Genomics of a maize disease accelerated through collaborations in the USA and Belgium

From left to right: Karen Utrecht (Africa Programme Manager: Borlaug and Scientific Exchange Programs, USDA), Prof Berger, Dr Burt Bluhm (University of Arkansas)

Genomics Research Institute member Prof Dave Berger from the Plant Science Department of the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa was awarded a 2013 US Department of Agriculture (USDA) Norman E Borlaug International Agricultural Science and Technology Fellowship.

These fellowships were established in honour of Norman Borlaug, recipient of the Nobel Peace Prize in 1972, for his role in breeding improved varieties of wheat, which led to the Green Revolution. The fellowships provide opportunities for agricultural researchers around the world to work with US scientists for periods up to three months.

Prof Berger spent three months of his sabbatical, hosted by Dr Burt Bluhm, in the Department of Plant Pathology at the University of Arkansas, Fayetteville. Dr Bluhm is a leading international researcher in the genetics of fungal pathogens of crops. The topic that Prof Berger researched during his visit was grey leaf spot disease of maize, a limiting factor in maize production globally and also in sub-Saharan Africa. The project that Prof Berger’s Molecular Plant-Pathogen Interactions research group focused on was the fungus Cercospora zeina, the causal agent of this disease in Africa. Genome sequencing of an African isolate of the fungus is underway, partially funded by the Genomics Research Institute at UP with additional funds leveraged from an NRF Bio-informatics and Functional Genomics grant. Prof Berger visited the Genomics Facility at Purdue University, USA, as well as the Yale Centre for Genome Analysis, New Haven, Connecticut which has a state-of-the-art PacBio single molecule sequencer. This technology has the advantage over current next-generation sequencing methods of direct sequencing of the fungal DNA and produces longer DNA sequence runs.

An outcome of the visit was the resolution to improve the C.zeina genome sequence using PacBio. Genome assembly and annotation are being carried out in collaboration with Prof Yves van der Peer, Professor in Bio-informatics and Genome Biology, Group Leader of Bio-informatics and Systems Biology, Ghent University, Belgium who also holds a joint appointment at the University of Pretoria. Prof Van der Peer hosted UP PhD student Nicky Olivier during 2013, and the C. zeina genome assembly was subsequently improved. This visit was funded by the NRF, the Department of Plant Science, the Faculty of Natural and Agricultural Sciences, the GRI and the NRF. The Ghent group will be visiting UP in April 2014, and a follow-up visit by Prof Berger to Ghent is planned for later in the year.

Further outcomes of the USDA Borlaug Fellowship are the planned visit of a student from Dr Bluhm’s laboratory to UP in May 2014 and a USDA-funded follow-up visit by Dr Bluhm to Prof Berger’s laboratory in mid-2014. This collaborative research, in which Dr Bridget Crampton of the Department of Plant Science and FABI is also involved, investigates the pathogenicity mechanisms and population genetics of C. zeina and has the long-term aim of finding weaknesses in the armoury of the fungus which can be exploited to develop novel control strategies.

Prof Berger in the Lab at the University of Arkansas
Prof Berger in the Lab at the University of Arkansas








Story by: D. Berger, UP News, University of Pretoria