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.

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.

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.

Unlocking the diversity of yam

IITA scientists inspect yam plants in the field gene bank. Photo by O. Adebayo, IITA.
IITA scientists inspect yam plants in the field gene bank. Photo by O. Adebayo, IITA.

The International Year of Biodiversity (IYB) has emphasized the need for global action that will unravel the genetic diversity of yam, a root crop that provides food security to 300 million people in sub-Saharan Africa.

Yam is grown in about 51 countries in the tropics and subtropics, with yields averaging about 11 t/ha in the major producing countries of West Africa (Nigeria, Cote d’Ivoire, Ghana, and Bénin). However, little is known about the tuber crop’s diversity.

“This aspect is important for yam improvement to meet the demand of people depending on this crop for food and livelihood,” says Ranjana Bhattacharjee, IITA Scientist working on fingerprinting the yam germplasm collection.

Yam provides calories and puts money in the pockets of farmers. The tuber-bearing climbing plant from the genus Dioscorea also plays a major role in sociocultural activities in West Africa including traditional marriages and the New Yam Festival.

Globally, there are over 600 species of yam but only a few are cultivated for food or medicine. Scientists fear that some species are threatened and might become extinct as a result of climate change and genetic erosion. This prompts the calls for conservation.

The major edible species of African origin are white Guinea yam (D. rotundata Poir.), yellow Guinea yam (D. cayenensis Lam.), and trifoliate or bitter yam (D. dumetorum Kunth). Edible species from Asia include water or greater yam (D. alata L.), and lesser yam (D. esculenta [Lour.] Burkill). Cush-cush yam (D. trifida L.) originated from the Americas. White Guinea yam and water yam are the most important in terms of cultivation and use.

Yam tuber. Photo by IITA.
Yam tubers. Photo by IITA.

This preferred staple is usually eaten with sauce directly after boiling, roasting, or frying. The tubers may also be mashed or pounded into dough after boiling, or cooked with sauces and oils. They can be processed into yam balls, chips, and flakes.

Fresh yam tubers are peeled, chipped, dried, and milled into flour that is used in preparing dough called amala (Nigeria) or telibowo (Bénin). Commercial products based on dry flakes or flours from the tuber are produced in Nigeria, Ghana, and Côte d‘Ivoire for export and sale in urban areas.

Though millions depend on the crop, especially in sub-Saharan Africa, not many outside of Africa know about the tuber’s potential for commercialization, and its role in enhancing food security in the region, according to Robert Asiedu, Director of the Program on Root and Tuber Systems at IITA.

“We talk about yam tubers as a food staple of millions of Africans to donors or investors who don’t even know what yam is, how it looks or tastes. So the question is: How would they even think of investing in research in a ‘little-known’ staple like yam?”

Perhaps yam’s low profile in the developed countries or in the West is the major limitation in attracting funding for research, but this hardy tuber is an important “part of man” especially in Africa, the Caribbean, Asia, and the South Pacific Islands where it is widely eaten. According to Asiedu, it is the “preferred and most appreciated staple food and calorie source” in areas where it is grown.

Yam faces constraints that include the high costs of planting material and of labor, decreasing soil fertility, the inadequate yield potential of varieties, and increasing levels of field and storage pests and diseases associated with intensive cultivation.

To tackle some of these constraints, work at IITA for the last few years has focused on improving the tuber, primarily white and yellow Guinea yam, and water yam.

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

The breeding program uses the 2,216 accessions of Guinea yam and 816 of water yam in IITA’s genebank to study resistance to anthracnose and virus diseases. Improved populations have been developed with partners in the national agricultural research and extension systems (NARES), who have released varieties in Nigeria (National Root Crops Research Institute, 7) and Ghana (Crops Research Institute, 3).

Despite the success in yam improvement, new challenges keep on coming, prompting researchers to use other tools, such as molecular characterization to unlock the genetic diversity of yam.

Recently, the Global Crop Diversity Trust funded a project in IITA to duplicate, document, and distribute the germplasm of yam to other partners in accordance with the International Treaty on Plant Genetic Resources for Food and Agriculture. Such support is indeed a milestone in yam research. The project also aims to fingerprint the entire germplasm collection at IITA. This will help in understanding the extent of genetic diversity present in the collection. From this, the genes for important traits can be determined through association mapping, a tool that could be used successfully to improve and sustain the crop.

As the world marks the IYB, serious attention from other donors is necessary to keep the crop as a “part of man.”