Cassava mosaic disease (CMD) causes devastating losses to cassava on the sub-Saharan African continent. CMD is caused by several distinct geminivirus species, including ACMV, EACMV and SACMV, which are transmitted by the whitefly Bemisia tabaci.  Cassava brown streak disease (CBSD) has also recently escalated and is now also a major problem in cassava in eastern and southern African countries, but to date has not been reported in SA. CBSD is caused by two distinct ipomoviruses.

Cassava research in our laboratory focuses on five main areas:

1.       Development of virus resistance to CMD

This project is the genetic engineering of virus resistance into cassava using RNA silencing as the induced mechanism. Different hairpin constructs have been made and transformed into cassava, and we are testing these for efficacy against SACMV, EACMV and ACMV.

2.       Characterization of cassava geminivirus and whitefly diversity

This project involves both discovery and molecular characterization of new and existing geminiviruses in cassava in South Africa and Mozambique.

3.       Sub-viral agents associated with geminiviruses

Several sub-viral agents have been associated with geminiviruses, and these are known to modify disease. Amongst these are beta- and alpha-satellites, and defective interfering DNAs.  Our laboratory is also looking at discovery, characterization and function of these agents in infected cassava .

4.       Functional genomics of geminivirus-cassava host interactions

This project involves next-generation sequencing and functional genomics techniques to examine global interactions between South African cassava mosaic virus (SACMV) and host plants (natural host cassava as well as experimental hosts, Arabidopsis and Nicotiana benthamiana).   Transcriptome studies provide information on potential genes involved in susceptibility and resistance in cassava and model hosts, while small RNAs (miRNA and siRNA) data provides clues as to epigenetic mechanisms involved in host responses to SACMV infection.  Resuts from this can be used in future to devise strategies for developing natural resistance.

5.       Cassava brown streak disease

I am involved with collaborators and PG students outside of SA as CBSD does not occur in SA.  Many of these projects are funded by Bill Gates Foundation and I collaborate with MARI in Tanzania, and Danforth Plant Center in the US.  I have four PhD students working on aspects of virus diversity; virus evolution and virus resistance (transgenic cassava) in Tanzania, Malawi, Uganda and Mozambique.

Cassava is an important root crop in unfavourable environments in poor areas of developing countries. As cassava is often cultivated in dry areas, research towards improvement of drought tolerance in cassava is needed. In order to accelerate the advance of genetic improvement of cassava, genomic resources must be made available to the community. A genome sequencing project for cassava has already been initiated at the U.S. D.O.E. Joint Genome Institute (JGI) in Maryland, USA. A partially inbred cultivar generated at CIAT has been selected for genomic sequencing to avoid the problem of heterozygosity.

The CGIAR Generation Challenge Programme has provided funding for a project aimed at developing a panel of single nucleotide polymorphism (SNP) markers on a genome-wide basis to localize favourable alleles in existing mapping populations, generated from contrasting drought tolerance genotypes. For this purpose, a bacterial artificial chromosome (BAC) library from the same genotype being sequenced at JGI is being fingerprinted. A set of minimally overlapping clones or minimal tiling path (MTP) will be selected and the ends of all BAC clones in the MTP will be sequenced for SNP discovery.

In the mean time, SSR markers in the parents of the mapping populations are to be tested to estimate the level of polymorphism. The genome-wide SNP marker set that this project will deliver will allow identification of quantitative trait loci (QTL) associated with drought tolerance by high-throughput genotyping of validated SNPs.

As cassava is a close relative of castor bean, whose genome has been sequenced, once the genome sequence and fingerprint map of cassava are released, it will be possible to conduct comparative analyses within the Euphorbiaceae family. This kind of information will facilitate the elucidation of the evolutionary history and domestication of cassava.

Furthermore, the availability of a fingerprint map and the genome sequence for one genotype of cassava will open the door for genome-wide diversity studies using other cultivated or wild cassava varieties in comparison with the reference genome. Next-generation sequencing technologies will make it affordable to re-sequence different cassava genomes and take full advantage of the broad genetic diversity of cassava for breeding and crop improvement.

This international project is being led by Dr Pablo Rabinowicz of the University of Maryland, involves the University of California, as well as two ACGT partner institutions, the University of Pretoria (Prof Zander Myburg) and University of the Witwatersrand (Prof Chrissie Rey). South African involvement was facilitated through the ACGT’s standing as a consortium member of the Generation Challenge Programme.