Mikocheni Agricultural Research Institute

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

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.

Spatial predictions of soil macro and micro-nutrient content across Sub-Saharan Africa at 250 m spatial resolution and for 0-30 cm depth interval are presented. Predictions were produced for 15 target nutrients: organic carbon (C) and total (organic) nitrogen (N), total phosphorus (P), and extractable-phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), sodium (Na), iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), aluminum (Al) and boron (B). Model training was performed using soil samples from ca. 59,000 locations (a compilation of soil samples from the AfSIS, EthioSIS, One Acre Fund, VitalSigns and legacy soil data) and an extensive stack of remote sensing covariates in addition to landform, lithologic and land cover maps. An ensemble model was then created for each nutrient from two machine learning algorithms- random forest and gradient boosting, as implemented in R packages ranger and xgboost-and then used to generate predictions in a fully-optimized computing system. Cross-validation revealed that apart from S, P and B, significant models can be produced for most targeted nutrients (R-square between 40-85%). Further comparison with OFRA field trial database shows that soil nutrients are indeed critical for agricultural development, with Mn, Zn, Al, B and Na, appearing as the most important nutrients for predicting crop yield. A limiting factor for mapping nutrients using the existing point data in Africa appears to be (1) the high spatial clustering of sampling locations, and (2) missing more detailed parent material/geological maps. Logical steps towards improving prediction accuracies include: further collection of input (training) point samples, further harmonization of measurement methods, addition of more detailed covariates specific to Africa, and implementation of a full spatiotemporal statistical modeling framework.

Sweetpotato is a member of the morning glory family that is thought to have originated in Central or South America but also has a secondary center of diversity in the southwest Pacific islands. It is grown in all tropical and subtropical areas of the world and consistently ranks among the 10 most important food crops worldwide on the basis of dry weight produced, yielding about 130 million metric tons per year on about 9 million hectares. Sweetpotato is an important crop for food security. It has been relied on as a source of calories in many circumstances. Vines and/or storage roots can be used for direct human consumption or animal feed. Growing awareness of health benefits attributed to sweetpotato has stimulated renewed interest in the crop. Orange-fleshed cultivars, a source of vitamin A, were introduced to developing countries with hope that they would replace the white-flesh varieties and help alleviate vitamin A deficiencies. In East Africa, sweetpotato virus disease, which is caused by the synergistic interaction of the whitefly-transmitted crinivirus and the aphid-transmitted potyvirus, can cause losses of 80 to 90% in many high-yielding genotypes. During the past 15 years, as molecular methods have been adopted, much has been learned about the composition of the sweetpotato virus complexes, the effects of virus diseases on production systems, the biology of the virus–plant interaction, and management approaches to sweetpotato virus diseases. This article is intended to summarize what has been learned since earlier reviews, integrate knowledge gleaned from experiences in tropical and temperate production systems, and suggest courses of action to develop sustainable management programs for these diseases.

Sustainable agriculture requires the careful optimization of the use of organic amendments to improve soil fertility while minimizing any harmful environmental effects. To understand the events that occur in soil after the addition of different organic amendments, we evaluated the nitrogen (N) mineralization dynamics in soil after adding organic amendments, and evaluated changes in the microbial population. The four organic amendments were fresh dairy cattle manure, fresh white clover, vegetable, fruit, and yard waste compost, and poplar tree compost. The N mineralization potential of each organic amendment was determined by analyzing total mineral nitrogen during a 97-day laboratory incubation experiment. Soils amended with clover released 240 μg N g−1 soil during the 97-day incubation, more than twice as much as that released from soils amended with manure or composts (76–100 μg N g−1 soil). At the end of the incubation, the net N mineralization in clover-amended soils was 54%, more than five times higher than that in soils amended with composts or manure (4%–9%). Nitrogen was mineralized faster in clover-amended soil (1.056 μg N g−1 soil day−1) than in soil amended with composts (0.361–0.417 μg N g−1 soil day−1). The microbial biomass carbon content was higher in clover-amended soil than in the soils amended with manure or composts. We monitored changes in the microbial population in amended soils by a phospholipid fatty acid (PLFA) analysis. On day 97, there were higher concentrations of total PLFAs in soils with organic amendments (e.g., 14.41 nmol g−1 in clover-amended soil) than in control soil without amendments (9.84 nmol g−1). Bacteria (Gram-positive and Gram-negative), actinomycetes, and fungi were more abundant in clover-amended soils than soils amended with manure or composts. The N mineralization potential varied among the four organic amendments. Therefore, the timing of application and the type of organic amendment should be matched to the nutrient needs of the crop.

Abstract Accelerated soil erosion is one of the major constraints to agricultural production in many parts of the Tanzanian highlands. Although several soil and water conservation technologies have been developed and promoted, the adoption of many recommended measures is minimal and soil erosion continues to be a problem. This research was conducted in order to determine the social and economic factors that influence adoption of soil and water conservation (SWC) measures in the West Usambara highlands, Tanzania. For this research a household survey, group discussions and transect walks were undertaken. A total of 104 households were interviewed and several fields were visited during the transect walks. Data was analysed with the use of cross‐tabulation, cluster analysis, factor analysis and chi‐squared methods. The results obtained indicate that involvement in off‐farm activities, insecure land tenure, location of fields and a lack of short‐term benefits from SWC are among the major factors that negatively influence adoption of SWC measures. Membership in farmer groups, level of education, contacts with extension agents and SWC programmes were found to be positively influencing the adoption of SWC measures. Recommendations to facilitate adoption of different SWC measures include: integration of social and economic factors into SWC plans; the creation of more awareness among farmers of soil‐erosion effects and long‐term benefits of SWC; the development of flexible SWC measures to cater for different farm patterns and a participatory approach to SWC at catchment level rather than at individual farmers' fields. Copyright © 2004 John Wiley & Sons, Ltd.

Although pesticides have a positive effect on plant health in terms of insect pests and diseases control, increased productivity and improved crop storage, their malpractice impacts on food safety negatively. Pesticide residues and corresponding metabolites are left as runoff to the environment affecting non-targeted organisms like fish, bees, butterflies, birds and other beneficial organisms in soil and water bodies. Moreover, the application of pesticides in non-agriculture activities goes unnoticed, such as spraying for anopheles mosquito to control malaria. Human health effects caused by pesticide residues in food include headache, vomiting, itching and skin irritation, restlessness, dizziness, breathing difficulties, neurotoxicity and chronic poisoning-related diseases such as cancer and death incidences. Maximum residue limits are the maximum pesticide residues limit in food considered safe to human as set by the Codex Alimentarius Commission and the joint Food and Agriculture Organization/World Health Organization meeting on pesticide residues. The residues of dichlorodiphenyltrichloroethane and chlorpyrifos are reported in various foods globally. Additionally, food safety is largely obstructed by illegal use of pesticides and the presence of counterfeit pesticides in the market. This review provides detail on pesticide control and regulations, residues in food, their health impacts and link approaches like good agricultural practices for ensuring sustainability on safe food production.

This paper introduces Rapid Appraisal of Agricultural Innovation Systems (RAAIS). RAAIS is a diagnostic tool that can guide the analysis of complex agricultural problems and innovation capacity of the agricultural system in which the complex agricultural problem is embedded. RAAIS focuses on the integrated analysis of different dimensions of problems (e.g. biophysical, technological, socio-cultural, economic, institutional and political), interactions across different levels (e.g. national, regional, local), and the constraints and interests of different stakeholder groups (farmers, government, researchers, etc.). Innovation capacity in the agricultural system is studied by analysing (1) constraints within the institutional, sectoral and technological subsystems of the agricultural system, and (2) the existence and performance of the agricultural innovation support system. RAAIS combines multiple qualitative and quantitative methods, and insider (stakeholders) and outsider (researchers) analyses which allow for critical triangulation and validation of the gathered data. Such an analysis can provide specific entry points for innovations to address the complex agricultural problem under study, and generic entry points for innovation related to strengthening the innovation capacity of agricultural system and the functioning of the agricultural innovation support system. The application of RAAIS to analyse parasitic weed problems in the rice sector, conducted in Tanzania and Benin, demonstrates the potential of the diagnostic tool and provides recommendations for its further development and use.

Abstract Brown streak virus disease is the most important biotic constraint to cassava production in the coastal areas of southern Tanzania. Symptoms include foliar chlorosis and sometimes stem lesions. The disease also affects the tuberous roots which develop a yellow/brown, dry, corky necrosis within the starch‐bearing tissues, sometimes accompanied by pitting and distortion, that is visible externally. The foliar symptoms of the disease often do not greatly affect plant growth, although the most sensitive cultivars may be stunted and defoliated. The main impact of the disease on the crop is by causing root necrosis. Field experiments were conducted at two sites in Tanzania to determine the effect of the disease on yield and quality of the roots. Cassava brown streak disease (CBSD) decreased root weight and patches of root necrosis made roots unmarketable, although the unaffected parts might still have been suitable for home consumption. The disease therefore has two effects, one on total root yield and one on root quality, which affects marketability. The field trials showed that CBSD can decrease root weight in the most sensitive cultivars by up to 70%. The length of time between the appearance of foliar symptoms and the development of root necrosis is a varietal characteristic. In the most susceptible cultivars, root necrosis may appear within 6 months of planting cuttings derived from symptomatic mother plants. A local cultivar known as cv. Nachinyaya exhibited a form of tolerance to CBSD in which foliar symptoms appeared but the development of root necrosis was delayed allowing the full yield potential to be realized.

SUMMARY Sweetpotato (Ipomoea batatas) is a widely grown food crop, in which the most important diseases are caused by viruses. Genetic variability of three widely distributed sweetpotato viruses was analysed using data from 46 isolates of Sweet potato feathery mottle virus (SPFMV), 16 isolates of Sweet potato mild mottle virus (SPMMV) and 25 isolates of Sweet potato chlorotic stunt virus (SPCSV), of which 19, seven and six isolates, respectively, are newly characterized. Division of SPFMV into four genetic groups (strains) according to phylogenetic analysis of coat protein (CP) encoding sequences revealed that strain EA contained the East African isolates of SPFMV but none from elsewhere. In contrast, strain RC contained ten isolates from Australia, Africa, Asia and North America. Strain O contained six heterogeneous isolates from Africa, Asia and South America. The seven strain C isolates from Australia, Africa, Asia, and North and South America formed a group that was genetically distant from the other SPFMV strains. SPMMV isolates showed a high level of variability with no discrete strain groupings. SPCSV isolates from East Africa were phylogenetically distant to SPCSV isolates from elsewhere. Only from East Africa were adequate data available for different isolates of the three viruses to estimate the genetic variability of their local populations. The implications of the current sequence information and the need for more such information from most sweetpotato-growing regions of the world are discussed in relation to virus diagnostics and breeding for virus resistance.

Bemisia tabaci whitefly species are some of the world's most devastating agricultural pests and plant-virus disease vectors. Elucidation of the phylogenetic relationships in the group is the basis for understanding their evolution, biogeography, gene-functions and development of novel control technologies. We report here the discovery of five new Sub-Saharan Africa (SSA) B. tabaci putative species, using the partial mitochondrial cytochrome oxidase 1 gene: SSA9, SSA10, SSA11, SSA12 and SSA13. Two of them, SSA10 and SSA11 clustered with the New World species and shared 84.8‒86.5% sequence identities. SSA10 and SSA11 provide new evidence for a close evolutionary link between the Old and New World species. Re-analysis of the evolutionary history of B. tabaci species group indicates that the new African species (SSA10 and SSA11) diverged from the New World clade c. 25 million years ago. The new putative species enable us to: (i) re-evaluate current models of B. tabaci evolution, (ii) recognise increased diversity within this cryptic species group and (iii) re-estimate divergence dates in evolutionary time.

Abstract A rather unique panel tracking more than 3,300 individuals from households in rural Kagera, Tanzania, during 1991/1994–2010 shows that about one out of two individuals/households who exited poverty did so by transitioning out of agriculture into the rural nonfarm economy or secondary towns. Only one out of seven exited poverty by migrating to the big cities, even though those moving to the city experienced on average faster consumption growth. Further analysis of a much larger cross‐country panel of 51 developing countries cannot reject that rural diversification and secondary town development lead to more inclusive growth patterns than metropolitization. Indications are that this follows because more of the poor find their way to the rural nonfarm economy and secondary towns, than to distant cities. The development discourse would benefit from shifting beyond the rural–urban dichotomy and focusing more instead on how best to urbanize and develop its rural nonfarm economy and secondary towns.

The complete positive-sense single-stranded RNA genome of Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae) was found to consist of 9,069 nucleotides and predicted to produce a polyprotein of 2,902 amino acids. It was lacking helper-component proteinase but contained a single P1 serine proteinase that strongly suppressed RNA silencing. Besides the exceptional structure of the 5'-proximal part of the genome, CBSV also contained a Maf/HAM1-like sequence (678 nucleotides, 226 amino acids) recombined between the replicase and coat protein domains in the 3'-proximal part of the genome, which is highly conserved in Potyviridae. HAM1 was flanked by consensus proteolytic cleavage sites for ipomovirus NIaPro cysteine proteinase. Homology of CBSV HAM1 with cellular Maf/HAM1 pyrophosphatases suggests that it may intercept noncanonical nucleoside triphosphates to reduce mutagenesis of viral RNA.

On-farm experiments were conducted in farmers’ fields at 12 different sites in the 2 districts of Moshi and Rombo in northern Tanzania during the 2000–01 cropping season to study the effects of (brady)rhizobial inoculation in combination with P supply on growth and grain yields of soybean and common bean, and to assess the economic returns of these different technologies to farmers. A low level of N was included as an indicator of endogenous soil N status. The treatments included (brady)rhizobial inoculation, N fertilisation (30 kg N/ha as urea), P application [26 kg P/ha as triple super phosphate (TSP)], (brady)rhizobial inoculation + P fertilisation (26 kg/ha as TSP) and unfertilised uninoculated control. The study was conducted as a randomised complete block design with each of the 12 farmers’ fields as a replicate. At harvest, plant growth of soybean and common bean was significantly (P=0.05) greater with (brady)rhizobial inoculation compared with N and P supply or uninoculated control in the 2 districts. Relative to uninoculated unfertilised plots, grain yields of common bean were markedly (P=0.05) increased by 60–78% from inoculation alone, and 82–95% from inoculation + 26 kg P/ha; with soybean there was 127–139% increase in grain yield from inoculation alone, and 207–231% from inoculation + P. Thus, the combined application of bacterial inoculants and P fertiliser to field plants of soybean and common bean significantly (P=0.05) increased biomass production and grain yield compared with the single use of N and P or (brady)rhizobial strains. From economic analysis, the increase in grain yield with inoculation translated into a significantly (P=0.05) higher marginal rate of return and dollar profit for soybean and common bean farmers in northern Tanzania. With common bean, there was a 66 and 92% increase, respectively, in dollar profit with inoculation at Moshi and Rombo districts respectively relative to control; these profit margins rose to 84 and 102% with provision of supplemental P (26 kg P/ha). With soybean, however, the increase in profit with inoculation was much larger, about 140 and 153% at Rombo and Moshi, respectively, and these rose to 224 and 250% with P supply.

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a pest species complex that causes widespread damage to cassava, a staple food crop for millions of households in East Africa. Species in the complex cause direct feeding damage to cassava and are the vectors of multiple plant viruses. Whilst significant work has gone into developing virus-resistant cassava cultivars, there has been little research effort aimed at understanding the ecology of these insect vectors. Here we assess critically the knowledge base relating to factors that may lead to high population densities of sub-Saharan African (SSA) B. tabaci species in cassava production landscapes of East Africa. We focus first on empirical studies that have examined biotic or abiotic factors that may lead to high populations. We then identify knowledge gaps that need to be filled to deliver sustainable management solutions. We found that whilst many hypotheses have been put forward to explain the increases in abundance witnessed since the early 1990s, there are little published data and these tend to have been collected in a piecemeal manner. The most critical knowledge gaps identified were: (i) understanding how cassava cultivars and alternative host plants impact population dynamics and natural enemies; (ii) the impact of natural enemies in terms of reducing the frequency of outbreaks and (iii) the use and management of insecticides to delay the development of resistance. In addition, there are several fundamental methodologies that need to be developed and deployed in East Africa to address some of the more challenging knowledge gaps.

Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production.

In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall-degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into nucleotide base called data locally in real-time, removing the need for high-specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and setup. To evaluate and validate capability of the system for unbiased pathogen identification by real-time sequencing in a farmer's field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint to its production. Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus-resistant or replacement planting. This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.

Cassava brown streak disease (CBSD) has occurred in the Indian Ocean coastal lowlands and some areas of Malawi in East Africa for decades, and makes the storage roots of cassava unsuitable for consumption. CBSD is associated with Cassava brown streak virus (CBSV) and the recently described Ugandan cassava brown streak virus (UCBSV) [picorna-like (+)ssRNA viruses; genus Ipomovirus; family Potyviridae]. This study reports the first comprehensive analysis on how evolution is shaping the populations of CBSV and UCBSV. The complete genomes of CBSV and UCBSV (four and eight isolates, respectively) were 69.0-70.3 and 73.6-74.4% identical at the nucleotide and polyprotein amino acid sequence levels, respectively. They contained predictable sites of homologous recombination, mostly in the 3'-proximal part (NIb-HAM1h-CP-3'-UTR) of the genome, but no evidence of recombination between the two viruses was found. The CP-encoding sequences of 22 and 45 isolates of CBSV and UCBSV analysed, respectively, were mainly under purifying selection; however, several sites in the central part of CBSV CP were subjected to positive selection. HAM1h (putative nucleoside triphosphate pyrophosphatase) was the least similar protein between CBSV and UCBSV (aa identity approx. 55%). Both termini of HAM1h contained sites under positive selection in UCBSV. The data imply an on-going but somewhat different evolution of CBSV and UCBSV, which is congruent with the recent widespread outbreak of UCBSV in cassava crops in the highland areas (>1000 m above sea level) of East Africa where CBSD has not caused significant problems in the past.

Sustainable intensification (SI) is promoted as a rural development paradigm for sub-Saharan Africa. Achieving SI requires smallholder farmers to have access to information that is context-specific, increases their decision-making capacities, and adapts to changing environments. Current extension services often struggle to address these needs. New mobile phone-based services can help. In order to enhance the public extension service in Tanzania, we created a digital service that addresses smallholder farmers’ different information needs for implementing SI. Using a co-design methodology – User-Centered Design – we elicited feedback from farmers and extension agents in Tanzania to create a new digital information service, called Ushauri. This automated hotline gives farmers access to a set of pre-recorded messages. Additionally, farmers can ask questions in a mailbox. Extension agents then listen to these questions through an online platform, where they record and send replies via automated push-calls. A test with 97 farmers in Tanzania showed that farmers actively engaged with the service to access agricultural advice. Extension agents were able to answer questions with reduced workload compared to conventional communication channels. This study illustrates how User-Centered Design can be used to develop information services for complex and resource-restricted smallholder farming contexts.

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity.