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 Although effects of virus infection on tuber size have not been accurately quantified, data from published and unpublished studies suggest about 20 to 50% reduction in tuber yield.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.

Developing clean seed systems for cassava

James Legg, j.legg@cgiar.org

Cassava stems for future crop. Photo by L. Kumar, IITA.
Cassava stems for future crop. Photo by L. Kumar, IITA.

Cassava is one of those crops that uses part of the plant for propagation. It is very convenient to use vegetative material from a previous crop to plant a new one. This is one of the beauties of vegetatively propagated crops. However, this convenience comes at a price. The use of planting material from a previous generation to establish the next provides an easy way for disease-causing pathogens, particularly viruses, to pass directly from one plant generation to another. So, while they offer convenience, vegetatively-propagated crops are often more widely affected by pathogens than those planted in the form of true seeds.

In Africa, cassava is the most widely cultivated of the vegetatively-propagated crops, being grown on more than 12 million ha across the continent. The exotic pest introductions, cassava mealybug and cassava green mite, caused great damage to Africa’s cassava crop in the 1980s and 1990s, but both have been effectively managed through the implementation of a classical biological control program.

The fungal diseases, cassava bacterial blight (Xanthomonas axonopodis pv. manihotis) and cassava anthracnose (Colletotrichum gloeosporioides f. sp. manihotis) are locally important. The greatest current constraints to cassava production, however, are the virus diseases, cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) and cassava brown streak disease (CBSD) caused by cassava brown streak viruses (CBSVs), which together cause crop losses worth more than US$1 billion annually.

One of the most important approaches to controlling these virus diseases, as well as other pathogens of cassava, is through the avoidance of infection. This can be achieved by starting out with pathogen-tested plants, and then bulking the planting material through a series of quality controlled multiplication steps. Although it sounds very simple, this can be difficult to achieve in practice.

Pathogen testing requires well-equipped laboratories run by adequately trained staff. Quality management in the field requires extensive grassroots knowledge of disease symptoms and the involvement of an appropriately trained and resourced national plant protection organization. In many parts of sub-Saharan Africa, capacity for these functions remains insufficient to meet the demands.

IITA and its partners have made significant progress in developing and implementing new systems to maintain the health of cassava through seed systems. For instance, through the Great Lakes Cassava Initiative (GLCI), a multi-partnered project implemented from 2007 to the present in Burundi, Democratic Republic of Congo, Kenya, Rwanda, Tanzania, and Uganda, a rigorous system has been put in place to assure the health of cassava planting material. This has been particularly important in view of the rapid recent spread of a devastating pandemic of CBSD in East Africa.

Healthy cassava plant. Photo by IITA.
Healthy cassava plant. Photo by IITA.

The key components of the quality and health management system are as follows: Primary (centralized seed production sites) managed by researchers or qualified seed producers, secondary, and tertiary multiplication sites (usually in farmers’ fields) are all assessed, at least once in a year, using the Quality Management Protocol (QMP). This sets out quality levels, primarily in terms of disease and pest incidence and material quality that must be met if the field is to “pass”.

The QMP standards for CMD and CBSD incidences ascertained by diagnostic tests are <10% for primary and secondary sites and <20% for tertiary sites in endemic areas. Planting materials from fields that fail to meet QMP standards are not distributed or used for further multiplication, although the tuberous roots can be used by the growers for consumption. Fields that meet the QMP standard and test negative for CBSVs are approved for more widespread dissemination.

This is the first time that this level of rigor has been applied to maintaining the health of cassava through multiplication programs in sub-Saharan Africa. It has been invaluable in assuring the health of the planting material provided to more than half a million beneficiaries in six countries, and provides an important model for other current and future cassava development programs.

Much remains to be done before such an approach can be used in a more sustainable way. Most importantly, basic capacity needs to be strengthened in most countries. Key elements of this include the laboratory and human capacity for virus indexing, as well as the knowledge of QMP and the capacity of the national plant quarantine organization to monitor cassava seed systems.

In addition, the management of cassava diseases could be greatly enhanced by the establishment of isolated nuclear multiplication sites planted with virus-tested cassava plantlets derived from tissue culture, as well as by raising awareness among growers about the importance of establishing the next crop with healthy planting material.

A long-term goal, as the commercial value of cassava increases, will be to provide a mechanism through which planting material certified through the QMP attracts a price premium. Creating added value is certain to be the key to the future development of clean seed systems for cassava in Africa. IITA and its partners are strongly committed to reaching this goal.