Yam genetic resources conserved at IITA

Badara Gueye (B.Gueye@cgiar.org) and Michael Abberton

Within CGIAR, IITA has the mandate for the collection, characterization, and exchange of yam species. IITA’s Genetic Resources Center (GRC) thus holds a major yam international germplasm collection in trust under the Multilateral System of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA).

With 3,872 accessions, the IITA yam collection is the world’s largest, including nine of the major cultivated species: Dioscorea rotundata, D. alata, D. bulbifera, D. cayenensis, D. dumentorum, D. esculenta, D. preussii, D. manganotiana, and D. praehensilis. Conserved in the field and through an in vitro genebank, it represents a large genepool for yam crop improvement to help the crop reach its full potential for food and income for poor farmers. To meet this objective, GRC is working on many themes for harnessing yam genetic resources in collaboration with a range of partners. The first one is the filling of genetic gaps to ensure the availability of a broader yam gene pool. In 2014, we are carrying out germplasm collection in Nigeria and Benin Republic. The entire yam collection is conserved in the IITA field bank at Ibadan, Nigeria, and the use of outstation sites offers different conditions for the regeneration of recalcitrant lines, which reduces germplasm losses. More than one-third of the yam collection is duplicated in the in vitro medium-term storage facility at IITA-Ibadan. The development of a yam cryopreservation protocol will allow long-term conservation.

To promote the use and distribution of yam germplasm, especially in breeding, the entire yam collection was characterized using agromorphological descriptors, leading to the identification of a core collection. Increasing collaboration with the yam breeders, germplasm health specialists, and national partners is ongoing to carry out genetic resources evaluation including for market demanded traits. Molecular tools and advanced phenotyping methods are also being employed to further characterize the germplasm and further promote its use. All the data are made available and accessible worldwide and efforts are ongoing to increase the proportion of quarantine pathogen free yam genetic resources for more distribution across borders. Viruses are important pathogens of yam, therefore germplasm use will also be promoted through production of virus-free material for exchange and production of planting material. Virus elimination methods (heat treatment, cryotherapy and chemotherapy) are being explored to establish a reliable protocol for yam virus cleaning.

GRC plays also a major role in training and capacity building of national programs with respect to collection, conservation and characterization of genetic resources of yam.

For further information visit: http://www.iita.org/genetic-resources.

Mobilizing yam farmers in Ghana and Nigeria to produce good quality seed yam

Beatrice Aighewi, a.aighewi@cgiar.org

The availability and quality of seed determine the success of any farmer and this has been an issue because the seed sector is poorly developed in many African countries. The challenges that result from poor seed are particularly serious with regard to vegetatively propagated crops such as yam. Several reasons are responsible for this situation: the resultant unavailability and poor quality of seed yams is compounded by the following reasons:

· Seed yam is mostly produced by traditional methods which are relatively slow.

· The high cost of seed yam causes most farmers to rely mainly on seed tubers saved from previous harvests.

· Lack of quality control and absence of formal seed yam production systems result in scarcity of genetically uniform and disease-free seed in markets.

· Poor understanding of the quality attributes of seed yam entrenches poor quality.

· Lack of capacity/knowledge on rapid multiplication methods to obtain clean planting material.

In trying to improve the current situation of seed yams, the Yam Improvement for Income and Food Security in West Africa (YIIFSWA) project is placing emphasis on improving the quality of seed yam on farmers’ fields and initiating the development of a formal seed yam system since ensuring quality is a hallmark of any formal seed system.

In most yam-producing systems in West Africa, seed yam production is not separated from ware yam production. Traditionally, a farmer plants setts to produce ware yams and in the process obtains seed by double harvest (milking), cutting some large tubers or using those that are too small for food. Due to the low rate of multiplication, the seed produced is rarely enough in quantity for expansion of yam cultivation and because the same seed is recycled over many generations, a build-up of disease on seed tubers reduces the productivity. In many seed yam markets, it is the left-over seed after the farmer has planted his field that is sold, and chances are high that the quality of such seed will be poor (Fig. 1) because a farmer will normally reserve the best to plant in his field).

The only region where relatively good quality seed yam is found in market is in parts of the River Niger area of Nigeria, particularly at Illushi and Otuocha Markets, where there are farmers who specialize in seed yam production. Seed yam in the market is sorted by size and variety and they look good in terms of quality (Fig. 2). Discussions with yam farmers in Nigeria and Ghana revealed that for most of them, the only reason why good seed yam is sold is if they are faced with a financial crisis and need immediate cash. Seed yam which is an inheritance for most farmers is a major component of their financial and food security, and in some instances anyone who takes seed yam to the market to sell is considered a thief. In Salaga District of Ghana, no seed yam is sold at any market; it can only be bought from a farmer on his farm.

Observations at Illushi market shows that even without the formal seed system, farmers can produce better quality seed if they are enlightened and specialize in seed yam production. If such seed yam markets could be developed in major yam-producing areas, most of the problems associated with unavailability and poor quality will be sorted out.

To improve the quality of seed yams on farmers’ fields and develop the seed yam market, YIIFSWA has targeted the small-holder farmer who forms the majority of producers. A multidisciplinary YIIFSWA team uses the platform of cross-objective workshops and capacity building to train farmers in some communities of major yam-producing regions of Nigeria and Ghana to produce and market good quality seed yam (Figs. 3 and 4). Many of the farmers trained belong to farmers’ groups that have already had some training on producing seed yams from minisetts on demonstration plots in their localities. Some of those who participated in previous training exercises had an opportunity to explain to other farmers what they had learned and encouraged other farmers to try the minisett technique to produce their seed yam, and remove barriers that have prevented them from getting more seed.

YIIFSWA also provided training for extension agents on high ratio propagation methods—minisett technique and use of vine cuttings which can produce more tubers of better quality than what farmers are currently producing (Fig. 5). It is expected that they will train farmers in their areas of operation, and sustain the campaign for production of better quality seed yam.

Countering yam anthracnose threat in West Africa

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Nematode pests of yam

Danny Coyne

Plant parasitic nematodes are ever-present and incidental with plant growth and crop production, occurring on just about every crop or plant known.

Nematodes are mostly microscopic and thus unseen; and the symptoms of nematode infection are difficult to determine in the field, as these are often nonspecific.

Yam farmers are very much aware of the physical damage that nematodes cause to the tubers, but are mostly completely unaware of what causes the damage. In the field, nematodes reduce crop vigor and performance, leading to lower yields. They cause significant damage to the tubers, resulting in deformed, unsightly tubers or tubers with cracked and flaking skin that conceals an underlying rot. Such symptoms have an immediate and direct impact on the marketability of tubers, but they also relate to reduced crop productivity. Infected tubers, when unwittingly used as planting material, due to low, unnoticeable levels of infection, affect the ability of seed to produce—or even to germinate.

A wide range of nematodes are associated with yam, but only two ‘types’ are of concern: root-knot nematodes (Meloidogyne spp.), which are evident by the disfigurement they cause to tubers (Figs. 1 and 2), and lesion nematodes (Scutellonema bradys, Pratylenchus spp.), which result in ‘dry rot’ and cracked tubers. Infected tubers can also develop erratically growing roots, referred to as ‘crazy roots’ (Fig. 1A).

Meloidogyne spp., are an especially damaging group of pests for numerous crops, which are becoming an increasingly serious problem on yam, likely due to gradual intensification of cropping practices. For example, a recent 2013 survey by IITA in Nigeria found that approximately a quarter of all harvested tubers have some level of tuber damage by Meloidogyne spp. (Fig. 1B).

The same survey also discovered, for the first time, a particularly aggressive species, M. enterolobii, infecting yam, among a number of other Meloidogyne species, which may occur simultaneously in the same field, and on the same plant. This has implication in breeding for resistance, and requires that the screening process takes into account the variety of species affecting the crop, such as is undertaken at IITA. Once infected by Meloidogyne spp., tubers become galled and disfigured. Symptoms will vary depending on conditions, nematode species, and yam variety. Tubers normally look ‘knobbled’ due to the development of galls on the surface, the severity of which depends on the level of infection.

Farmers do not understand how this disfigurement occurs, believing it to be a supernatural occurrence in some cases. Tuber galling damage will not generally develop further once harvested. During storage, galled tubers lose weight and deteriorate much faster than healthy tubers. Galled tubers used for seed will (if they survive) result in the development of more heavily damaged (galled) tubers at harvest.

Dry rot, caused by lesion nematodes, results from their feeding action as they ‘migrate’ from cell to cell, destroying them as they pass through the yam tissue. This damage occurs first in the subsurface tissue, just below the tuber skin, moving deeper with time. A relatively healthy looking skin can also often mask the underlying damage, which may not be visible until the surface is damaged or cut back (e.g., Fig. 2A), to reveal the brown, discolored, necrotic tissue beneath. Surface cracking is also a typical symptom of lesion nematode infection, but the relation between the nematodes and cracking is less clear-cut, with cracked tubers occurring in the absence of nematodes in tubers.

The species of nematodes responsible for dry rot and cracking on yam is intriguing for several reasons. One is that S. bradys is a key species, which feeds as an endoparasite, while the remaining species in the genus are better known as ectoparasitic feeders, remaining in the soil and feeding on the outside of roots. The other is that at least two species of Pratylenchus (P. coffeae and P. sudanensis) also cause the same symptoms as S. bradys. The species distribution and occurrence is geographically related; the more research we undertake, the more we unravel the story. We have determined the center of origin for S. bradys, for example, as the central Nigeria/Benin area, although the nematode has since been distributed around the globe on infected yam tubers. At harvest, severely affected tubers may be obvious, but lower levels of infection may go unnoticed. However, during storage the nematodes continue to feed, which is a major consequence of lesion nematode infection. Heavy infections result in the complete deterioration of tubers, while less damaged tubers can, to some extent, be consumed after removing the rotted sections. Low levels of infection may not be detected, and can contribute to the disease cycle when tubers are used as seed material.

A particular characteristic of yam is that the nematode problem is perpetuated through the use of infected planting material. Heavily damaged tubers are obvious, and are not generally used as seed, and usually consumed at home. Less visibly damaged tubers may be sold in the market or stored, for sale or consumption later or for use as a planting material in the next season. The use of poor quality planting material thus serves to maintain the disease cycle, by returning inoculum from the store back to the field. This adversely affects crop establishment, yield, and storability of harvested tubers, ensuring a continued and negative impact on quality, especially of highly susceptible cultivars. It is likely even, that nematode damage, in particular, has been a major contributing factor to the loss of some traditional (susceptible) varieties.

To overcome nematode problems on yam, a key area of focus is to target the seed system, and farmer awareness and understanding of the problem. This has become an increasingly important focus for IITA and its partners in recent years. It also forms the central pillar for a large IITA-led yam project. By generating and maintaining sustainable healthy seed systems, farmers will have greater access to seed material that will result in more productivity that will be less likely disfigured at harvest. In-field infection will occur, especially by root-knot nematodes, but damage will be less severe and yields higher.


From yam production and postharvest constraints to opportunities

D.B. Mignouna, d.mignouna@cgiar.org, T. Abdoulaye, A. Akinola, and A. Alene

Food insecurity remains a huge concern in West Africa. Agriculture, without doubt remains the main source of food and livelihood. Over the past two decades, agricultural yields have stayed the same or declined. Although there has been a recent rise in agricultural productivity, it derived more from expanded planting areas for staple crops than from yield increases. Thus, increasing and sustaining agricultural productivity should be a critical component of programs that seek to reduce poverty and attain food security in the region.

Yam (Dioscorea spp.), a vegetatively propagated crop cultivated for its underground edible tubers, is the mainstay for about 300 million people in West Africa. It is a very important food and income source for millions of producers, processors, and consumers in the region. About 48 million tons are produced annually in this subregion on 4 million ha. The five major yam-producing countries (Bénin, Côte d’Ivoire, Ghana, Nigeria, and Togo) account for 93% of the world’s production, with Nigeria alone accounting for 68% of global production (36 million t on 3 million ha) with 31.8% of the population depending on yam for food and income security. The crop contributes substantially to the amount of protein in the diet, ranking as the third most important source, much more than the more widely grown cassava, and even higher than some sources of animal protein. Hence, yam is important for food security and income generation with a domestic retail price of US $0.49/kg. Yam is also integral to the sociocultural life in the subregion.

In present-day Nigeria, yam is still culturally significant because it plays an important role in betrothal ceremonies or traditional marriages. It is one of the significant items a suitor presents to his in-laws to obtain their approval to marry their daughter. Some grooms are compelled to present as many as 40 pieces of long and fat yam tubers, aside from gallons of palm oil, baskets of kola nuts, bags of salt, and other sundry items, the nonprovision of which could invalidate the union. The cultural importance of yam is higher in some regions in Nigeria as it is a crop celebrated annually during the New Yam Festival, with rituals to thank the god of agriculture, to seek its blessings for a bumper harvest in the forthcoming years. Yam is produced more in the middle belt zone of Nigeria and is consumed more in the South, but those making commercial gains from its sales are core northerners from the North West, the North Central, and the North East.

Despite its importance in the economy and lives of many people, the crop faces several constraints that significantly reduce its potential to support rural development and meet consumers’ needs for improved food security and enhanced livelihood. Constraints limiting yam production and postharvest handling need to be identified to provide a basis for appropriate interventions. This was the reason behind the interventions through the Yam Improvement for Income and Food Security in West Africa (YIIFSWA) project. YIIFSWA was initiated to work with other stakeholders in West Africa to identify the opportunities of interventions that could potentially help to increase productivity in the region. This report documents production and postharvest constraints and opportunities in yam.

Using Nigeria and Ghana as cases, important worldwide yam-producing countries, a study was carried out using a multistage, random sampling procedure in selecting a total of 800 and 600 households, respectively. All surveyed households were interviewed using a structured questionnaire.

Survey results indicated that a range of factors limited yam production and storage. These include insect pests, diseases, water-logging, drought, rodents, low soil fertility, shortage of staking material, inadequate input supply and storage facility, land shortage, high cost of labor, lack of improved varieties, and others such as theft (Fig. 1).

High cost of labor stands out as the most pressing problem in all the surveyed zones, both in Nigeria and Ghana. For instance, mounding as a seedbed preparation method, is laborious, and hence expensive. But apart from mound making all yam production operations are labor intensive because they are performed with hand hoes, machetes, and digging sticks without any form of a labor-saving technology.

Another main constraint are insect pests and diseases. The unavailability and high cost of good quality disease-free seed yam had been on one hand a result of pests and diseases and on the other hand a serious hidden constraint due to the fact that farmers do not purchase seed yam. Other important constraints mentioned were the inadequate input supply that was very pronounced in Ghana, low soil fertility more reported in Nigeria, rodents and drought (Ghana), water-logging (Nigeria), lack of improved varieties more prominent in Ghana, shortage of land and staking material (Ghana), and others such as theft that were not negligible in both countries.

It is clear that there are shared priority constraints in the two countries, indicating no specificity of problems by country. The YIIFSWA research agenda needs to be informed by the constraints facing yam farmers and based on these the following interventions were identified: (i) Key investments for lowering farmers’ production cost using agricultural research (breeding, agronomy) and extension (improved agronomic and management practices; and (ii) Managing pests and diseases.

As regards opportunities, yam could be be a formidable force in the fight against poverty, hunger, and deadly diseases if research and development measures are implemented to develop and disseminate technologies that can bring the crop into central focus in national food policies. This will enable it to benefit from policy programs that can drive down production costs. Yam is a preferred food in the region; some varieties, especially yellow varieties, are sources of betacarotene. The crop is produced mostly for sale, and it is increasingly becoming a major source of foreign exchange in the region as an export crop.

Therefore, YIIFSWA, through its initiatives, should ensure that all constraints are turned into opportunities for all the yam value chain players in general and farmers in particular.

Enhancing yam improvement for West Africa

Hiroko Takagi

EDITS Project: JIRCAS International Collaborative Research for West African crops

In the past, most agricultural investments and international agricultural research in Africa were focused on developing major cereals and crops for export. Recently, however, the focus has shifted to approaches to diversify agricultural innovations in defined locations to contribute to productivity and profitability increase and achieving sustainable food security to overcome poverty and malnutrition. In addition to so-called “major global crops”, attention has also been placed on many more crops that are regionally or locally important for nutrition and income and that are often underresearched but are nutritious, valued culturally, adapted to local environments, and contribute to diversifying regional agriculture systems.

The Japan International Research Center for Agricultural Sciences (JIRCAS), together with several Japanese research institutions and IITA, initiated in 2011 a 5-year collaborative research project called “Evaluation and Utilization of Diverse Genetic Materials in Tropical Field Crops (EDITS)”. The project focuses on yam (EDITS-Yam) and cowpea (EDITS-Cowpea), and aims to generate a solid understanding of the available wide genetic resources in these West African traditional crops, and develop efficient evaluation techniques for effective crop improvement. The outputs from these collaborative efforts are expected to contribute to breeding programs in West Africa.

JIRCAS is playing a key role by linking the Japanese scientific capacities to African communities through IITA, which is the entry point for many overseas research institutions to overcome the various constraints in African agriculture. The knowledge and techniques gained from the collaborative research project is expected to enhance the development of improved yam and cowpea varieties that can help promote rural livelihoods in West Africa.

EDITS-Yam

Yam is a traditional staple crop of significant economic and sociocultural importance in West Africa. The demand for yam is projected to increase, mostly due to population growth in the region. However, little improvement of farm yields has been registered in this crop in the last few decades, indicating an urgent need for more investment in yam research and development. To increase its productivity and enhance the income generation capacity of small-holder farmers, research-for-development should focus on increasing productivity through improved varieties and production technologies to meet the regional needs.

The last couple of years saw a breakthrough in genome sequencing technologies, and in the application genomic information to plant breeding. Genome analysis and improved molecular techniques would tremendously facilitate germplasm characterization, genetic mapping and tagging, and functional genomics of yam. These new tools, if incorporated into the breeding program, will pave the road for effective genetic improvement of yam. Since April 2011, JIRCAS together with the Iwate Biotechnology Research Center (IBRC) and IITA, has been implementing EDITS-Yam to develop and use advanced genomic and molecular tools to enhance germplasm evaluation and improvement for D. rotundata in West Africa.

EDITS-Yam is designed to strengthen genotyping using molecular tools and develop phenotyping protocols to facilitate yam breeding. The project aims to (1) generate the first reference genome of D. rotundata (Guinea yam), (2) develop and apply genomic information and molecular tools in yam breeding, (3) provide improved tools for biodiversity analysis and identification of potentially useful germplasm, and (4) develop phenotyping protocols for important agronomic traits. The outputs from this collaborative research are expected to contribute to the enhancement of yam breeding activities in the region. Consequently, new improved varieties will provide better food security and income for the small-holder farmers in West Africa and beyond.

Progress in 2011-2013

Sequencing of Guinea yam genome

To enhance Guinea yam breeding by fully exploiting modern genomics tools, generating a reliable reference sequence is a prerequisite. To this end, we have been gathering efforts to obtain the first whole genome sequence (WGS) of D. rotundata. The de novo assembly is currently in its final stage. The reference of genome will be completed soon, and the finding will be shared with the global yam community (Fig. 1).

Whole-genome sequencing-based analysis of diversity in Guinea yam

Next generation sequencing (NGS) allows large-scale genome-wide discovery of genetic markers that are important for genomic and genetic applications such as construction of genetic and physical maps, and analysis of genetic diversity. As a component of the on-going effort to construct the first draft sequence of D. rotundata and accelerate the breeding program, WGS-based genetic diversity analysis of D. rotundata accessions is under way. So far, 10 D. rotundata breeding materials, including five landraces and five breeding lines, have been resequenced. These materials are diverse with respect to traits such as maturity time, yield, tuber quality, and resistance to nematode and Yam mosaic virus (YMV), and have been extensively used as parental lines in the IITA yam breeding program.

Aligning the Illumina paired-end short reads obtained from resequencing of the breeding materials to D. rotundata scaffold sequence allowed genome-wide extraction of single nucleotide polymorphism (SNP) and insertion/deletion (indel) markers, which are being used to estimate the genetic relatedness among the lines/accessions studied and reveal the genetic diversity available to breeders. Findings of this study will have huge implications for genetic and genomic studies in yams, including among others, the application of SNPs, the most abundant genetic markers in genomes, for the development of high throughput genotyping platforms and for marker-assisted breeding. More accessions will be considered for resequencing in the future to mine the diversity in D. rotundata in detail.

Diversity Research Set (DRS) as a tool for diversity evaluation of D. rotundata germplasm

The availability of genotypic and phenotypic tools is critical to understand the diversity present in germplasm collections and enhance the active use of genetic resources. IITA currently holds over 2,000 accessions of D. rotundata. Of these, we selected a subset of experimental materials called Diversity Research Set to develop genotyping and phenotyping tools and protocols for germplasm evaluation.

In principle, DRS should be small in size for ease of handling and to allow a detailed analysis of diversity, but retain most of the diversity present in the original collection both at molecular and morphological levels. Accordingly, 106 accessions have been selected as the DRS-EDITS based on 21 key morphological traits, ploidy level, and SSR polymorphisms. The materials are currently being used for (1) detailed genotyping using DNA markers generated from the ongoing WGS, (2) morphological characterization and identification of key descriptors for regional D. rotundata collection, and (3) detailed phenotyping of economically important traits (Fig. 2)

Developing phenotyping protocols

In yam, as well as other root and tuber crops, phenotyping remains the major bottleneck to fully use genotyping information in germplasm evaluation and breeding. EDITS-Yam is also aiming to develop phenotyping protocols on key traits such as tuber yield, earliness of tuber growth and maturation, starch content and properties in collaboration with agronomists and food science specialists. These protocols, once developed, will be used for large-scale phenotyping applied to genetic and diversity studies (Fig. 3).

The information generated and tools developed in the framework of the EDITS-Yam project are expected to contribute immensely to broadening the knowledge base in yam, thereby facilitating the management of available genetic resources and aiding efficient use of yam germplasm for future improvement of the crop. This project and the collaboration it forged are expected to contribute to raising the profile of yam, and trigger the initiation of more and concerted international approaches to yam research for development. The preliminary outputs from the EDITS-Yam project suggest that there is a need for complementary studies to effectively use genetic and genomic tools being generated for yam improvement. To this effect, possibilities for additional resources are being explored.

Viral disease threats to yam in West Africa

Lava Kumar, l.kumar@cgiar.org

Virus diseases pose serious challenges to seed and ware yam production and also impede international exchange of yam planting material in West Africa, which is home to about 91% of the global edible yam production. Current efforts to control virus threats are directed towards propagation of virus-free seed yam. However, deployment of genetic resistance in farmer-preferred cultivars is critical for sustainable virus disease control in West Africa.

One disease and several viruses

‘Mosaic disease’ is a common disorder caused by several different viruses infecting yam in West Africa. About 17 viruses have been identified in edible and medicinal yam in different parts of the world1. The virus species belonging to the genera Potyvirus and Badnavirus are most widespread. Two potyviruses, Yam mosaic virus (YMV) and Yam mild mosaic virus (YMMV), and several badnaviruses—generically referred as yam badnaviruses (YBVs) —are frequently detected in farmer-grown yam in the West African yam belt that stretches from western regions of Cameroon to Cote d’Ivoire, including Nigeria, Bénin, Togo, and Ghana. About 88% of the global yam production area and 91% of the global production is confined to this region. Six Dioscorea species, viz., D. rotundata (white yam), D. alata (water yam), D. cayenensis (yellow yam), D. dumetorum (bitter yam), D. bulbifera (aerial yam), and D. esculenta (lesser yam) are widely cultivated for food use in West Africa. Virus infections are known in all these species but most prevalent in D. rotundata and D. alata, the two most predominant species covering >70% of the cultivated area in West Africa.

Different viruses cause almost similar symptoms and are difficult to distinguish from one another based on symptoms alone. In general virus symptoms in yam consist of deformation of leaf lamina, mottling, yellowing, vein banding, mosaic pattern on leaves, stunting, and poor growth (Fig. 1). Symptom expression can differ based on the genotype, time of infection, environmental conditions and cultivar. Mixed infection with more than one virus often results in severe symptoms. Although effects of virus infection on tuber size have not been accurately quantified, data from published and unpublished studies suggest about 20 to 50% reduction in tuber yield. In addition, ‘internal brown spot disease’ reported from Côte d’Ivoire is known to cause dry corky necrosis in tubers (Fig. 1b). The cause of this disease is not known, but based on symptoms it is regarded as viral in nature. In addition, badnavirus sequences have been found to be integrated in the yam genome. These are termed as endogenous pararetrovirus sequences (EPRVs) or endogenous yam badnaviruses (eYBVs) and have been detected in almost all yam species grown in West Africa, the Caribbean, and South-Pacific regions2. However, the pathological significance of yam EPRVs is not known.

Virus spread along with plant parts and insect vectors

Viruses infecting yam are systemically distributed in all plant tissues, including tubers. Consequently, tubers, setts, or any plant tissue from infected plants serves as a source for virus spread through vegetative propagation (Fig. 2). In addition, some of the yam viruses are transmitted from plant to plant by insect vectors. For instance, YMV and YMMV are transmitted by aphids and YBVs are transmitted by mealybugs. Insect vectors play an important role in spreading virus from infected plants to uninfected plants. A recent study demonstrated YMV transmission through botanical seeds of yam, albeit only a small percentage of seed serves as virus carriers.

Infected seed yams contributing to high virus incidence in West Africa

Farmers in West Africa mainly cultivate yam by planting small tubers (seed yam) or pieces of tubers (setts and minisetts) derived from larger tubers, which are sourced from their own harvest, brought from neighbors, or markets. This practice contributes to the accumulation and perpetuation of tuber-borne viruses. Considering that about one quarter of the yam tuber harvest each year in West Africa is used for propagation, the risk of virus perpetuation dramatically increases through infected tubers from generation togeneration. Historical data and recent surveys conducted as part of the Yam Improvement for Income and Food Security in West Africa (YIIFSWA) project estimated an average virus incidence of >70% in almost all the farmers’ fields, reflecting the perpetual use of infected tubers due to lack of availability of virus-free seed yams. Lack of virus resistance in the popular landraces and improved cultivars, poor awareness about viral diseases, and severe shortage of virus-free planting material are other factors that continue this prevailing situation in West Africa. Coordinated action is required to control the unabated spread of yam viruses through use of virus-infected seed yams.

Multipronged approach for yam virus disease control

Virus disease management of clonally propagated crops which are also transmitted by insect vectors requires a multipronged strategy: (i) reduce virus inoculum in the field by phytosanitation (removal and destruction of infected sources) and replacement of infected seed stock with virus-free propagation material, (ii) use resistant cultivars to prevent infection, and (iii) control insect vectors to prevent further spread. Unfortunately, many of these tactics are not being practiced due to lack of appropriate resources such as virus-free seed stock or highly resistant varieties.

YIIFSWA impetus

In the ongoing Bill & Melinda Gates Foundation-funded YIIFSWA initiative, surveys were conducted in the major yam production regions in Ghana and Nigeria to determine the situation of virus incidence and severity during the 2012-13 seasons. Mean virus disease incidence in both countries was greater than 85% and mean severity was 3, based on a 1 to 5 rating scale (1 = no symptoms and 5 = most severe symptoms). Local landraces were dominantly used by farmers compared to released cultivars. Virus diagnostics tests by reverse-transcription polymerase chain reaction (RT-PCR) assays detected YMV in D. rotundata in all the locations, sometimes in mixed infection with YMMV. YBVs were also detected in all the locations, however it was not clear if these positive results were from episomal? infection or eYBVs. Knowledge on virus diversity determined by sequencing of portion of viral genomes was incorporated into the diagnostic test development to further enhance sensitivity and specificity of yam virus diagnostic tools.

Efforts are also ongoing to produce virus-free yam stocks of the most popular farmer-preferred cultivars (landraces and improved cultivars) in Nigeria and Ghana. A suite of macro and micropropagation technologies combined with thermo- and chemotherapy techniques have been employed to generate stocks free of YMV, YMMV, and CMV. Such virus-free stocks have been established for the cultivars Adaka, Aloshi, Alumaco, Ame, Amula, Danachia, Gbangu, Kemi, Makakusa, Obiaturugo, Ogini, Ogoja, TDr 89/02475, and TDr 89/02665. They are being mass propagated for use as nucleus stock for breeder-class seed yam production. Similar efforts are ongoing to generate virus-free stocks of a wider range of D. rotundata and D. alata cultivars. This, in combination with YIIFSWA activities on strengthening the seed yam systems through improved seed production techniques and capacity development is anticipated to regularly infuse stocks of high quality seed yams produced from virus-free sources by specialist seed growers and contribute to productivity gains.

‘Positive selection’ (PS) is another approach piloted as part of YIIFSWA and allied initiatives to prevent reuse of tubers from severely infected plants for seed purpose. PS is a simple on-farm method of selectively harvesting seed yam tubers from healthy looking plants or plants showing mild symptoms, when asymptomatic plants are not available. This eliminates tubers with high virus concentration and infected with multiple viruses, the two conditions responsible for severe symptoms, poor plant performance, and degeneration of seed yams. Implementation of PS over several seasons is expected to reduce virus inoculum in the fields, improves the quality of farmer-saved seed yam, and reduces the need for regular seed replacement. However, this approach requires additional effort in the form of monitoring crops before senescence, tagging, and separate harvesting of tubers from selected plants. Awareness creation among growers about the benefits of PS and training in selection of healthy looking plants is critical to the sustainable implementation of this approach.


Resistant varieties required for sustainable management

Resistant varieties offer the most convenient, economical, and sustainable option for controlling virus diseases. In addition, they are easy for dissemination and adoption. Almost all the popular landrace cultivars were found to be susceptible. Some were found to have tolerance showing mild symptoms at the later crop growth stage (e.g., Amula). Germplasm sources with high levels of host plant resistance to virus diseases have been identified in the Dioscorea landraces3. However, all the improved varieties released as of 2013 were found to be susceptible. Limited breeding efforts for virus disease resistance demonstrated dominantly inherited resistance to YMV in certain D. rotundata crosses4,5, indicating the promise of breeding for developing cultivars with high levels of virus resistance with end-user preferred traits.

Conclusions

Virus diseases pose a major threat to West African yam production, affecting tuber yields and seed yam quality. Reuse of farmer-saved seed in successive seasons has contributed to high virus incidence and seed yam degeneration. In the absence of high levels of virus resistance in farmer-preferred varieties, it is imperative to infuse clean stocks of popular cultivars through seed systems, coupled with approaches such as phytosanitation and positive selection to reduce virus inoculum in the fields. Concerted efforts in this direction started recently through initiatives such as YIIFSWA. However, these efforts need to be complemented with breeding programs to develop cultivars with high levels of resistance and end-user preferred attributes for sustainable control of virus diseases and also to ensure sustainability of quality seed yams.

References

1. Kenyon et al. 2003. An overview of viruses infecting yams in sub-Saharan Africa. In: Eds. Hughes, J. d’A and Odu, B.O. Plant virology in sub-Saharan Africa, Proceedings of a conference organized by IITA, IITA, Nigeria. pp432-439.

2. Seal et al. (2014). The prevalence of badnaviruses in West African yam (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes. Virus Research (in press) [doi:10.1016/j.virusres.2014.01.007]

3. Asiedu R. 2010. Genetic improvement of yam. In: Yam Research for Development in West Africa – Working Papers. IITA-BMGF Consultation Documents, IITA. pp 81-108.

4. Mignouna J. et al. 2002. Identification and potential use of RAPD markers linked to Yam mosaic virus resistance in white yam (Dioscorea rotundata Poir.). Ann. Appl. Biol. 140: 163­169.

5. Odu et al. 2011. Analysis of resistance to Yam mosaic virus, genus Potyvirus, in white guinea yam (Dioscorea rotundata) genotypes. J. Agri. Sci. 56: 1-13.

Yam breeding at IITA: achievements, challenges, and prospects

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

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

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

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

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

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

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

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

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

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

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