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 IITAâ€™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 farmersâ€™ 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: 5â€“7.
2 Eastwood, R. and M. Lipton. 2011. Demographic transition in sub-Saharan Africa: how big will the economic dividend be? Population Studies 65: 9â€“35.
Countries need strong leadership to introduce changes in implementing agricultural development programs.
â€” Dr Nteranya Sanginga, Director General, IITA
Abebe Menkir (email@example.com), Baffour Badu-Apraku, and Sam Ajala Maize Breeders, IITA, Ibadan, Nigeria
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 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 farmersâ€™ 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 IITAâ€™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 IITAâ€™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 IITAâ€™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.
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.
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 farmersâ€™ fields that help to achieve higher yield gains to support improved farming in WCA.
Ousmane Boukar (firstname.lastname@example.org), Tahirou Abdoulaye, Manuele TamÃ³, Hesham Agrama, Hailu Tefera, Christian Fatokun, and Steve Boahen O. Boukar, Cowpea Breeder; T. Abdoulaye, Socioeconomist, IITA, Ibadan, Nigeria; M. TamÃ³, 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.
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.
Cowpeaâ€•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 farmersâ€™ 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 IITAâ€™s breeding nurseries are shared with interested colleagues from the national research institutions who evaluate these at their stations and in farmersâ€™ 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 â€˜hopeâ€™.
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 farmersâ€™ 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.
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 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 farmersâ€™ access to the PICS bags through a better distribution network.
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 rustâ”€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.
Several elite lines from IITAâ€™s breeding nursery have been evaluated in many countries in SSA and found to perform well in farmersâ€™ 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 farmersâ€™ 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.
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.
Jim Lorenzen (email@example.com) 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.
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.
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.
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 5â”€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.
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.
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.
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.
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.
Ismail Yusuf Rabbi (firstname.lastname@example.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
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.
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 â€œnext-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 IITAâ€™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).
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)â€•which is ravaging cassava production in Eastern and Southern Africaâ€•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 Energyâ€™s Joint Genome Institute and 454 Life Sciences2.
The progress in next- generation technologies has drastically reduced the costs of DNA sequencing so that genotyping-by-sequencing (GBS) is now feasible for species such as cassava, ushering in a new era of agricultural genomics5. This will revolutionize the application of genomic tools for cassava improvement. GBS involves the cutting of genomic DNA into short pieces at specific locations using a restriction enzyme. The ends of these pieces are sequenced using techniques that allow sequencing of many samples at the same time. The beauty of this method is the use of adaptors containing barcodes (unique tags) that are enzymatically joined to the digested DNA fragments, enabling simultaneous sequencing or multiplexing of up to 384 samples in one sequencing reaction. This economy of scale greatly reduces the cost of processing each individual DNA to less than $10/sample. Approximately 200,000 markers can be identified and mapped in a very short time. With this powerful tool, breeders may conduct genomics-based research that was inconceivable a couple of years ago. Some of the exciting new research applications include polymorphism discovery, high-density genotyping for QTL detection and fine mapping, genome-wide association studies, genomic selection, improving reference genome assembly, and kinship estimation.
High-density QTL mapping and fine mapping
In the past, a limitation for QTL mapping was the number of markers on a genetic linkage map. With new SNP-based technologies this is no longer a limitation. This allows for fine mapping of QTLs so long as a sufficient number of individuals in the mapping population can be developed. IITA, in collaboration with national partners [ARI-Tanzania and National Crops Resources Research Institute (NaCRRI), Uganda], is using SNPs to discover QTLs associated with sources of tolerance for CBSD.
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 IITAâ€™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 breederâ€™s collection. This approach of â€œallele miningâ€ 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.
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 â€œtraining populationâ€. For cassava, phenotyping is the slowest and most expensive phase of the cropâ€™s breeding cycle because of the cropâ€™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 â€engine of evolution,â€ 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 IITAâ€™s long-standing conventional breeding pipeline means that the best days of cassava improvement lie ahead. These efforts will ultimately satisfy the increasing need for more healthy and nutritious food produced in environmentally sustainable ways.
1 Lokko et al. 2007. Cassava. In: Kole et al (ed). Genome mapping and molecular breeding in plants, Vol. 3. Pulses, Sugar and Tuber Crops. Springer-Verlag Berlin Heidelberg.
2 Prochnik S., P.R. Marri,B. Desany, P.D. Rabinowicz, et al. 2011. Tropical Plant Biol. doi:10.1007/s12042-011-9088-z. 3 Ferguson M., I.Y. Rabbi, D-J.Kim, M. Gedil, L.A.B. Lopez-Lavalle, and E. Okogbenin. 2011a. Tropical Plant Biol. DOI 10.1007/s12042-011-9087-0.
4 Ferguson M.E., S.J. Hearne, T.J. Close, S. Wanamaker, W.A. Moskal, C.D. Town, J. de Young, P.R. Marri, I.Y. Rabbi, and E.P. de Villiers. 2011b. Theor Appl Genet. DOI: 10.1007/s00122-011-1739-9.
5 Elshire R., J. Glaubitz, Q. Sun, J. Poland, and K. Kawamoto. 2011. PLoS ONE 6:e19379.
Melaku Gedil (email@example.com) and Ismail Rabbi M. Gedil, Head, Bioscience Center; I. Rabbi, Postdoctoral Fellow (Molecular Genetics), IITA, Ibadan, Nigeria
Harnessing state-of-the art genomics technologies
The potential application of â€œOmicsâ€ technology, as demonstrated by the steadily growing impact of biosciences, in alleviating the multitude of constraints in agricultural production is rapidly becoming a reality with the advent of next-generation DNA sequencing and genotyping technologies, high throughput (HTP) metabolomics and transcriptomics, informatics, and decision-making tools. These technologies, together with rapidly evolving bio-computational tools, are accelerating the discovery of genes and closely linked molecular markers underlying important traits, leading to the rapid accumulation of genomic resources necessary for devising an efficient and effective breeding strategy geared toward the faster development of varieties of choice.
The state-of-the-art technologies including the next-generation sequencing (NGS) for genome and transcriptome analysis, as well as genotyping-by-sequencing (GBS) are being adopted in R4D programs at IITA. For instance, the NGS through outsourcing and multi-partner collaboration; the RNAseq for HTP expression study in cassava; the Illuminaâ€™s Golden Gate Assay for HTP single nucleotide polymorphism (SNP) genotyping in cassava, soybean, and maize as well as GBS in maize and cassava. Data generated by these techniques are being applied for marker-assisted recurrent selection (MARS) of drought-tolerant maize, and genome selection (GS) for high-yielding, disease-resistant cassava.
Development of an integrated molecular breeding platform
The new technologies, however, are very data-intensive and demand advanced computational and communication technologies and infrastructure for data acquisition, analysis, and management. For the effective integration of genomics technologies in our breeding schemes, we are building capacity (connectivity to the internet, the necessary hardware/software, and skilled personpower) to acquire, store, and analyze terabytes of data.
The Generation Challenge Program (GCP) of the CGIAR is developing an integrated breeding platform (IBP) to build a comprehensive and integrated crop information system enabling linkages among molecular, phenotypic, and pedigree data. The maize version of International Crop Information System (ICIS), dubbed International Maize Information System (IMIS), has been expanded to include all pedigrees of IITA maize under the Drought Tolerant Maize for Africa (DTMA) project. It has some functionality in terms of molecular data storage but this is limited and we are now generating data sets of hundreds of thousands of markers per line that require different storage solutions. The GCP is consulting with other initiatives such as iPlant and DArT and is working on collaboratively creating solutions for the needs of several user-cases including DTMA, Tropical Legumes (TL)-I, and TL-II projects. In the IBP initiative, IITA is the leading crop center to host the main web-accessible databases of cassava, cowpea, yam, and soybean. The form and functionality of the databases are still a work in progress although activities are ongoing in the application of current versions of ICIS to cassava, yam, and cowpea.
In view of the IBP initiative, we are developing a bioinformatics capacity to (a) manage the newly generated genomic resources of IITAâ€™s research crops, particularly those clonally propagated, (b) use the genomic resources in the public sector for soybean and maize, (c) use comparative genomics techniques for other African orphan crops of high importance, such as cassava, yam, and cowpea, and (d) create a bioinformatics center of excellence to train and provide access for African research scientists.
HTP by genotyping and informatics support tools
The increasing affordability of the NGS technologies has shifted critical consideration from genotyping to phenotyping. According to leading experts, it is now cheaper to genotype than to phenotype a plant. Quality phenotypic data are essential for the interpretation and use of the deluge of genomic data to identify the changes in DNA sequences that influence important traits. The fact that priority agronomic traits are complex and polygenic and interact with the environment necessitates conducting extensive and precise multi-environment evaluations of candidate breeding materials (over several years and in several locations). Therefore, there is a need to invest in precision phenotyping of traits and data capture (from electronic sample tracking to non-invasive HTP) through the use of hand-held devices such as barcode readers and near-infrared spectroscopy. Efforts are being made to develop rapid and accurate phenotyping protocols to integrate with genomic tools in establishing breeding schemes at IITA.
A wide array of techniques and tools is being deployed to associate molecular markers with desirable phenotypic traits. Associated markers can be used to accelerate germplasm enhancement via MARS, marker-assisted backcrossing for the introgression of disease resistance and other simple traits, hence bypassing the necessity of evaluating breeding materials in the field; MARS for rapid cycle population improvement in bi-parental crosses based on genomic estimated breeding value; and GS based on a model developed with a training population to select untested samples.
Our efforts to harness the unparalleled scientific progress in the fields of genomics and bioinformatics are expected to find solutions to the recalcitrant problems confronting small-holder farmers in sub-Saharan Africa.
Leena Tripathi (firstname.lastname@example.org) Biotechnologist, IITA, Nairobi, Kenya
Biotechnology has opened unprecedented avenues for exploring biological systems. Transgenics is one of the key techniques particularly useful for the genetic improvement of crops that are not amenable to conventional breeding, such as those that are vegetatively propagated. In IITA, transgenic technologies are being used for improving banana/plantain (Musa sp.), cassava (Manihot esculenta), and yam (Dioscorea sp.).
Genetic transformation platform
An efficient protocol for plant regeneration and transformation is a prerequisite for the successful use of transgenic technologies. Despite the technical difficulties in transforming monocot species, efficient transformation protocols that are embryogenic cell suspension based and Agrobacterium mediated have been established for many cultivars of banana/plantain. This system, however, is a lengthy process and cultivar dependent. Therefore, a transformation protocol using meristematic tissues was also established which is rapid and genotype independent. These protocols have paved a way for the genetic manipulation of banana/plantain by incorporating agronomically important traits such as those conferring resistance to diseases or pests as well as tolerance to abiotic stress factors.
Agrobacterium-mediated transformation protocols for three popular cassava varieties preferred by African farmers were established through somatic embryogenesis. A regeneration and transformation protocol is also established for yam (Dioscorea rotundata and D. alata) using nodal explants, but transformation efficiency needs to be improved. A transformation protocol using somatic embryogenic callus for yam is under development.
Development of disease- and pest-resistant transgenic crops
Banana Xanthomonas wilt (BXW), caused by the bacterium Xanthomonas campestris pv. musacearum (Xcm), is the most devastating disease of banana in the Great Lakes region of Africa. In the absence of natural host plant resistance, IITA, in partnership with NARO-Uganda and the African Agricultural Technology Foundation, has developed transgenic banana by constitutively expressing the Hypersensitive Response Assisting Protein (Hrap) or plant ferredoxin-like protein (Pflp) gene from sweet pepper (Capsicum annuum). The transgenic plants have exhibited strong resistance to BXW in the laboratory and screenhouse tests. The best 65 resistant lines were planted in a confined field trial at the National Agricultural Research Laboratories (NARL), Kawanda, Uganda, for further evaluation.
Based on results from mother plants and their first ratoon plants, 12 lines were identified that show absolute resistance. The plant phenotype and the bunch weight and size of transgenic lines are similar to those of nontransgenic plants. These lines will be further tested in a multilocation trial in Uganda. They will be evaluated for environmental and food safety in compliance with Ugandaâ€™s biosafety regulations, risk assessment and management, and procedures for seed registration and release, and are expected to be released to farmers in 2017.
Cassava brown streak disease (CBSD) has emerged as the biggest threat to cassava cultivation in East Africa. As known sources of resistance are difficult to introgress by conventional methods into the cultivars that farmers prefer, the integration of resistance traits via transgenics holds a significant potential to address CBSD. Of the available transgenic approaches, RNA silencing is a very promising strategy that has been successfully employed to control viral diseases. IITA, in collaboration with Donald Danforth Plant Science Centre (DDPSC), USA, is developing CBSD-resistant cassava for East Africa.
Nematodes pose severe production constraints, with losses estimated at about 20% worldwide. Locally, however, losses of 40% or more occur frequently, particularly in areas prone to tropical storms that topple the banana plants. IITA, in collaboration with the University of Leeds, UK, has generated transgenic plantain using maize cystatin that limits the digestion of dietary protein by nematodes, synthetic peptide that disrupts chemoreception, or both of these traits. These lines expressing the transgenes were challenged in a replicated screenhouse trial with a mixed population of the banana nematodes, Radopholus similis and Helicotylenchus multicinctus. Many lines were significantly resistant to nematodes compared with nontransgenic controls. The promising transgenic lines showing high resistance will be planted in confined fields in Uganda for further evaluation in mid-2012.
Transgenic technologies for abiotic stress tolerance
Cassava roots undergo rapid deterioration within 24â€“48 hours after harvest, the so-called postharvest physiological deterioration (PPD), which renders the roots unpalatable and unmarketable. IITA, in collaboration with the Swiss Federal Institute of Technology (ETH) Zurich, is developing cassava tolerant of PPD through the modification of ROS (reactive oxygen species) scavenging systems. The potential is being assessed of various ROS production and scavenging enzymes, such as superoxide dismutase, dehydroascorbate reductase, nucleoside diphosphate kinase 2, and abscisic acid responsive element-binding protein 9 genes, to reduce the oxidative stress and the extent of PPD in transgenic cassava plants.
Future road map
Efforts at IITA over the last 10 years to establish transformation protocols for all the IITA crops have been paying off and have led to the establishment of a genetic transformation platform for cassava, banana/plantain, and yamâ€•the three most important food crops in sub-Saharan Africa. These technologies have contributed to significant advances in incorporating resistance to pests and diseases in banana and cassava. Some of these technologies have the potential to offer additional benefits. For instance, the transgenic technology to control Xanthomonas wilt may also provide an effective control of other bacterial diseases of banana (Moko, blood, and bugtok diseases), and of bacterial blight in other crops such as cassava and cowpea.
Banana and plantain (Musa spp.) are major staple foods and a source of income for millions in tropical and subtropical regions. Most of the banana grown worldwide are produced by small-scale farmers for home consumption or sale in local and regional markets.
Many pests and diseases significantly affect banana cultivation. Nematodes pose severe production constraints, with losses estimated at about 20% worldwide. Locally, however, losses of 40% or more occur frequently, particularly in areas prone to tropical storms that topple the plants.
Pest management in banana is based on several principles, primarily through the use of clean, healthy planting material, crop rotation, and in commercial settings, chemical control. However, crop rotation is often impractical, especially for small-scale farmers, while nematicides are locally unavailable or not affordable for subsistence farmers. These pesticides are also highly toxic, environmentally unacceptable, and increasingly being withdrawn from use.
Limited sources of nematode resistance and tolerance are present in the banana gene pool. Some resistance has been identified against one of the most damaging nematode species, the burrowing nematode (Radopholus similis), but this needs to be combined with consumer-acceptable traits. Furthermore, several species of nematodes are often present together, requiring a broad spectrum resistance able to control not just Radopholus but other damaging nematodes, such as species of Pratylenchus, Meloidogyne, and Helicotylenchus.
Enter biotechnology. Biotechnology offers sustainable solutions to the problem of controlling plant parasitic nematodes. Several approaches are possible for developing transgenic plants with improved resistance; these include strategies against invasion and migration and against nematode feeding and development.
Some successes in genetic engineering of banana have been achieved, enabling the transfer of foreign genes into the plant cells. An efficient transformation protocol for African banana cultivars has been established at IITA using meristematic tissues. The protocol avoids the callus and cell suspension culture requirements of other approaches. It is rapid, genotype independent, and avoids the somaclonal variation that often results from regenerating embryogenic cell suspensions.
Prof. Howard Atkinsonâ€™s group in Leeds has demonstrated that more than one independent basis for transgenic resistance provides an additive effect for nematode control. Our use of three independent additive approaches is designed to ensure a resistance level that prevents the buildup of damaging populations, even if virulent individuals completely challenge one line of defense or partially compromise them all. We intend to demonstrate that this additive approach can provide durable resistance.
The three approaches are a cysteine proteinase inhibitor (a cystatin), a potato tuber serine/aspartic proteinase inhibitor, and a repellent peptide. Cysteine proteinases are used by a wide range of plant parasitic nematodes to digest dietary protein. The cystatin prevents this digestion and slows nematode growth. Transgenic expression of both proteinase inhibitors provides effective control of both cyst and root-knot nematodes and cystatin has also been shown to be effective against Radopholus.
Cysteine proteinases are not present in mammals and those we will use lack toxicity or allergenicity for humans. They occur in common foods, such as the seeds of maize, rice, and cowpea, and people rapidly digest them. The other, very distinct, novel approach is the use of a repellent. This is also not lethal to nematodes or other organisms. Nematodes do not invade roots applied with repellent because they fail to detect the hostâ€™s presence. This approach is effective against a wide range of nematode species.
We will also be using a novel RNA interference (RNAi) approach. The use of RNAi for functional analysis of plant parasitic nematode genes was first established in the University of Leeds. The approach relies on the production of double-stranded RNA molecules by banana cells. When they are ingested by the nematode, they specifically interfere with the expression of the essential nematode gene they target. The advantage of the RNAi approach is that no novel protein production is required to achieve resistance to nematodes. This offers a considerable biosafety advantage, given that RNA molecules represent no food risk and there is little likelihood of nontarget effects. The challenge is to provide an effective level of resistance to all banana nematodes by this approach. Genetic transformation of plantain using these approaches is in progress at IITA.
Gene flow is not an issue for this crop, making the transgenic approach even more attractive. Banana and plantain lack cross-fertile wild relatives in many production areas. Most edible banana are male- and female-sterile and depend on vegetative propagation. The new defense will be integrated with other pest management strategies already developed at IITA to maximize resistance levels and safeguard durability. This work is part of a new, interdisciplinary research partnership between IITA and the University of Leeds, directed at enhancing human health and food security in sub-Saharan Africa.
We also plan to stack genes for Xanthomonas wilt and nematode resistance into one line to produce a high-value product for farmers. Gene stacking is becoming common, adding multiple traits at once into the plant genome. Resistance to diseases and pests can be achieved by integrating several genes with different targets or modes of action into the plant genomes. We already have promising results with genes for resistance to banana Xanthomonas wilt (BXW) (R4D Review Edition 1), which we would like to combine with nematode resistance. Banana cultivars with resistance to multiple diseases and pests will be a breakthrough in banana improvement.