Disparity between leaf and root symptoms and crop losses associated with cassava brown streak disease in four countries in eastern Africa

Cassava brown streak disease is endemic to the coastal regions of East Africa, and from around 2004, the disease resurged and became epidemic in the Great Lakes Region, where it continues to spread. In both these areas, cassava brown streak disease (CBSD) leaf symptoms occur at high incidences. However, it is the associated symptom of root rot (necrosis) in the starch-bearing tissues that renders the root unfit for human consumption. Because the extent of root necrosis is not known until the crop is harvested and surveys require destructive sampling, root symptoms are much less frequently assessed than are the above-ground symptoms on the leaves and stems. Surveys were undertaken in selected villages in Tanzania, Kenya, Uganda and Malawi to assess the incidence of CBSD leaf symptoms and the incidence and severity of root symptoms, to estimate the impact of the disease on household food security and on cassava processing. CBSD leaf symptoms were recorded at high incidences (40–90% in individual fields) in all fields visited throughout East Africa, but root necrosis incidence was lower than would be expected from the high incidence of leaf symptoms. Severe root necrosis at high incidence was found only on a few varieties, usually grown to a limited extent. It appears that varieties that are prone to root necrosis are being abandoned in favour of those with a lower propensity to develop root necrosis after infection by the virus

High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.Bill and Melinda Gates Foundation (BMGF) Grant OPPGD1493. University of Arizona. CGIAR Research Program on Roots, Tubers, and Bananas. Next Generation Cassava Breeding grant OPP1048542 from BMGF and the United Kingdom Department for International Development. BMGF grant OPPGD1016 to IITA. National Institutes of Health S10 Instrumentation Grants S10RR029668 and S10RR027303.http://www.g3journal.orghb201

The process and lessons of exchanging and managing in-vitro elite germplasm to combat CBSD and CMD in Eastern and Southern Africa

Varieties with resistance to both cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) can reverse food and income security threats affecting the rural poor in Eastern and Southern Africa. The International Institute of Tropical Agriculture is leading a partnership of five national (Malawi, Mozambique, Kenya, Tanzania and Uganda) cassava breeding programs to exchange the most elite germplasm resistant to both CMD and CBSD. This poster documents the process and the key learning lessons. Twenty to 25 stem cuttings of 31 clones comprising of 25 elite clones (5 per country), two standard checks (Kibandameno from Kenya and Albert from Tanzania), and four national checks (Kiroba and Mkombozi from Tanzania, Mbundumali from Malawi, and Tomo from Mozambique) were cleaned and indexed for cassava viruses at both the Natural Resources Institute in the United Kingdom and Kenya Plant Health Inspectorate Services, in Kenya. About 75 in-vitro plantlets per clone were sent to Genetic Technologies International Limited, a private tissue culture lab in Kenya, and micro-propagated to ≥1500 plantlets. Formal procedures of material transfer between countries including agreements, import permission and phytosanitary certification were all ensured for germplasm exchange. At least 300 plantlets of each elite and standard check clones were sent to all partner countries, while the national checks were only sent to their respective countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transplanted for field multiplication as a basis for multi-site testing. Except for Tomo, a susceptible clone, all the clones were cleaned of the viruses. However, there was varied response to the cleaning process between clones, e.g. FN-19NL, NASE1 and Kibandameno responded slowly. Also, clones responded differently to micro-propagation protocols at GTIL, e.g. Pwani, Tajirika, NASE1, TME204 and Okhumelela responded slowly. Materials are currently being bulked at low disease pressure field sites in preparation for planting at 5-8 evaluation sites per country. The process of cleaning, tissue culture mass propagation, exchange and local hardening off/bulking has been successful for the majority of target varieties. Two key lessons derived from the process are that adequate preparations of infrastructure and trained personnel are required to manage the task, and that a small proportion of varieties are recalcitrant to tissue culture propagation

Risk assessment of gene flow from genetically engineered virus resistant cassava to wild relatives in Africa:an expert panel report

Published online: 14 December 2015The probability and consequences of gene flow to wild relatives is typically considered in the environmental risk assessment of genetically engineered crops. This is a report from a discussion by a group of experts who used a problem formulation approach to consider existing information for risk assessment of gene flow from cassava (Manihot esculenta) genetically engineered for virus resistance to the ‘wild’ (naturalized) relative M. glaziovii in East Africa. Two environmental harms were considered in this case: (1) loss of genetic diversity in the germplasm pool, and (2) loss of valued species, ecosystem resources, or crop yield and quality due to weediness or invasiveness of wild relatives. Based on existing information, it was concluded that gene flow will occur, but it is not likely that this will reduce the genetic diversity in the germplasm pool. There is little existing information about the impact of the virus in natural populations that could be used to inform a prediction about whether virus resistance would lead to an increase in reproduction or survival, hence abundance of M. glaziovii. However, an increase in the abundance of M. glaziovii should be manageable, and would not necessarily lead to the identified environmental harms

Cut, Root, and Grow: Simplifying Cassava Propagation to Scale

Cassava (Manihot esculenta Crantz) is an essential crop with increasing importance for food supply and as raw material for industrial processing. The crop is vegetatively propagated through stem cuttings taken at the end of the growing cycle and its low multiplication rate and the high cost of stem transportation are detrimental to the increasing demand for high-quality cassava planting materials. Rapid multiplication of vegetative propagules of crops comprises tissue culture (TC) and semi-autotroph hydroponics (SAH) that provide cost-effective propagation of plant materials; however, they contrast the need for specific infrastructure, special media and substrates, and trained personnel. Traditional methods such as TC and SAH have shown promise in efficient plant material propagation. Nonetheless, these techniques necessitate specific infrastructure, specialized media and substrates, as well as trained personnel. Moreover, losses during the intermediate nursery and adaptation stages limit the overall effectiveness of these methods. Building upon an earlier report from Embrapa Brazil, which utilized mature buds from cassava for rapid propagation, we present a modified protocol that simplifies the process for wider adoption. Our method involves excising single nodes with attached leaves from immature (green) cassava stems at 2 months after planting (MAP). These nodes are then germinated in pure water, eliminating the need for specific growth substrates and additional treatments. After the initial phase, the rooted sprouts are transferred into soil within 1–8 weeks. The protocol demonstrates a high turnover rate at minimal costs. Due to its simplicity, cost-effectiveness, and robustness, this method holds significant promise as an efficient means of producing cassava planting materials to meet diverse agricultural needs

Breedbase: a digital ecosystem for modern plant breeding

Modern breeding methods integrate next-generation sequencing (NGS) and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to 1) track breeding materials, 2) store experimental evaluations, 3) record phenotypic measurements using consistent ontologies, 4) store genotypic information, and 5) implement algorithms for analysis, prediction and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/). Originally initiated as Cassavabase (https://cassavabase.org/) with the NextGen Cassava project (https://www.nextgencassava.org/), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web-based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/) and packaged in a Docker image for deployment (https://dockerhub.com/breedbase/). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem