BackgroundProduction of cassava (Manihot esculenta Crantz), a food security crop in sub-Saharan Africa, is threatened by the spread of cassava brown streak disease (CBSD) which manifests in part as a corky necrosis in the storage root. It is caused by either of two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), resulting in up to 100% yield loss in susceptible varieties.MethodsThis study characterized the response of 11 cassava varieties according to CBSD symptom expression and relative CBSV and UCBSV load in a field trial in Uganda. Relative viral load was measured using quantitative RT-PCR using COX as an internal housekeeping gene.ResultsA complex situation was revealed with indications of different resistance mechanisms that restrict virus accumulation and symptom expression. Four response categories were defined. Symptom expression was not always positively correlated with virus load. Substantially different levels of the virus species were found in many genotypes suggesting either resistance to one virus species or the other, or some form of interaction, antagonism or competition between virus species.ConclusionsA substantial amount of research still needs to be undertaken to fully understand the mechanism and genetic bases of resistance. This information will be useful in informing breeding strategies and restricting virus spread.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-014-0216-x) contains supplementary material, which is available to authorized users.

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

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Cassava varieties resistant to cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are needed for the food and income security of the rural poor in eastern and southern Africa (ESA). The International Institute of Tropical Agriculture led five national cassava breeding programs (Malawi, Mozambique, Kenya, Tanzania and Uganda) in virus-cleaning and exchanging elite cassava germplasm resistant to both diseases. This paper documents the experiences and lessons learned from the process. Thirty-one clones (25 elite, two standard and four national) were submitted by the five breeding programs to the Natural Resources Institute and Kenya Plant Health Inspectorate Services for virus cleaning and indexing. Subsequently, ca 75 invitro virus-indexed plantlets per clone were sent to Genetic Technologies International Limited (GTIL), a private tissue culture (TC) lab in Kenya, and micro-propagated to produce ≥1500 plantlets. After fulfilling all the formal procedures of germplasm exchange between countries ≥300 plantlets per clone were sent to each partner country. National check clones susceptible to CMD/CBSD were sent only to their countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transferred to clean isolated sites for field multiplication. All the clones were cleaned of the viruses, except Tomo. The cleaning process was slow for F19-NL, NASE1, and Kibandameno and TC micro-propagation at GTIL was less efficient for Pwani, Tajirika, NASE1, and Okhumelela than for the other clones. Difficulties in cleaning recalcitrant clones affected the timeline for establishing the multi-site evaluation trials in target countries. The initiative is the one of the kind to successfully clean and exchange elite germplasm as a joint action to combat CBSD in ESA. Adequate preparation in terms of infrastructure and personnel are critical to successfully receiving and adapting the indexed in-vitro plants as new germplasm.

Cassava (Manihot esculenta Crantz) is a major source of dietary carbohydrates for >700 million people globally. However, its long breeding cycle has slowed the rate of genetic gain for target traits. This study aimed to asses genetic variation, the level of inbreeding, and trait correlations in genomic selection breeding cycles. We used phenotypic and genotypic data from the National Crops Resources Research Institute (NaCRRI) foundation population (Cycle 0, C0) and the progeny (Cycle 1, C1) derived from crosses of 100 selected C0 clones as progenitors, both to evaluate and optimize genomic selection. The highest broad‐sense heritability (H2 = 0.95) and narrow‐sense heritability (h2 = 0.81) were recorded for cassava mosaic disease severity and the lowest for root weight per plot (H2 = 0.06 and h2 = 0.00). We observed the highest genetic correlation (rg= 0.80) between cassava brown streak disease root incidence measured at seedling and clonal stages of evaluation, suggesting the usefulness of seedling data in predicting clonal performance for cassava brown streak root necrosis. Similarly, high genetic correlations were observed between cassava brown streak disease severity (rg= 0.83) scored at 3 and 6 mo after planting (MAP) and cassava mosaic disease, scored at 3 and 6 MAP (rg= 0.95), indicating that data obtained on these two diseases at 6 MAP would suffice. Population differentiation between C0 and C1 was not well defined, implying that the 100 selected progenitors of C1 captured the diversity in the C0. Overall, genetic gain for most traits were observed from C0 to C1.

Cassava brown streak disease (CBSD) is the most devastating disease of cassava in southern, eastern and cntral Africa, and can cause up to 100% yield loss. Limited progress has been made in breeding for host plant resistance due to limited knowledge on the resistance variability to the disease. Reaction of promising cassava genotypes to CBSD in multi-environments are also unknown. Therefore, this study intended to: (1) Identify additional sources of resistance to CBSD; (2) Determine the stability of resistance to CBSD, and (3) mega-environments for screening resistance to CBSD. Field evaluation of 19 genotypes was conducted in RCBD with three replications at three agro-ecologies of Uganda for two cropping cycles. Additive Main Effects and Multiplicative Interaction (AMMI) and (GGE) biplot models were used to analyze genotype-environment interactions. Based on mean field reaction, the six best genotypes identified for resistance to CBSD were: TZ/06/140, TMS30572, TZ /06/130, N3/66/1, N3/58/1 with N3/104/3 and N3/66/1 being the most stable. While N3/66/1, N3/58/1 and N3/104/3, Mzungu and Kigoma Red were reported to be putative new sources of resistance to CBSD in Uganda. Genotypes (G), Environments (E), and GxE interactions were all significant, with no genotype exhibiting complete resistance. The significant result for GxE interaction to CBSD indicates the need for multi-environment screening and is suggestive of quantitative nature of CBSD resistance.

This study aimed to identify cassava quality attributes preferred by users along the food chain, in order to provide breeders with criteria for prioritization. Survey, and consumer-testing studies were conducted within Apac and Luwero districts in Uganda. Additionally, sensory evaluation by trained panelists was conducted to determine descriptors for assessing quality of boiled roots. Results revealed softness of boiled roots and in-ground storability as key attributes influencing varietal preference besides high yield, non-bitter roots, disease resistance, early maturity and drought resistance. For some attributes like in-ground storability, preference differed significantly between locations, and showed differentiation by gender. Local varieties were found to be superior in quality attributes. From sensory evaluation, 21 descriptors associated with appearance, texture, taste and aroma of boiled roots were determined. Findings from this study are vital for breeders to adopt gender-responsive approaches in order to develop varieties that meet the needs and preferences of end-users.