The Molecular Plant-Pathogen Interactions (MPPI) Group is located in the Plant Sciences Complex at the University of Pretoria. The group is part of the Department of Plant & Soil Sciences and the Forestry and Agricultural Biotechnology Institute (FABI) and is headed by Prof Dave Berger. Research focuses on the molecular basis of plant-pathogen interactions and the mechanisms of plant defence using a range of approaches from whole plant phenotyping to functional genomics, as well as developing bioinformatics tools. The MPPI group has particular experience in transcriptomics using microarrays and RNAseq.

The main research projects in the MPPI lab involves maize, the staple food of sub-Saharan Africa. We are interested in understanding mechanisms underlying quantitative disease resistance in maize to grey leaf spot (GLS) disease. GLS is an important constraint to maize production in many maize growing regions of the world, particularly in Africa.

We collaborate with maize breeders and field pathologists to understand the disease in its Agricultural context, which gives postgraduate students the opportunity to temporarily "escape" from the lab. Apart from glasshouse bioassays, the MPPI group is employing genomics, such as high density molecular markers, and transcriptomics to study maize defence mechanisms against GLS, with the long term aim to develop tools for maize improvement, such as marker assisted selection.

The MPPI group, together with the CFPRG in FABI, is also elucidating pathogenicity strategies employed by Cercospora zeina, the causal agent of GLS. We are taking a comparative genomics approach, through whole genome sequencing of C. zeina isolates. The research is followed up using functional genomics tools developed in the CFPRG. In addition, we are carrying out genetic diversity studies of C.zeina.

The MPPI group is hosted in the Plant Sciences Complex with excellent laboratories for plant biotechnology research, and access to phytotron and glasshouse facilities. Several bioinformatics software packages and databases have been developed by the group in collaboration with the Centre for Bioinformatics and Computational Biology at the University of Pretoria.

New Publications

Abkallo HM, Arbuthnot P, Auer TO, Berger DK, Burger J, Chakauya E, Concordet J-P, Diabate A, Di Donato V, Groenewald J-H, Guindo A, Koekemoer LL, Nazare F, Nolan T, Okumu F, Orefuwa E, Paemka L, Prieto-Godino L, Runo S, Sadler M, Tesfaye K, Tripathi L, Wondji C. (2024) Making genome editing a success story in Africa. Nature Biotechnology :1-4. https://rdcu.be/dBJUa
Omondi DO, Dida MM, Berger DK, Beyene Y, Nsibo DL, Juma C, Mahabaleswara SL, Gowda M. (2023) Combination of Linkage and Association Mapping with Genomic Prediction to Infer QTL Regions Associated with Gray Leaf Spot and Northern Corn Leaf Blight Resistance in Tropical Maize. Frontiers in Genetics 14:1-16. 10.3389/fgene.2023.1282673
Welgemoed T, Duong TA, Barnes I, Stukenbrock EH, Berger DK. (2023) Population genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems. G3 Genes|Genomes|Genetics 10.1093/g3journal/jkad214
Wingfield BD, Berger DK, Coetzee MPA, Duong TA, Martin A, Pham NQ, Van den Berg N, Wilken PM, Arun-Chinnappa KS, Barnes I, Buthelezi S, Dahanayaka BA, Durán A, Engelbrecht J, Feurtey A, Fourie A, Fourie G, Hartley J, Kabwe ENK, Maphosa M, Narh Mensah DL, Nsibo DL, Potgieter L, Poudel B, Stukenbrock EH, Thomas C, Vaghefi N, Welgemoed T, Wingfield MJ. (2022) IMA genome‑F17 Draft genome sequences of an Armillaria species from Zimbabwe, Ceratocystis colombiana, Elsinoë necatrix, Rosellinia necatrix, two genomes of Sclerotinia minor, short‑read genome assemblies and annotations of four Pyrenophora teres isolates from barley grass, and a long-read genome assembly of Cercospora zeina. 13:19. 10.1186/s43008-022-00104-3
Craze HA, Pillay N, Joubert F, Berger DK. (2022) Deep Learning Diagnostics of Gray Leaf Spot in Maize under Mixed Disease Field Conditions. Plants 11(1942):1-17. https://bit.ly/3vg484g
Luo G-F, Podolyan A, Kidanemariam D, Pilotti C, Houliston G, Sukal AC. (2022) A review of viruses infecting Yam (Dioscorea spp.). Viruses 14(662) 10.3390/v14040662
Nsibo DL, Barnes I, Omondi DO, Dida MM, Berger DK. (2021) Population genetic structure and migration patterns of the maize pathogenic fungus, Cercospora zeina in East and Southern Africa. Fungal Genetics and Biology 149(103527) 10.1016/j.fgb.2021.103527
Pillay N, Gerber M, Holan K, Whitham SA, Berger DK. 2021. Quantifying the Severity of Common Rust in Maize Using Mask R-CNN. In: Artificial Intelligence and Soft Computing. ICAISC 2021. Lecture Notes in Artificial Intelligence, vol 12854. Rutkowski L, Scherer R, Korytkowski M, Pedrycz W, Tadeusiewicz R, Zurada J. (eds). Springer, Cham., pp 202-213.
Aveling TAS, De Ridder K, Olivier NA, Berger DK. (2020) Seasonal variation in mycoflora associated with asymptomatic maize grain from small-holder farms in two provinces of South Africa. Journal of Agriculture and Rural Development in the Tropics and Subtropics (JARTS) 121(2):265-275. 10.17170/kobra-202011262275 PDF
Berger DK, Mokgobu T, De Ridder K, Christie N, Aveling TAS. (2020) Benefits of maize resistance breeding and chemical control against northern leaf blight in smallholder farms in South Africa. South African Journal of Science 12(11) 10.17159/sajs.2020/8286