National Science and Technology Forum (NSTF)

Prof. David Berger

Studying what makes crops sick, and how this happens

The UN has estimated that by 2050 food production will need to increase by 70% to meet demand. With only so much land left, the focus will be on smarter ways to grow crops. This is where Professor Dave Berger steps in, pioneering crop biotechnology research for food security in South Africa.

A professor at the department of plant and soil sciences, University of Pretoria, Berger works in molecular plant pathology. It’s the magical world of genetics. Since the human genome was sequenced in 2003, the technology and applications have expanded exponentially.

To understand his work, we need a little Genetics 101. A genome is an organism’s complete set of DNA. DNA contains the information needed to build the entire organism. Each DNA strand is made of four chemical units. The order of these units determines the meaning of the information encoded in that part of the DNA molecule.

DNA sequencing means determining the exact order of the units. A gene refers to the part of DNA that carries the instructions for making a specific protein or set of proteins. Proteins are the “engines” of the cell that create specific structures, control chemical reactions and carry signals from A to B.

International Year of Pulses

“I work on the genetics of how crops interact with pathogens. For example, understanding what makes one variety of maize more resistant than another,” says Berger. Pathogens are microorganisms that cause disease.

He primarily focuses on finding the genetic master regulators in crops. These master regulators control a process, such as when a plant flowers or when it fights disease. It boils down to finding the regulatory switch in an organism.

Throughout his career, his research has been linked with crop science and food security. This is of particular importance as the UN has declared 2016 the International Year of Pulses. Pulses (dry beans) are a big part of sustainable food production, food security and nutrition.

Working on nitrogen fixation

His post-doctoral research was at the University of California Berkeley, from 1991 to 1993. Prior to Berger’s PhD in 1990 and his post-doctoral research, little was known about the master regulators of nitrogen fixation genes at the molecular and biochemical level.

Nitrogen fixation involves symbiotic bacteria that colonise plant roots, including pulse crops. They capture nitrogen from the atmosphere and convert it into natural fertiliser.

Berger’s PhD and post-doctoral research contributed to several discoveries. These include a nitrogen fixation master regulator from a “gold-mining” bacterium, and the biochemical mechanisms of the master regulator that required DNA to be bent to switch on the nitrogen fixation genes.

Crop disease research at ARC

On return to South Africa in 1993, Berger worked as a senior researcher at the Agricultural Research Council (ARC). In an ARC/CSIR collaboration, he was part of the team involved in biotechnological solutions for Anthracnose disease of the lupin plant, a pulse crop used for animal feed.

The team identified which fungus was causing the disease. A master regulator for an anti-fungal lupin gene was identified and patented as part of this research. However, this was not sufficient to control the disease.

ACGT Microarray Facility

Berger joined the Forestry and Agricultural Biotechnology Institute at the University of Pretoria in 2000 and established the ACGT Microarray Facility. It is one of two such facilities in the country, serving genetic research that covers plant, veterinary and medical applications.

Microarrays are a leap forward in genetic technology. All of the genes from an organism are printed on a microscope slide in a grid pattern by a robot. This means scientists can study all 32 000 maize genes, for example, in a single experiment rather than one at a time.

Microarray research produces millions of data points. This accelerated the new career path of “bioinformatics”, which combines computer science and biology. Berger has co-ordinated many training courses in experimentation and analysis for local scientists, through the facility, and this technology has been taken up in laboratories throughout the country.

The maize disease, grey leaf spot

Currently Berger is looking at grey leaf spot (GLS), a global disease that seriously affects maize production. Maize is our staple diet and GLS can have a devastating effect on maize crops.

The research focuses on finding genetic resistance against the disease in the maize plant. The other research focus is on which genes in the fungus cause the disease. Berger and his team are also looking at the disease impact on commercial and smallholder farmers in SA. Prior to the research, little was known about these areas.

“SA has a dichotomy,” says Berger. “The agricultural landscape consists of large-scale commercial maize farmers with 100 hectares or more, plus access to technology and other services, as well as smallholder farmers with 100 square metres of maize and little access to services.”

The maize GLS project was launched as an interdisciplinary public-private partnership between maize breeders, agricultural extension officers, plant pathologists, geneticists, bioinformaticians, and farmers.

To date, outputs include improved disease-resistant maize lines and identifying the unique QTL for GLS resistance in maize. (The QTL is part of the genome and an early step in identifying and sequencing the actual genes that cause resistance.)

There are also patents on the GLS-resistance DNA markers and maize gene master regulators. The team has developed a novel genetics approach for research into complex traits in crop plants.

DNA markers are signals in DNA. For example, with a DNA test the DNA marker can indicate which maize line is resistant and which is not. These markers are used by companies that breed maize hybrids and the seeds are then sold on to the farmers.

To give some idea of the importance of this work, the maize seed market in SA is estimated at R900-million per year.

To determine the extent of the GLS threat, Berger is also looking at the genetics of fungus. The study with commercial farms has been completed but the smallholder farm study is ongoing.

The research has shown a high diversity of the fungus across SA. “This means a potentially high risk of fungicide resistance in the pathogen and the need for diversified resistance breeding,” says Berger. Other outputs include identifying the fungus that causes GLS in maize in South Africa.

International recognition

Berger has received numerous awards. These include the US department of agriculture’s Norman E Borlaug International Agricultural Science and Technology Fellowship (2013). He has published more than 50 international journals articles and has supervised or co-supervised 42 master’s and PhD students.

“I encourage the youth to go into the plant sciences. It’s an exciting field,” says Berger. He notes that you need to be inquisitive, meticulous, and a team player. He says doing a plant sciences PhD is like doing three years of MasterChef — it’s about working accurately and consistently, coping with the pressure, and producing that perfect result.

 Professor Dave Berger is recognised for his lifetime contribution to SET in crop science and food security in honour of the UN’s 2016 International Year of Pulses. Read more.

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