
Maize streak virus disease causes severe stunting and extreme yield reduction in maize. Creating Maize streak virus-resistant varieties is one of the major successes of IITA's maize breeding program. Source: L. Kumar.
Maize is an important food security and income-generating crop for millions of people in West and Central Africa (WCA). Maize breeding at IITA was initiated around 1970. Using as base materials two composites created from diverse sources in Nigeria under a West African project supported by the Scientific and Technical Research Committee of the Organization for African Unity, breeders at IITA formed several broad-based populations and improved them through recurrent selection. The main research focus at that time was the development of open-pollinated maize varieties (OPVs) with resistance to diseases, and adapted to the humid forest and moist savannas of WCA. The products generated from this research were channelled to research and development partners for further testing, multiplication, and dissemination in various countries in the subregion.

The widespread outbreak of the maize streak virus (MSV) disease in the late 1970s prompted IITA to develop two resistant populations. These were crossed to high-yielding and broad-based germplasm from the International Maize and Wheat Improvement Center, eastern and southern Africa, the temperate zone, central and south America, Thailand, DECALB, and other sources to create populations and varieties resistant to MSV. IITA has supplied MSV-resistant inbred lines, OPVs, hybrids, and populations to partners within and outside WCA through diverse delivery pathways for more than 25 years. Direct use of MSV-resistant maize germplasm that also had resistance to southern leaf rust, southern leaf blight, downy mildew, and leaf spot has been recorded in several countries in Africa.

The significant breakthrough in the development and release of high-yielding extra-early, early, intermediate, and late-maturing varieties with resistance to leaf rust, leaf blight, and leaf spot has caused a phenomenal increase in maize production in WCA, notably in Bénin, Burkina Faso, Cameroon, Chad, The Gambia, Guinea, Ghana, Mali, Nigeria, Senegal, and Togo. Further expansion in production has also occurred in many countries in this subregion because of the adoption of extra-early maturing improved varieties identified from regional trials coordinated by the Semi-Arid Food Grain Research and Development (SAFGRAD) and the West and Central frica Collaborative Maize Research Network (WECAMAN).

IITA maize breeders in action, maize breeding program. Source: L. Kumar.
IITA maize breeders in action, maize breeding program. Source: L. Kumar.
The development of extra-early maturing varieties enabled production to expand into new areas, especially to the Sudan savannas where the short rainy season hitherto had precluded maize cultivation. The highest growth in maize area, yield, and production in sub-Saharan Africa since 1961 occurred in WCA. These productivity gains, achieved through farmers’ adoption of improved varieties in the 1980s, were driven by the suitability of the cultivars to the major production environments, the availability of inexpensive fertilizer and extension services, as well as favorable government policies that encouraged the use of these technologies.

In a recent impact assessment study conducted in nine countries, the number of varieties annually released in WCA had increased from fewer than one in 1970s to 12 in the late 1990s. The availability of such high-yielding and adapted varieties resulted in a 2% annual increase in land area planted to maize and a 3.5% annual increase in grain yield from 1971 to 2005. Among the varieties released from 1998 to 2005 in the nine countries, 67% were derived from IITA’s maize germplasm. Of the 4 million ha planted to improved maize in these countries, about 43% of the area was planted to varieties derived from IITA’s germplasm. The joint IITA-NARS investment in maize research in the nine countries had lifted an average of 1.6 million people out of poverty annually from 1980 to 2004.

While working with diverse partners to promote the dissemination of maize varieties in the various countries, IITA realized that the major constraint to the adoption of improved varieties in WCA was the absence of an effective seed production and delivery system. To promote the establishment of indigenous private seed companies, IITA embarked on the development of hybrids in 1979 with financial support from the Federal Government of Nigeria and the active participation of Nigerian scientists. This led to the release of the first generation of hybrids in 1983, with a spill-over effect of the establishment of seed companies in Nigeria for marketing hybrid maize seeds. The official announcement of IITA’s maize OPVs and hybrids in the catalogs of indigenous seed companies in Nigeria provide further evidence of the adoption, deployment, and commercialization of IITA-bred varieties and hybrids.

In recent years, IITA has also made significant progress in the development of a large number of maize inbred lines, OPVs and hybrids with resistance to Striga hermonthica, stem borers, and aflatoxin contamination, with tolerance to drought, efficient nitrogen use, and enhanced contents of lysine, tryptophan, and pro-vitamin A. We have the first generation of extra-early, early, intermediate, and late-maturing OPVs and hybrids that combine drought tolerance with resistance to S. hermonthica developed under the Drought Tolerant Maize for Africa Project and supplied to partners for testing through regional trials. The number of drought-tolerant OPVs identified from these trials and released for production since 2007 were 7 in Bénin Republic, 5 in Ghana, 3 in Mali, and 13 in Nigeria.

On the other hand, only one drought-tolerant hybrid selected in Mali and six drought-tolerant hybrids selected in Nigeria were released for production. Furthermore, three varieties with high lysine and tryptophan content, two varieties resistant to S. hermonthica, two varieties that are nitrogen use efficient, a stem borer-resistant variety, two yellow and two white hybrids were released from 2008 to 2011 in Nigeria.

Maize production in Saminaka area in Kaduna State, Nigeria. Photo. by A. Menkir.
Maize production in Saminaka area in Kaduna State, Nigeria. Photo. by A. Menkir.
To accelerate the release and commercialization of hybrids with different maturity classes, high yield potential, combining resistance to Striga and drought tolerance, and other desirable traits in different countries in WCA, IITA has supplied parental lines of promising hybrids to private seed companies for further testing, production, and commercialization. The institute has also trained technical and management staff of seed companies to strengthen their human capacity to produce and market hybrid maize.

In addition, IITA has promoted community-based seed production schemes through its work with WECAMAN and more recently with diverse partners to make improved seeds available to farmers in countries where the private sector is less developed and in areas with limited access to markets.
Despite the impressive strides that have been made so far, continued investment in maize productivity research still remains critical to sustain agricultural growth, food security, improved nutritional quality, and safe harvests. Considering the predominance of the crop in diverse farming systems, heterogeneous landscapes, and the diets of millions of people in WCA, enhanced yield gains have the potential to further expand production in WCA, thus contributing to bridging the gap between food supply and demand in the region, because research has led to and will continue to deliver excellent results.

Increased investment not only in research but also in strengthening the private seed sector will still be needed to promote the rapid turnover of maize hybrids on farmers’ fields that help to achieve higher yield gains to support improved farming in WCA.

A success tale on improving two legume crops in Africa

Ousmane Boukar (o.boukar@cgiar.org), Tahirou Abdoulaye, Manuele Tamó, Hesham Agrama, Hailu Tefera, Christian Fatokun, and Steve Boahen
O. Boukar, Cowpea Breeder; T. Abdoulaye, Socioeconomist, IITA, Ibadan, Nigeria; M. Tamó, Legume Entomologist, IITA, Benin; H. Agrama and H. Tefera, Soybean Breeders, IITA, Malawi; C. Fatokun, Cowpea Breeder, IITA, Ibadan, Nigeria; S. Boahen, Legume Specialist/Agronomist, IITA, Mozambique

Cowpea and soybean are cultivated by poor and middle-income farmers as a sole crop or as intercrop with maize and other cereals for their protein-rich grains which are consumed in different forms. The haulms from plant residues and the dry pod walls of both crops are good sources of quality fodder for livestock.

Improved cowpea varieties being tested in a field trial. Photo by L. Kumar.
Improved cowpea varieties being tested in a field trial. Photo by L. Kumar.

The two crops contribute substantially to sustain crop production through their ability to fix atmospheric nitrogen, some of which is left behind in the soil after harvesting for subsequent crops. IITA and its partners have been involved in improving legume production systems for several decades. An overview of these efforts is presented in this article.

Cowpea
Cowpea―indigenous to sub-Saharan Africa (SSA), is grown on about 14 million ha worldwide, with over 84% of this area in SSA. Between 1985 and 2007, the rate of growth was 4.5% in land area planted to cowpea, 4.5% in grain yields/ha, and 5.9% in quantity of cowpea produced. These data indicate that the increase in the quantity of grain produced over the period resulted mainly from an expansion in the land area and less from an improved yield/unit area. In well-managed experimental stations, yields of up to 2 t/ha can be obtained but globally the average yield is about 450 kg/ha.

Several abiotic and biotic factors keep the productivity of cowpea low in African farmers’ fields. Notable among these are drought, poor soil fertility, inappropriate agronomic practices, an array of fungal, viral, and bacterial diseases, and parasitic flowering plants (Striga and Alectra). Cowpea is particularly susceptible to infestation by several insects with devastating effects on plants in the field and seeds in storage.

Efforts in genetic improvement have been and are still being made to develop varieties with resistance to these various yield-limiting factors and in various research institutions across SSA, iIITA, and other advanced research institutions. Cowpea breeders from these various institutions meet regularly to share information and exchange ideas on the way forward.

Elite lines generated from IITA’s breeding nurseries are shared with interested colleagues from the national research institutions who evaluate these at their stations and in farmers’ fields. Those that perform well are recommended for release in the respective countries. For example, in Mali, a cowpea line IT99K-499-35 was recently adopted by many farmers in the Segou area and because of its superior performance and resistance to Striga, given a local name, Jinguiya which means ‘hope’.

Under the Tropical Legumes II (TL II) project, several new cowpea varieties [IT97K-499-35 (in 2008), IT89KD-288 and IT89KD-391 (in 2009), IT99K-573-1-1 and IT99K-573-2-1 (in 2011)] were released in Nigeria. Regional trials are being conduced for two cowpea lines (IT97K-1122 and IT00K-1263) identified through farmers’ participatory selection as part of the TL II project in Tanzania to facilitate their official release. In 2011, three IITA cowpea lines (IT97K-1069-6, IT00K-1263, and IT82E-16) were released in Mozambique; and IT99K-494-6 was released by Bunda College in Malawi as an Alectra-resistant variety in 2011.

Legume scientists in a disease resistance screening trial. Photo by L. Kumar.
Legume scientists in a disease resistance screening trial. Photo by L. Kumar.

Research into integrated pest management (IPM) for cowpea has resulted in the development and deployment of biopesticides including the use of entomopathogenic organisms combined with botanicals, and biological control agents such as hymenopteran parasitoids which attack and feed on some of the cowpea pests. An example is the mixture of a specific entomopathogenic virus capable of infecting and killing the legume pod borer Maruca vitrata with aqueous formulations of neem oil. This has proved to be as effective as the use of conventional insecticidal sprays. With regard to biological control, a small parasitic wasp which attacks the flower bud thrips, another major pest of flowering cowpea, has been introduced and established in most of Bénin and parts of Ghana, It has been reported to reduce the thrips population on wild alternative host plants by up to 40%.

The development of improved cowpea varieties has so far depended on conventional breeding methods. However, efforts are being made to apply molecular breeding tools to cowpea improvement. Fairly saturated genetic linkage maps of cowpea have been produced in several laboratories. The linkage maps have been used for the detection of DNA markers associated with resistance/tolerance to Striga, drought, macrophomina, and bacterial blight, and seed characteristics such as size. A few of the markers have been converted to user-friendly markers which will make them readily available for breeders in the national systems. Molecular markers are contributing to progress in variety development.

IITA is collaborating with Purdue University, USA, in implementing the Purdue Improved Cowpea Storage (PICS) project on the hermetic storage of cowpea grain in Nigeria, Bénin, Togo, and Cameroon. From 2008 to 2010, IITA and its partners disseminated hermetic triple-layer bags for storage in more than 13,500 villages in the cowpea-producing areas of Nigeria, Cameroon, Togo, and Bénin. This project addresses one of the most important constraints to cowpea production which is grain damage in storage. Furthermore, by not using any type of chemical, this hermetic storage method is protecting farming families and consumers from accidents from the mishandling of and poisoning by the chemicals used in cowpea storage. To date, farmers have purchased more than 30,000 PICS bags in these countries.

IITA is also collaborating in an adoption study that will provide information about the reach of the technology. Another study on analysis of the supply chain of the PICS bags in the same four countries will help to improve the farmers’ access to the PICS bags through a better distribution network.

Soybean
Soybean is a fairly new crop in SSA and has few biotic constraints. Fewer than 400 ha were planted to soybean in SSA during the 1980s but this exceeded the 1-million ha mark by 2007. Grain yield/ha increased from about 900 kg/ha in the 1980s to >1000 kg/ha between 2005 and 2007. Initially most varieties grown in parts of SSA had the problem of seed longevity. Farmers could not store seeds successfully from one cropping season to the next. This problem has now been solved so that seeds of the newly developed varieties remain viable over a longer period. Another constraint to soybean production was pod shattering, which resulted in seeds being lost in the field. Farmers could not leave their crop to dry in the field before harvesting without losing some of the grain. The varieties that have been developed at IITA have tolerance to pod shattering, and resistance to rust─a fungus (Phakopsora pachyrhizi) that causes significant yield losses, especially in the moist savanna agroecology. Some genotypes of soybean are noted for their abilities to reduce the seed bank of Striga hermonthica, a parasitic weed which can cause serious damage to cereal crops.

Farmers admiring improved soybean varieties. Photo by IITA.
Farmers admiring improved soybean varieties. Photo by IITA.

Several elite lines from IITA’s breeding nursery have been evaluated in many countries in SSA and found to perform well in farmers’ fields. Some of these have been recommended for release in the different countries. For example, rust-resistant TGx1835-10E and TGx1987-62F have been released in Nigeria; TGx1740-2F was released in Malawi; TGx-1485-1D, TGx1740-2F, TGx1904-6F, TGx1908-8F, and TGx1937-1F were released in Mozambique in 2011. These were the first batch of varieties ever released in Mozambique. The development of improved varieties also involved farmers’ participation in selection, which made it possible for farmers to have some knowledge on performance of the lines being selected, thus facilitating rapid adoption and dissemination. IITA, in collaboration with Laval University in Canada, completed genotypic [using single nucleotide polymorphism (SNP) markers] and phentotypic characterization of 300 soybean genotypes for rust resistance and symbiotic performance.

In addition to efforts on genetic improvement of soybean, major emphasis has been placed on promoting and using soybean to encourage consumption, and thus create markets for farmers to sell their produce. Recipes were developed to promote the use of soybean grain for food. This promotional activity was necessary because the crop was new in many parts of the region and people were not familiar with how it could be best used as food. Vegetable oil millers were also encouraged to accept soybean as a raw material from where good quality oil could be extracted.

Legumes fix atmospheric nitrogen in their root nodules through the symbiotic association between the crop and rhizobium, a free-living soil bacterium. Legume seeds are inoculated with the rhizobium before sowing to increase the number of rhizobium available to the plant for infection and nodule formation, and subsequently enhance the quantity of the nitrogen fixed. Soybean is one such crop that requires rhizobium inoculation if a good crop is to be established on soils with no existing rhizobia or inadequate number if rhizobia.

At IITA, some soybean varieties have been developed which are capable of fixing atmospheric nitrogen using the native rhizobium present in the soil. These varieties which require no inoculation before sowing are characterized by promiscuous nodulation. Growing such varieties will save the farmers some expense and the time needed to purchase the inoculants with which the seeds are treated.

Conclusions
Decades of collaborative research efforts on genetic improvement of these two important legume crops involving scientists in the national agricultural research systems of different countries in SSA, IITA, and advanced research institutions in Europe and North America have resulted in the development and promotion of different improved varieties to meet the preferences of farmers and consumers. Improved varieties developed through this partnership have been released in over 70 countries around the world, which signifies the success of this partnership for legume crop improvement.

Further efforts will focus on use of innovative approaches to pyramid pest and disease resistance genes into improved lines and varieties; application of molecular markers to rapidly introduce genes for simply inherited desirable traits into popular varieties; and genetic modification using recombinant DNA technology to produce insect-resistant cowpea varieties (Bacillus thuringiensis or Bt cowpea for resistance to the Maruca pod borer). Efforts will be continued to address diseases, such as the need to develop improved cowpea and soybean lines with combined resistance to different fungal, bacterial, and viral pathogens. The factors that influence tolerance to drought in cowpea require further elucidation, as this would facilitate progress in developing new varieties with enhanced drought tolerance.

Breeding superior banana/plantain hybrids

Jim Lorenzen (j.lorenzen@cgiar.org)
Banana Breeder, IITA, Tanzania

Banana (the term includes plantain in this article, Musa species), is a major staple crop in Africa. Although it originated in Asia and was introduced to Africa long ago, it has become more important as a food security crop in its new home in Africa than in its region of origin. From its early domestication in Southeast Asia and the islands extending toward Australia, banana spread to Africa before recorded history. Archaeological evidence suggests that it reached Central Africa several millennia ago.

Pollination of banana flowers. Photo by L. Kumar.
Pollination of banana flowers. Photo by L. Kumar.
The main types of cooking banana in Africa include plantain (AAB genome), East African Highland Banana (EAHB, AAA genome), and a wide range of other types including sweet dessert banana (AAA or AAB genome), starchy but sweet roasting or brewing banana (ABB genome), and a number of other types. The “genome” refers to the portion of the chromosomes that come from one of the progenitor species of banana, Musa acuminata (A genome) or Musa balbisiana (B genome). However, most banana production in sub-Saharan Africa (SSA) consists of the East Africa Highland type or plantains, two sets of varieties with very limited genetic diversity in either. This lack of genetic diversity is a serious concern. About 60% of African production occurs in Uganda and its immediate neighbor countries (Tanzania, Rwanda, Kenya, D.R. Congo; also including Burundi).

Since banana production is year-round, it serves as a buffering bridge crop to provide food in times of scarcity between cereal harvests. As a long-lived clonal crop, it (like cassava) also can serve as a famine-avoidance crop because it is less susceptible than annual crops to catastrophic failure in the event of unseasonable drought and can act as a survival crop during cereal crop failure. Banana also provides important ecological functions for sustainable agriculture by reducing erosion in sloping highland agriculture, and recycling nutrients through the crop residue returned to the soil in each production cycle. In some locations banana leaves and cut stems are an important fodder component in the livestock sector, providing some fodder even during the dry season.

Production constraints
While precolonial banana production may have been relatively stable, pests and diseases introduced into Africa in the last century have destabilized production in some areas. Some important introduced diseases and pests include black leaf streak (also known as Black Sigatoka), Banana bunchy top virus (BBTV), burrowing nematode, banana weevil, and Fusarium wilt. More recently, banana Xanthomonas wilt (BXW) has emerged as an important bacterial disease that apparently originated in Ethiopia and caused a major disease epidemic in much of East Africa in the last decade. Breeding for resistance to these diseases and pests provided the initial motivation for IITA and partners to initiate breeding in Africa.

Manual pollination of banana flowers. Photo by IITA.
Manual pollination of banana flowers. Photo by IITA.
Banana breeding history
Although early efforts to breed banana using modern breeding concepts were initiated by British scientists in the Caribbean about 80 years ago, even today the world has only about seven significant banana breeding programs. IITA initiated a plantain breeding program at the Onne High Rainfall research station in southeast Nigeria in the 1980s as a new epidemic disease, Black leaf streak, arrived in the region. This program made relatively rapid progress, identified fertile plantain varieties to cross to wild sources of resistance, optimized and implemented embryo rescue as a means of boosting germination from <1% to 5─30%, and produced resistant high-yielding hybrids by the early 1990s. Realizing that the bigger portion of African banana production was in highland East Africa and also threatened by black leaf streak, in 1995, IITA initiated a banana breeding program in Uganda in collaboration with the National Agricultural Research Organization (NARO). Working together, scientists identified fertile EAHB varieties, produced resistant high-yielding tetraploid hybrids to serve as parents, and initiated a program to produce resistant high-yielding triploid hybrids that were more likely to remain seedless.

Banana breeding process
Although most of the world eats banana, few realize that wild banana are full of hard seeds and domestication resulted in the seedless fruits that we now eat. Most varieties are triploids (have 3 sets of each chromosome), which are both more productive and more likely to remain sterile and seedless. However, some edible varieties retain a bit of residual fertility and will set a few seeds if pollinated with a strong source of viable pollen. Banana breeders serve as surrogates to natural pollinators (bats), climb ladders in the early morning to collect male flowers, and carry them and the ladders over to the intended female plants to hand-pollinate female flowers. The flowers open sequentially each day, so each floral bunch is pollinated daily for a week. While many pollinations produce no seeds, some produce a few and a very few produce many seeds. Unfortunately, due to the complex background of domesticated banana, most seeds will not germinate on their own. Therefore breeding programs extract embryos from surface-sterilized seeds and germinate them in test tubes in nutritious media, from which they can later be transplanted to sterile soil, hardened, and eventually planted in the field. Triploid hybrids are evaluated as potential new varieties, while diploid (2 sets of chromosomes) and tetraploid (4 sets) hybrids are evaluated as potential improved parents.

Progress
The original plantain hybrids, as well as superior hybrids developed later, are currently being tested for agronomic performance, yield, and consumer acceptability in a number of countries in West and Central Africa, including Nigeria, Cameroon, Ghana, and Coté d’Ivoire. In the meantime, IITA’s original East African partner in banana breeding, NARO, has grown to be one of the largest banana research programs in the world, with internationally recognized capacity in several disciplines.

Fittingly, in 2010 NARO became the first national program in Africa to officially release a banana variety bred in Africa. Kabana6 (nicknamed Kiwangaazi) is a high-yielding variety with resistance to black leaf streak and partial resistance to nematodes and weevils. More encouragingly, newer selections likely to be more acceptable to Ugandan consumers are “in the pipeline,” and procedures are now in place to move some jointly developed NARO-IITA hybrids to countries where their cooked texture and appearance fit the traditional variety “type” better than they do the “matooke” variety type of Uganda. A couple of promising hybrids are finding acceptability in Burundi and eastern D.R. Congo, and hopefully will also be released as varieties. IITA recently opened a second East African breeding site near Arusha, Tanzania, a country with a broader range of environments and irrigation opportunities, potentially better to breed widely adapted varieties and providing the opportunity to screen more systematically for drought tolerance.

Physical measurements of banana fruits. Photo by IITA.
Physical measurements of banana fruits. Photo by IITA.
Other aspects
To support the breeding program, other genetics studies are being conducted, including development of populations for molecular mapping studies, mapping genes controlling important traits, manipulating ploidy to try to create fertility in “sterile” lines, developing molecular “tools” to make breeding more efficient, and investigating gene expression in response to drought. IITA has excellent capacity for screening for resistance to pests and diseases.

The entire banana improvement program depends on collaborative relationships, both within IITA and from a range of partners within Africa and in other continents. The pending release of the reference genome sequence from La recherche agronomique pour le développement (CIRAD)/Genoscope in France should greatly accelerate genetics research on banana and its relatives. In light of the challenges of breeding and the lack of good sources of resistance for two important pathogens (BXW and BBTV), IITA is also investing in biotechnology approaches to banana improvement, with promising signs of resistance in early laboratory, screenhouse, and confined field trials (companion article by Tripathi).

Challenges
While encouraging progress is being made, banana breeding is challenging, slow, and expensive. Low fertility, poor seed set, and low germination rates mean that it is difficult to produce large numbers of progeny to evaluate. Banana plants are large, so evaluation plots are likewise large and expensive, and plants require up to 3 years to progress through two fruiting cycles. Much of the background genetics underlying key traits have yet to be properly investigated, so the list of research opportunities to make breeding more efficient and productive is long.

Musa is one of the major crops in the world for which wild relatives have yet to be systematically collected, so access to wild species for breeding for more resistant or more nutritious hybrids is problematic. Unfortunately, the global gene pool with the resistance and quality genes for future breeders remains at risk. Hopefully arrangements can be made for collection expeditions in the center of origin (Southeast Asia) in the near future while wild Musa still remain.

Future
Although banana has been a neglected crop in terms of research investment and scientists’ effort in many countries, key decision makers are beginning to realize the essential role of banana/plantain in food security, enhanced livelihoods, and resilient agricultural systems for Africa. The potential to breed superior hybrids has been demonstrated, and there are numerous opportunities for improving both the process and the product, and for realizing impact from already developed hybrids. The future for banana crop improvement looks promising.

Cassava improvement in the era of “agrigenomics”

Ismail Yusuf Rabbi (i.rabbi@cgiar.org), 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.

Genotyping-by-sequencing
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.

References
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.

Yam breeding at IITA: achievements, challenges, and prospects

Antonio Lopez-Montes (a.lopez-montes@cgiar.org), Ranjana Bhattacharjee, and Gezahegn Tessema
A. Lopez-Montes, Yam Breeder; R. Bhattacharjee, Molecular Geneticist; G. Tessema, Associate Professional Officer, IITA, Ibadan, Nigeria

Yam is an impotant staple food in West Africa. Photo by IITA.
Yam is an impotant staple food in West Africa. Photo by IITA.
Yam—an integral part of the West African food system
Yam (Dioscorea spp.) is a multi-species, clonally propagated crop cultivated for its starchy tubers. About 10 species are widely cultivated around the world, but only D. rotundata, D. alata, and D. cayenensis are the most widely cultivated species in West Africa, accounting for 93% of the global yam production. Since its inception, IITA R4D efforts have focused on developing new varieties of yam with desired agronomic and quality traits and to improve yam-based cropping systems.

Largest collection of yam genetic resources
IITA maintains the largest world collection of yam, accounting for over 3,000 accessions mainly of West African origin. The collection represents eight species: D. rotundata (67%), D. alata (25%), D. dumetorum (1.6%), D. cayenensis (2%), D. bulbifera (2%), D. mangenotiana (0.25%), D. esculenta (0.7%), and D. praehensilis (0.3%). The passport data and characterization information on these accessions are maintained in databases accessible at http://genebank.iita.org/. On request, these germplasm accessions are distributed following Standard Material Transfer Agreements (SMTA). As in many other crops, the request for gene bank accessions has been low for use in national and international yam improvement programs. Of a total of 3170 accessions, only 1077 accessions have been distributed in the last 10 years.

To increase the use of yam germplasm, which are a wealth of rare alleles for target traits, a core collection (391 accessions) was established in 2006 representing 75% of genetic diversity of the entire collection using data on 99 morphological descriptors and country of origin. The germplasm collection is being genotyped using 18 DNA-based markers. Presently, research efforts are under way in collaboration with CIRAD for cryopreservation, using liquid nitrogen, to reduce the cost of maintenance of such a large collection. Efforts to improve yam germplasm conservation and use will be continued under the framework of the CGIAR Research Program (CRP) on Roots, Tubers and Bananas (RTB) for Food Security and Income. As part of this program efforts will be made to (a) optimize ex situ and in situ yam conservation methodologies; (b) increase coverage of yam gene pools; (c) evaluate, genotype, and phenotype yam collections for important traits; (d) enrich databases with information on yam collections and make it freely accessible to users; and (e) improve procedures for safe exchange of RTB genetic resources.

Making the difference
IITA’s yam breeding program has mainly focused on clonal selection from landraces and hybridization of elite clones of D. alata and D. rotundata. Conventional breeding efforts in yam have resulted in substantial achievements leading to release of high-yielding and disease-resistant cultivars. For instance, through collaborative evaluation of IITA-derived breeding lines with national research institutes (National Root Crop Research Institute, Umudike, Nigeria, and the Crops Research Institute, Ghana), 10 varieties of D. rotundata (10 during 2001–2009 in Nigeria and 1 in 2007 in Ghana) and 5 varieties of D. alata (during 2008–2009 in Nigeria) were released. More lines are in the pipeline to be released by these institutions in Nigeria and Ghana, and also in Benin, Burkina Faso, Côte d’Ivoire, Sierra Leone, Togo, and Liberia. The released varieties have multiple pest and disease resistance, wide adaptability, and good organoleptic attributes.

Novel vertical sacs method for seed yam production using vine cuttings. Photo by L. Kumar.
Novel vertical sacs method for seed yam production using vine cuttings. Photo by L. Kumar.
Some work has also been carried out in interspecific hybridization, but it is faced with a lot of challenges, including cross-compatibility and synchronization of flowering. For instance, D. rotundata can be crossed to D. cayenensis, but crossing either of the two to D. alata has not been successful. Research effort in interspecific hybridization has been geared towards the genetic improvement of yam, primarily on D. rotundata, D. cayenensis, and D. alata by transferring complementary traits from one to the other, e.g., higher carotenoid in D. cayenensis transferred to D. rotundata by interspecific hybridization.

Besides success in hybridization, efforts of the breeding program resulted in identification of resistance to nematodes (D. dumetorum), fungi and viruses (D. alata and D. rotundata); selection of germplasm for their response to soil nutrients and nutrients use efficiency; physicochemical characterization of D. alata for food quality, sensory evaluation of ‘amala’ (yam flour paste) and pasting characteristics of fresh yam as indicators of textural quality in major food products. Studies are ongoing to determine the variation in nutrient retention during processing of yam into food products; characterization of tuber micronutrient density, specifically for iron, zinc, total carotenoids, ascorbic acid (vitamin C), phytate, and tannin content. Traits, such as photoperiod response, flowering, and dormancy are also being studied in D. rotundata.

The future thrust will be on reducing the breeding period required to develop improved varieties with consumer-preferred traits, as well as increased participation of stakeholders for improved efficiency and impact of the yam breeding program. Developing participatory value chain strategy will set priorities not only for research and development but also for a consistent value chain articulation and low risk models to link farmers to markets. Yam for food security, food industry (flour, pasta, noodles, pancakes etc.), and pharmacology (drugs, cosmetics) needs prioritized by stakeholders will drive the development of new varieties, that are high yielding, resistant to diseases and pests, and with good adaptability to specific production systems, low fertility soils, and dry environments. GIS-based characterization of yam production systems, yam growth models and genome sequencing will provide strategic knowledge for the success of the yam breeding program. Rapid and high-ratio seed yam propagation systems will support the variety development and dissemination efforts to breeders and other stakeholders. The implementation of the new scheme is expected to reduce the time to develop and recommend new varieties from 9 to 3.5 years and facilitate rapid release of consumer-preferred varieties by the national programs.

Genomic resources for yam improvement
Research on biotechnology of yam includes tissue culture, genetic transformation, and development and use of molecular markers. However, no genetically modified yam has been produced so far although this approach could be used to transfer resistance to virus and anthracnose diseases into popular commercial varieties. Progress on yam genomics and transformation is covered in Bhattacharjee et al.

Researchers in accelerated yam breeding trial plot. Photo by L. Kumar.
Researchers in accelerated yam breeding trial plot. Photo by L. Kumar.
Future prospects
Review of constraints in yam production in West Africa identified the high cost of planting material, high labor costs, poor soil fertility, low yield potential of local varieties, pests and diseases (on-farm and in storage), and shortage of quality seed yam of popular landraces and released varieties as major limitations. To overcome these challenges, in the next five years under the CRP-RTB framework, yam breeding efforts will focus on (a) development of new breeding tools and strategies, (b) trait capture and gene discovery, (c) pre-breeding for new traits, (d) development of new varieties incorporating consumer-preferred characters, and (e) aligning research with farmer and end-user priorities.

These efforts will be supported by the ongoing R4D programs on developing efficient phenotyping protocols for nutrient use efficiency, moisture stress tolerance and biotic stresses in different yam species; regeneration protocol for transformation of various species (D. rotundata, D. alata, and D. cayenensis); methods for efficient interspecific hybridization among D. alata, D. rotundata, D. bulbifera, D. cayenensis, and D. dumetorum; establishment of marker-assisted breeding platform; techniques for rapid propagation of high quality seed yam; protocol for double haploids from yam microspores; and adoption of stakeholder participatory approaches in development and release of new varieties. Ongoing efforts to strengthen seed yam systems for ensuring sustainable production and supply of quality seed yam in West Africa, and communication and promotional strategies for the dissemination of breeding materials and improved varieties underpin the success of these efforts.

Genomics for transforming yam breeding

Ranjana Bhattacharjee (r.bhattacharjee@cgiar.org), Melaku Gedil, and Antonio Lopez-Montes
R. Bhattacharjee, Molecular Geneticist; M. Gedil, Head, Bioscience Center; A. Lopez-Montes, Yam Breeder, IITA, Ibadan, Nigeria

Breeding challenges in yam
Yam (Dioscorea spp.), a multi-species, polyploidy, and vegetatively propagated crop, is an economically important staple food for more than 300 million people in West Africa, Asia, Oceania, and the Caribbean. The five major yam-producing countries in West Africa (Bénin, Côte d’Ivoire, Ghana, Nigeria, and Togo) account for 93% of worldwide production. Dioscorea rotundata and D. alata are the species most commonly cultivated in West Africa1.

Scientists strategizing genomics for precision breeding. Photo by L. Kumar.
Scientists strategizing genomics for precision breeding. Photo by L. Kumar.
The genetic improvement of yam is faced with several constraints, including the long growth cycle (about 8 months or more), dioecy, plants that flower poorly or not at all, polyploidy, vegetative propagation, heterozygous genetic background, and poor knowledge about the genetics of the crop2. Progress has been made in breeding to develop F1 full-sib mapping populations from crossing male and female parents of D. rotundata for traits such as multiple tuber production, improved cooking quality, and virus disease resistance; and of D. alata for resistance to anthracnose, improved cooking quality, and reduced tuber oxidation3. These are valuable sources of populations for genetic analysis in yam for its improvement.

Current status of yam genomics
There is no convenient model system for yam genomics. In recent years, some progress has been made in the development of molecular markers to assess their potential for germplasm characterization and phylogenetic studies in D. rotundata-cayenensis and their wild progenitors, such as D. abyssinica and D. prahensilis. Two framework linkage maps were constructed using D. alata that included 338 AFLP markers on 20 linkage groups with a total map length of 1055 cM; and D. rotundata in which 107 AFLP markers were mapped on 12 linkage groups (585 cM) for the male and 13 linkage groups (700 cM) for the female. Three quantitative trait loci (QTLs) on the male and one QTL on the female were identified for resistance to yam mosaic virus (YMV). Similarly, one AFLP marker was found to be associated with anthracnose resistance on linkage group 2, explaining about 10% of the total phenotypic variance.

Another linkage map was generated for D. alata based on 508 AFLP markers that covered a total length of 1233 cM on 20 linkage groups, accounting for about 65% of the entire genome. Genes conferring resistance to YMV have been identified in D. rotundata and to anthracnose in D. alata by the successful use of bulked segregant analysis (BSA). Two RAPD markers, OPW18850 and OPX15850, closely linked in coupling phase with the dominant YMV-resistance locus Ymv-1 were identified. Similarly, two RAPD markers, OPI171700 and OPE6950, closely linked in coupling phase with anthracnose resistance gene, Dcg-1, were identified2.

Designing molecular markers using a bioinformatics platform. Photo by A. Alonge, IITA.
Designing molecular markers using a bioinformatics platform. Photo by A. Alonge, IITA.
Enriching the repertoire of molecular markers
In an effort to develop additional genomics resources, IITA was involved in sequencing ESTs from a cDNA library constructed from floral tissue. However, the first several hundred sequences were predominantly housekeeping genes. Recently, in a collaborative project with University of Virginia through USAID-Linkage funds, several thousand ESTs were generated using cDNA libraries from yam leaf tissues challenged with Colletotrichum gloeosporioides, the fungal pathogen responsible for yam anthracnose disease. This resulted in the identification of >800,000 EST sequences, from which about 1152 EST-SSRs were generated in D. alata for use in a yam improvement program. Although AFLP markers have been used for generating linkage maps so far, efforts are under way to saturate the maps with these EST-SSRs to identify the genomic regions associated with resistance to anthracnose disease.

DNA barcoding
Species identification in the genus Dioscorea has remained a challenge when active domestication is continuing in several parts of West Africa. Research on DNA barcoding is under way using chloroplast markers (rbcL, matK, and trnH-psbA) to understand the phylogenetic relationship between different species and also to get an insight into the ongoing domestication process.

Whole genome sequencing
Important considerations for the whole genome sequencing of yam include the genome size, ploidy level, and availability of homozygous clones. Estimation of the genome sizes of various Dioscorea species showed widely variable figures: D. alata and D. rotundata have genome sizes of about 800 mega base pairs (Mbp). Recently, an initiative was launched at IITA in collaboration with the Japan International Research Center for Agricultural Sciences (JIRCAS) to complete the whole genome sequencing of D. rotundata. Preliminary data yielded reasonable sequences. Further work is in progress to generate additional sequence data from the BAC library to facilitate the assembly of the genome which will culminate in producing the first draft genome sequence of Dioscorea species. Additional genomic information produced by resequencing several breeding materials and a parallel project in transcriptome analysis are poised to result in the discovery of a large number of molecular markers and help in the annotation of the genome.

Transcriptome analysis
In contrast to the genome sequence, which is fixed and uniform in all cells of a particular organism, transcriptome refers to the study of the total set of transcripts (expressed genes) in a given cell/tissue at a particular developmental stage or external environmental condition that could influence the physiology of the cell/tissue. IITA, in collaboration with USDA-Agricultural Research Service, Stoneville, embarked on RNAseq, the latest revolutionary tool for transcriptome profiling, based on differential gene expression for anthracnose disease. One of the expected outcomes of this project is to enrich the genomic resources available for yam improvement, including the discovery of SNPs. The latest informatics and statistical methods will be applied to saturate the available linkage map and high resolution mapping of the QTL(s) for anthracnose resistance in different genetic backgrounds.

Genotyping-by-sequencing
With advances in the next generation technologies, the costs of DNA sequencing have come down to such an extent that genotyping-by-sequencing (GBS) is now possible in almost all crops. IITA has recognized the potential of such innovative techniques in accelerating the breeding of clonally propagated crops, such as yam. Hence, in an ongoing USAID-Linkage project, a diverse panel of D. alata genotypes, including parents of available mapping population progenies segregating for anthracnose disease will be genotyped by sequencing to identify a large set of SNPs and determine the divergence among the parents.

Yam roots. Photo by IITA.
Yam roots. Photo by IITA.
Conclusions
To meet the steadily increasing demand, the viable approach is to adopt the innovative plant breeding strategies for yam that integrate the latest innovations in molecular technologies with conventional breeding practices. As efforts are under way to obtain the complete genome sequences and the development of additional genomic resources, the groundwork for deploying yam molecular breeding has been laid. With the availability of new genomic markers and GBS, it would be possible to fingerprint yam germplasm to identify duplicates/mislabeled accessions, to conduct diversity analysis and association mapping. As the genus Dioscorea contains several other useful species, comparative genomic tools can be used to transfer or deduce genetic and genomic information in other species.

References
1 Gedil, M. and A. Sartie. 2010. Aspects of Applied Biology 96:123–135.
2 Mignouna, H.D., M.M. Abang, and R. Asiedu. 2007. Yams. Pages 271–296 in: Genome mapping and molecular breeding Vol. 3: Pulses, Sugar and Tuber Crops, edited by C. Kole. Springer, Heidelberg, Berlin, New York, and Tokyo.
3 Sartie, A. and R. Asiedu. 2011. Development of mapping populations for genetic analysis in yams (Dioscorea rotundata Poir. and Dioscorea alata L.). African Journal of Biotechnology 10: 3040–3050.