Mikocheni Agricultural Research Institute

Dar es Salaam, Tanzania

Mikocheni Agricultural Research Institute

Dar es Salaam, Tanzania
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PubMed | International Institute Of Tropical Agriculture, University of Pretoria, Mikocheni Agricultural Research Institute, North Carolina State University and 3 more.
Type: Journal Article | Journal: Journal of virology | Year: 2016

Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies.Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.

Fisher M.,Oregon State University | Abate T.,ICRAF House United Nations Avenue | Lunduka R.W.,CIMMYT Southern Africa Regional Office SARO | Asnake W.,CIMMYT Ethiopia | And 2 more authors.
Climatic Change | Year: 2015

In sub-Saharan Africa (SSA), “maize is life,” due to its importance to food security and economic wellbeing. Around 40 % of Africa’s maize-growing area faces occasional drought stress, resulting in yield losses of 10–25 %. Around 25 % of the maize crop suffers frequent drought, with losses of up to half the harvest. To reduce vulnerability and improve food security, the Drought Tolerant Maize for Africa (DTMA) project has made releases of 160 drought tolerant (DT) maize varieties between 2007 and 2013. These have been tested in experimental and farmers’ fields, and disseminated to farmers in 13 African countries through national agricultural research systems and private seed companies. Yields of the new varieties are superior to those of currently available commercial maize varieties under both stress and optimum growing conditions. Although the benefits of DT maize for African farmers have been repeatedly predicted, realization of those benefits depends on farmer uptake, which has received limited empirical study. We use new plot-level data from surveys of 3,700 farm households in six countries (Ethiopia, Tanzania, Uganda, Malawi, Zambia, and Zimbabwe) to measure DT maize adoption rates and their determinants. The data reveal considerable inter-country variation in farmer uptake of DT maize, from 9 % of maize plots in Zimbabwe to 61 % in Malawi. The major barriers to adoption include unavailability of improved seed, inadequate information, lack of resources, high seed price, and perceived attributes of different varieties. Based on the results, we recommend that seed companies and agro-dealers ensure adequate supply of DT maize seed in local markets and sell seed in affordable micro-packs (1 or 2 kg). Furthermore, the DTMA project and partners should ramp up promotional efforts to ensure widespread awareness and understanding of the benefits of the new DT maize varieties. © 2015 The Author(s)

Rodenburg J.,Africa Rice Center | Riches C.R.,University of Greenwich | Kayeke J.M.,Mikocheni Agricultural Research Institute
Crop Protection | Year: 2010

Significant areas of rain-fed rice in the Sahel, savannah and derived savannah zones of sub-Saharan Africa (SSA), Madagascar and other Indian Ocean Islands are infested by parasitic weeds. The affected area accommodates some of the poorest farmers of the world. Without appropriate management parasitic weeds in rice are expected to increase in importance in SSA due to their general invasive nature and their abilities to adapt to changing conditions such as imposed by predicted climate changes. The most important parasitic weeds in rice are: Striga hermonthica, Striga asiatica, Striga aspera and Rhamphicarpa fistulosa. The first two are primarily found in free-draining uplands while S. aspera is also found on hydromorphic soils and R. fistulosa is restricted to unimproved lowlands including inland valleys. As parasitic weeds are typical production constraints in subsistence rice production, targeting them would directly contribute to poverty alleviation and food security. This paper provides an overview of the problems caused by parasitic weeds in rice and discusses management options and opportunities for research for development. © 2009 Elsevier Ltd. All rights reserved.

Kabiri S.,Wageningen University | Rodenburg J.,Africa Rice Center | Kayeke J.,Mikocheni Agricultural Research Institute | Van Ast A.,Wageningen University | And 4 more authors.
Weed Research | Year: 2015

Striga asiatica and Rhamphicarpa fistulosa are important parasitic weeds of rain-fed rice, partly distributed in similar regions in sub-Saharan Africa (SSA). It is not evident whether their ecologies are mutually exclusive or partially overlapping. In Kyela, a rice-growing area in south Tanzania where both parasites are present, three transects of about 3 km each across the upland-lowland continuum were surveyed in June 2012 and 2013. A total of 36 fields were categorised according to their position on the upland-lowland continuum as High, Middle or Low and soil samples were taken. In each field, parasitic and non-parasitic weed species were identified in three quadrats. Additionally, in two pot experiments with four different moisture levels ranging from wilting point to saturation, influence of soil moisture on emergence and growth of parasites was investigated. Striga asiatica was observed in higher lying drier fields, while R. fistulosa was observed in the lower lying wetter fields. Furthermore, non-parasitic weed species that were exclusive to S. asiatica-infested fields are adapted to open well-drained soils, while species that were exclusive to R. fistulosa fields are typical for wet soils. The experiments confirmed that S. asiatica is favoured by free-draining soils and R. fistulosa by waterlogged soils. These results imply that changes in climate, specifically moisture regimes, will be crucial for future prevalence of these parasitic weeds. The non-overlapping ecological range between their habitats suggests that their distribution and associated problems might remain separate. Thus, management strategies can be focused independently on either species. © 2014 European Weed Research Society.

PubMed | National Crops Resources Research Institute, University of Malaga, Mikocheni Agricultural Research Institute and University of Kent
Type: | Journal: Archives of virology | Year: 2016

The complete genomes of a monopartite begomovirus (genus Begomovirus, family Geminiviridae) and an associated betasatellite found infecting Vernonia amygdalina Delile (family Compositae) in Uganda were cloned and sequenced. Begomoviruses isolated from two samples showed the highest nucleotide sequence identity (73.1% and 73.2%) to an isolate of the monopartite begomovirus tomato leaf curl Vietnam virus, and betasatellites from the same samples exhibited the highest nucleotide sequence identity (67.1% and 68.2%) to vernonia yellow vein Fujian betasatellite. Following the current taxonomic criteria for begomovirus species demarcation, the isolates sequenced here represent a novel begomovirus species. Based on symptoms observed in the field, we propose the name vernonia crinkle virus (VeCrV) for this novel begomovirus and vernonia crinkle betasatellite (VeCrB) for the associated betasatellite. This is the first report of a monopartite begomovirus-betasatellite complex from Uganda.

Rakotomalala M.,British Petroleum | Pinel-Galzi A.,Montpellier University | Mpunami A.,Mikocheni Agricultural Research Institute | Randrianasolo A.,CRRSO | And 3 more authors.
Virus Research | Year: 2013

Rice yellow mottle virus (RYMV), of the genus Sobemovirus, is a major threat to rice cultivation in Africa. Long range transmission of RYMV, difficult to study experimentally, is inferred from a detailed analysis of the molecular diversity of the virus in Madagascar and in the Zanzibar Archipelago (Zanzibar and Pemba Islands; Tanzania) compared with that found elsewhere in Africa. A unique successful introduction of RYMV to Madagascar, which is ca. 400. km from mainland Africa, contrasted with recurrent introductions of the virus to the Zanzibar Archipelago, ca. 40. km from the East African coast. Accordingly, RYMV dispersal over distances of hundreds of kilometers is rare whereas spread of the virus over distances of tens of kilometers is relatively frequent. The dates of introduction of RYMV to Madagascar and to Pemba Island were estimated from three sets of ORF4 sequences of virus isolates collected between 1966 and 2011. They were compared with the dates of the first field detection in Madagascar (1989) and in Pemba Island (1990). The estimates did not depend substantially on the data set used or on the evolutionary model applied and their credible intervals were narrow. The estimated dates are recent - 1978 (1969-1986) and 1985 (1977-1993) in Madagascar and in Pemba Island, respectively - compared to the early diversification of RYMV in East Africa ca. 200 years ago. They predated by 5-10 years the first field detections in these islands. The interplay between virus sources, rice cultivation and long range dispersal which led to RYMV emergence and spread is enlightened. © 2012 Elsevier B.V.

McQuaid C.F.,Rothamsted Research | Sseruwagi P.,Mikocheni Agricultural Research Institute | Pariyo A.,National Crops Resources Research Institute | van den Bosch F.,Rothamsted Research
Plant Pathology | Year: 2016

One method of reducing disease in crops is the dissemination of disease-free planting material from a multiplication site to growers. This study assesses the validity and sustainability of this method for cassava brown streak disease, a threat to cassava crops across East Africa. Using mathematical modelling, the effects of different environmental and control conditions on pathogen spread were determined in a single-field multiplication site. High disease pressure, through large vector populations and disease in the surrounding area, combined with poor roguing practice, resulted in unsuccessful disease suppression. However, fields may produce sufficiently clean material for replanting if these factors can be overcome. Assessing the sustainability of a low-pressure system over multiple harvests, well-managed fields were found to maintain low disease levels, although producing sufficient cuttings may prove challenging. Replanting fields from the previous harvest does not lead to degeneration of planting material, only cutting numbers, and the importation of new clean material is not necessarily required. It is recommended that multiplication sites are only established in areas of low disease pressure and vector population density, and the importance of training in field management is emphasized. Cultivars displaying strong foliar symptoms are to be encouraged, as these allow for effective roguing, resulting in negative selection against the disease and reducing its spread. Finally, efforts to increase plant multiplication rates, the number of cuttings that can be obtained from each plant, have a significant impact on the sustainability of sites, as this represents the primary limiting factor to success. © 2016 British Society for Plant Pathology.

Mbanzibwa D.R.,Mikocheni Agricultural Research Institute | Tugume A.K.,Makerere University | Chiunga E.,Uyole Agricultural Research Institute | Mark D.,Mikocheni Agricultural Research Institute | Tairo F.D.,Mikocheni Agricultural Research Institute
Annals of Applied Biology | Year: 2014

Small interfering RNA deep sequencing (SRDS) was used to detect viruses in 23 sweetpotato plants, collected from various locations in Tanzania. Alignment of small RNA reads using a MAQ program recovered genomes of viruses from five families, namely Geminiviridae (2), Closteroviridae (1), Betaflexiviridae (1), Caulimoviridae (1) and Potyviridae (1). This was in agreement with the variation of symptoms observed on sweetpotato plants in fields and screen house, which included leaf curl, vein yellowing, chlorosis, stunted growth and brown blotches. PCR was also used to confirm the occurrence of viruses associated with leaf curl and symptomless infections. A complete genome (2768 nucleotides) was obtained for a sweepovirus that was 89.9% identical to the strain of Sweet potato leaf curl Sao Paulo virus (SPLCSPV; Begomovirus) reported in South Africa. Sweepoviruses are known to undergo frequent recombinations and evidence for this was found in the SPLCSPV sequence studied. The SRDS-based results indicated occurrence of the poorly studied Sweet potato badnavirus B (SPBV-B) and Sweet potato badnavirus A (collectively known as Sweet potato pakakuy virus; SPPV; Caulimoviridae) in sweetpotato plants in Tanzania. A 5′-end partial sequence (3065 nucleotides), encoding hypothetical, movement and coat proteins, was obtained and found to be 86.3% and 73.1% identical to SPBV-B and SPBV-A, respectively. A survey for the distribution of SPPV and Sweet potato symptomless mastrevirus 1 (SPSMV-1) showed that these viruses were wide spread and co-infecting sweetpotato plants in Tanzania. The importance of East Africa as a hot spot for the diversity and evolution of sweet potato viruses is discussed. © 2014 Association of Applied Biologists.

Seguni Z.S.K.,Mikocheni Agricultural Research Institute | Way M.J.,Imperial College London | Van Mele P.,British Petroleum
Crop Protection | Year: 2011

In tropical Africa and Asia, two species of the predatory ant genus, Oecophylla, play a crucial role in protecting tree crops against pests and enhancing the quality of fruits and nuts. As predatory effectiveness is influenced by the presence of other dominant ant species, understanding the ecological factors at work in agroecosystems lies at the basis of conservation biological control. Over three and a half years, the effect of ground vegetation management on the beneficial tree-nesting ant Oecophylla longinoda (Latreille) and its competitor, the ground-nesting ant, Pheidole megacephala (Fabricius), was studied in a citrus orchard in Tanzania. When ground vegetation was present, P. megacephala tolerated O. longinoda and to some extent cohabited with this ant in citrus trees. However, after clean cultivation, P. megacephala displaced O. longinoda from tree crowns and became the sole occupant of the majority of trees. Displacement could be reversed by reversing the weed management regime, but this took time. Two years after the establishment of ground vegetation about half of the trees were colonized by Oecophylla only. Maintaining ground vegetation in tree crop plantations benefits the establishment and abundance of Oecophylla over Pheidole and is recommended in order to improve the efficiency of biological control of tree pests. The use of Amdro ant bait (hydramethylnon) to control P. megacephala is discussed. Boosting agroecological innovations, such as the one described in this paper, could benefit smallholder producers. © 2011 Elsevier Ltd.

PubMed | Mikocheni Agricultural Research Institute, Kenya International Livestock Research Institute and Makerere University
Type: | Journal: Archives of virology | Year: 2017

Four isolates of a bipartite begomovirus from naturally infected Deinbollia borbonica plants exhibiting yellow mosaic symptoms in Kenya and Tanzania were molecularly characterised. The DNA-A was most closely related to that of tomato leaf curl Mayotte virus (AM701764; 82%), while the DNA-B shared the highest nucleotide sequence identity with that of East African cassava mosaic virus (AJ704953) at 65%. Based on the current ICTV species demarcation criterion for the genus Begomovirus (91% sequence identity for the complete DNA-A), we report the full-length genome sequence of this novel bipartite begomovirus. The results reveal additional diversity and reservoir hosts of begomoviruses in East Africa.

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