Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease

Cassava (Manihot esculenta) is a major food staple in sub-Saharan Africa, which is severely affected by cassava brown streak disease (CBSD). The aim of this study was to identify resistance for CBSD as well as to understand the mechanism of putative resistance for providing effective control for the disease. Three cassava varieties; Kaleso, Kiroba and Albert were inoculated with cassava brown streak viruses by grafting and also using the natural insect vector the whitefly, Bemisia tabaci. Kaleso expressed mild or no disease symptoms and supported low concentrations of viruses, which is a characteristic of resistant plants. In comparison, Kiroba expressed severe leaf but milder root symptoms, while Albert was susceptible with severe symptoms both on leaves and roots. Real-time PCR was used to estimate virus concentrations in cassava varieties. Virus quantities were higher in Kiroba and Albert compared to Kaleso. The Illumina RNA-sequencing was used to further understand the genetic basis of resistance. More than 700 genes were uniquely overexpressed in Kaleso in response to virus infection compared to Albert. Surprisingly, none of them were similar to known resistant gene orthologs. Some of the overexpressed genes, however, belonged to the hormone signalling pathways and secondary metabolites, both of which are linked to plant resistance. These genes should be further characterised before confirming their role in resistance to CBSD

Extending a system with verified components

The verification of component-based systems can be extremely complicated because it is usually not possible for system developers to pre-check the compatibility of the individual parts before the actual integration takes place. A system cannot be considered correct if its components do not work properly. Unfortunately, all the information on the correctness of the individual components become irrelevant and out-of-date from the moment they are used anywhere but the original environment. The solution to this problem can be based on the idea of building correct programs in which reliability is built-in. In this paper open incremental model checking - addressing the changes to a system rather than re-checking the entire system model including the new extensions - is discussed and compared to traditional modular model checking methods. In our paper we study the practical aspects and the efficiency of using Open Incremental Model Checking by working out a sample system consisting of verified components

A global alliance declaring war on cassava viruses in Africa

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Case studies of Roots, Tubers and Bananas seed systems.

The seed systems of RTB (root, tuber, and banana) crops are unique because they are propagated from vegetative parts of the plant, not from true seed. RTB seed is thus bulkier, more perishable, and more subject to the attacks of pests and diseases than is true seed. Because of this, there is often a gap between potential and real crop yields, which seed interventions seek to narrow. Seed systems are formal or informal networks of people and organizations that produce, plant, and distribute seed. Informal systems may deliver low quality seed, but not always. This book describes 13 RTB seed system interventions, using a framework based on the concepts of seed availability, access, and quality. The 13 case studies included (1) a potato-growers’ association in Ecuador, (2) a hydroponic seed potato in Peru, (3) a yam seed technology in Nigeria, (4) a banana and plantain project in Ghana, (5) a sweetpotato seed project in Tanzania and (6) one in Rwanda, (7) a seed potato system in Kenya, (8) cassava in Nicaragua, (9) seed potato in Malawi, (10) disease-resistant cassava varieties in seven African countries, (11) a tissue culture banana project, (12) an emergency plantain and banana project in East Africa, and (13) a large cassava seed project in six African countries

Molecular diagnostics, genetic diversity and generating infectious clones for cassava brown streak viruses

Cassava brown streak disease (CBSD) threatens cassava production in eastern and southern African countries. Diagnostic protocols currently available for the causal agents of CBSD, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV), were unreliable but were urgently needed. In this study, sampling procedures and diagnostic protocols were developed for accurate and reliable detection of both CBSV and CBSUV. The cetyltrimethylammonium bromide (CTAB) method of RNA extraction was optimized for sample preparation from infected cassava plants and compared with the commercial kit RNeasy (Qiagen) for sensitivity and reproducibility. Results showed that both protocols were reliable but CTAB was more cost-effective and ideal for resource-poor laboratories. Mixed infections of cassava mosaic begomoviruses (CMBs) that cause cassava mosaic disease (CMD), CBSV and CBSUV have become more common with the recent spread of CBSD at mid-altitudes. A multiplex PCR for the simultaneous detection of viruses that cause both diseases, the first of its kind for cassava, was therefore developed to detect CBSV and CBSUV along with the three commonly occurring CMBs (African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and East African cassava mosaic virus-Uganda (EACMVUG) in eastern Africa. Similarly, a duplex PCR was developed for the simultaneous detection of CBSV and CBSUV, both viruses being detected in field-collected samples from Tanzania and Kenya. The genetic diversity of more than 40 CBSD isolates from Kenya, Tanzania, Uganda, and Mozambique was further examined by sequencing the coat protein (CP) gene and partial HAM1 gene sequences. The phylogenetic tree clustered the CBSD isolates into two groups reflecting the two virus species causing CBSD. In this study, various strategies were carried out for generating infectious clones of CBSV; gateway cloning, in vivo and in vitro transcription methods, and amplification of the viral genome in three fragments. Although 3 overlapping CBSV fragments were successfully cloned, the presence of an unexpected mutation at one of the cloning sites unfortunately did not allow reassembling of the fragments to construct the full-length cDNA