Prof Dave Berger
Plant and Soil Sciences
|Nkosinathi Sthembiso Ndaba|
- 2019 David Nsibo PhD
- 2019 Miekie Human PhD
- 2020 MPPI students: Corteva mini-symposium at SAPBA
- 2016 NSTF South32 Award
- 2016 NSTF South32 Awards Video
- 2016 Food Security TV interview (English/Afrikaans)
- 2016 International Year of Pulses (NSTF)
- 2016 IS-MPMI congress
- 2017 Fall Armyworm (maize farmers)
- 2017 Future of farming talk
- 2017 Kenya project launch
- 2017 Radio interview (maize diseases) [download podcast]
- 2017 Velushka Swart PhD
- APPS congress (2015)
- Cassava genomics project (2014)
- DSG visits FABI (March 2014)
- DuPont Symposium announcement (2014)
- DuPont Symposium announcement (2015)
- DuPont Symposium on Crop Genomics (2014)
- DuPont Symposium on insect control in crops (2015)
- FABI puts UP on the Mycological World Map
- Five MSc students graduate (2015)
- Fungal transformation workshop (2014)
- Jeanne PhD oral (2015)
- Maize farmers day (2016)
- MPPI hosts visitor student from UC Davis (2015)
- Nanette PhD oral (July 2014)
- New Phytologist Symposium (2015)
- Prof David Collinge visit (2015)
- Regional Plant Biotechnology Forum (2014)
- Small-holder maize farmer workshop (2014)
- Spring graduation (2014)
- Spring graduation (2015)
- Steven Biotech Fundi award
- Steven PhD oral (2014)
- UP with Science (2014)
- USDA Fellowship news (April 2014)
- Waheed PhD oral (2016)
My research aims to gain a better understanding of the molecular dialogue between plants and pathogens with the long term goal of developing sustainable strategies to control crop diseases of relevance in Africa. The MPPI research group is currently focused on understanding the host-pathogen interaction in grey leaf spot disease of maize. We implement a range of approaches from whole plant phenotyping to genomics to investigate this pathosystem.
Prior to joining the University of Pretoria, I completed a PhD in Microbiology at the University of Cape Town, South Africa (1990), where I cloned, sequenced and characterized a key transcriptional regulator involved in nitrogen metabolism of the "gold mining" bacterium, Thiobacillus ferrooxidans. A key part of this study was developing a novel screen that exploited the gene’s regulatory role in gas production of bacteria.
My Postdoctoral stint was spent at the University of California, Berkeley, USA (1991-1993). The host laboratory was at the cutting edge of describing the transcriptional regulation of nitrogen metabolism in bacteria. My research contributed to understanding the biochemistry of DNA bending by integration host factor and phosphorylation-based two-component transcriptional activation.
On return to South Africa, I joined the Plant Biotechnology Group of the Agricultural Research Council, where I developed a research focus on polygalacturonase inhibiting proteins and their role in defence against fungal pathogens (1993 – 2000).
I joined the Plant Science Department at the University of Pretoria as a member of FABI and setup a DNA microarray facility (2000– ), which formed the basis of a gene expression profiling service. This laid the foundation for the genomics and bioinformatics approaches that have been implemented subsequently in the MPPI research programme.
Prof. Dave Berger of the MPPI group presented an invited talk at the recent British Society for Plant Pathology Conference in the UK.
Professor Eva Stukenbrock from the Max Planck Institute for Evolutionary Biology, presented a workshop on Population Genomics at FABI.
FABI hosted the 52nd Congress of the Southern African Society for Plant Pathologists (SASSP) at the Future Africa campus from 1-3 August.
Prof. Dave Berger was interviewed on the topic “Artificial intelligence in crop health monitoring” by PlaasTV / FarmTV, which is a YouTube channel targeted at local farmers.
The MPPI research group hosted a visit by the members of the Fungicide Resistance Action Committee (FRAC) South Africa and Grain SA.
FABI shone at the recent South African Society for Bioinformatics and the South African Genetics Society's first joint hybrid conference.
Two FABIans have been featured in the BSPP's “Forty Faces of Plant Pathology” that forms part of the Society’s 40th anniversary celebrations.
Dennis Omondi spent two research visits in the MPPI lab at FABI and Department of Plant and Soil Sciences during his MSc degree as part of a bilateral NRF Kenya-South Africa project on maize foliar diseases.
Several academics and researchers submitted a letter last week to the Ministers of DALRRD and DHEST asking them to reconsider the new GMO regulations.
Prof. Dave Berger presented in the genome editing session of the recent Science Forum South Africa 2021, where he gave an overview of current research in the field in South Africa.
AI and its role in crop health monitoring was featured in an article written by Prof. Dave Berger for a special edition of the newspaper Business Day.
FABI MSc student Ingrid Marais attended the National Association of Plant Breeders (NAPB) 2020 annual meeting thanks to a South-African Plant Breeders Association (SAPBA) sponsorship.
The 13th South African Plant Breeders Symposium was held at the University of Pretoria’s Future Africa campus from 8-11 March. A special afternoon session was set aside for University of Pretoria students to organise and was sponsored by Corteva™Agriscience.
FABI congratulates Miekie Human, who on 25 November marked the successful completion of her PhD thesis with a prestige seminar.
FABI celebrated the completion of the Institute’s 13th PhD candidate in 2019 with David Nsibo successfully defending his PhD on 21 November.
The biennial Congress on Molecular Plant-Microbe Interactions (MPMI), hosted by the International Society for Molecular Plant-Microbe Interactions took place from 14-18 July in Glasgow, Scotland.
Was this the first ever maize pathology workshop held on the “on the equator”? Possibly! Maseno University in Western Kenya, not far from Lake Victoria, is situated in a hot and humid region. Fungal foliar diseases and pests of maize abound in the region since chemical control is seldom applied and maize production continues all year round.
My Book Chapters
|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.
|Carstens M, Berger DK. 2016. Biotechnology and Crop Disease Resistance in South Africa. In: Biotechnology for Plant Disease Control. Collinge DB. (eds). Wiley, New York and London, pp 16 (Chapter).
My Journal Articles
|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. 13:19.
|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.
|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)
|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.
|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)
|Welgemoed T, Pierneef R, Read DA, Schulze SE, Pietersen G, Berger DK. (2020) Next generation sequencing reveals past and current widespread occurrence of maize yellow mosaic virus in South Africa. European Journal of Plant Pathology 158(1):237-249.
|Human MP, Berger DK, Crampton BG. (2020) Time-course RNAseq reveals Exserohilum turcicum effectors and pathogenicity determinants. Frontiers in Microbiology 11(360)
|Welgemoed T, Pierneef R, Sterck L, Van de Peer Y, Swart V, Scheepers KD, Berger DK. (2020) De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase. Frontiers in Plant Science
|Nsibo DL, Barnes I, Kunene NT, Berger DK. (2019) Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa. Fungal Genetics and Biology 125:36-44.
|Read DA, Featherstone J, Rees DJG, Thompson GD, Roberts R, Flett BC, Mashingaidze K, Berger DK, Welgemoed T, Pietersen G, Schulze SE, Kiula B, Kullaya A, Mbega E. (2019) First report of maize yellow mosaic virus (MaYMV) on maize (Zea mays) in Tanzania. Journal of Plant Pathology 101:203.
|Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG. (2018) Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. Journal of Molecular Evolution 86(3-4):216-239.
|Liversage J, Coetzee MPA, Bluhm BH, Berger DK, Crampton BG. (2018) LOVe across kingdoms: Blue light perception vital for growth and development in plant–fungal interactions. Fungal Biology Reviews 32(2):86-103.
|Wingfield BD, Berger DK, Steenkamp ET, Lim H-J, Duong TA, Bluhm BH, De Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier NA, Lin Y, Van der Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, Van der Nest MA, Van der Merwe NA, Van Wyk S, Wilken PM, Wingfield MJ. (2017) IMA Genome-F 8 Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus 8 (2):385‑396.
|Meyer J, Berger DK, Christensen SA, Murray SL. (2017) RNA-Seq analysis of resistant and susceptible sub-tropical maize lines reveals a role for kauralexins in resistance to grey leaf spot disease, caused by Cercospora zeina. BMC Plant Biology 17:197.
|Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. (2017) A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Scientific Reports 7:9747.
|Swart V, Crampton BG, Ridenour JB, Bluhm BH, Olivier NA, Meyer JJM, Berger DK. (2017) Complementation of CTB7 in the maize pathogen Cercospora zeina overcomes the lack of in vitro cercosporin production. Molecular Plant-Microbe Interactions 30(9):710-724.
|Zwart L, Berger DK, Moleleki LN, Van der Merwe NA, Myburg AA, Naidoo S. (2017) Evidence for salicylic acid signalling and histological changes in the defence response of Eucalyptus grandis to Chrysoporthe austroafricana. Scientific Reports 7:45402.
|Christie N, Myburg AA, Joubert F, Murray SL, Carstens M, Lin Y-C, Meyer J, Crampton BG, Christensen SA, Ntuli JF, Wighard SS, Van de Peer Y, Berger DK. (2017) Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem. The Plant Journal 89(4):746-763.
|Reitmann A, Berger DK, van den Berg N. (2017) Putative pathogenicity genes of Phytophthora cinnamomi identified via RNA-Seq analysis of pre-infection structures. European Journal of Plant Pathology 147(1):211-228.
|Muller MF, Barnes I, Kunene NT, Crampton BG, Bluhm B, Phillips S, Olivier NA, Berger DK. (2016) Cercospora zeina from maize in South Africa exhibits high genetic diversity and lack of regional population differentiation. Phytopathology 106(10):1194-1205.
|Oelofse D, Gazendam I, Veale A, Djami-Tchatchou A, Berger D, Dubery I. (2016) Functional characterization of a defense-related class-III chitinase promoter from Lupinus albus, active in legume and monocot tissues. European Journal of Plant Pathology 146(4):923-936.
|Daru B, Berger DK, Van Wyk AE. (2016) Opportunities for unlocking the potential of genomics for African trees. New Phytologist 210:772-778.
|Meyer FE, Shuey LS, Ramsuchit S, Mamni T, Berger DK, van den Berg N, Myburg AA, Naidoo S. (2016) Dual RNA-sequencing of Eucalyptus nitens during Phytophthora cinnamomi challenge reveals pathogen and host factors influencing compatibility. Frontiers in Plant Science 7:191.
|Meyer J, Murray SL, Berger DK. (2016) Signals that stop the rot: Regulation of secondary metabolite defences in cereals. Physiological and Molecular Plant Pathology 94:156-166.
|Ronishree Magwanda, Lizahn Zwart, Nicolaas A. van der Merwe, Lucy Moleleki, Dave Kenneth Berger, Alexander A. Myburg, Sanushka Naidoo. (2016) Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors. Front. Microbiol.
|Hussey SG, Mizrachi E, Groover A, Berger DK, Myburg AA. (2015) Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. BMC Plant Biology 15:117.
|Mizrachi E, Maloney VJ, Silberbauer J, Hefer CA, Berger DK, Mansfield SD, Myburg AA. (2014) Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. New Phytologist 204(6):1351-1363.
|Berger DK, Carstens M, Korsman JN, Middleton F, Kloppers FJ, Tongoona P, Myburg AA. (2014) Mapping QTL conferring resistance in maize to gray leaf spot disease caused by Cercospora zeina. BMC Genetics 15:60.
|Van der Linden L, Bredenkamp J, Naidoo S, Fouche-Weich J, Denby KJ, Genin S, Marco Y, Berger DK. (2013) Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis. Molecular Plant-Microbe Interactions 26:398-406.
|Naidoo R, Ferreira L, Berger DK, Myburg AA, Naidoo S. (2013) The identification and differential expression of Eucalyptus grandis pathogenesis-related genes in response to salicylic acid and methyl jasmonate. Frontiers in Plant Science 4:43.
|Van Schalkwyk A, Wenzl P, Smit S, Lopez-Cobollo R, Kilian A, Bishop G, Hefer C, Berger D. (2012) Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum X Solanum pennellii introgression lines. Theoretical and Applied Genetics 124:947-956.
|Korsman J, Meisel B, Kloppers F, Crampton B, Berger D. (2012) Quantitative phenotyping of grey leaf spot disease in maize using real-time PCR. European Journal of Plant Pathology 133:461-471.
|Hussey SG, Mizrachi E, Spokevicius AV, Bossinger G, Berger DK. (2011) SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus. BMC Plant Biology 11:173.
|Coetzer N, Myburg AA, Berger DK. (2011) Maize microarray annotation database. Plant Methods 7(31)
|Hussey S, Mizrachi E, Berger D, Myburg AA. (2011) The role of SND2 in the regulation of Arabidopsis fibre secondary cell wall formation. BMC Proceedings 5(7):P114.
|Naidoo S, Fouche-Weich J, Law P, Denby KJ, Marco Y, Berger DK. (2011) A Eucalyptus bacterial wilt isolate from South Africa is pathogenic on Arabidopsis and manipulates host defences. Forest Pathology 41:101-113.
|Coetzer N, Gazendam I, Oelofse D, Berger DK. (2010) SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. Plant Methods 6(10)
|Solomon OL, Berger DK, Myburg AA. (2010) Diurnal and circadian regulation of carbon allocation in developing xylem of Eucalyptus trees. South African Journal of Botany 76:425-439.
|Coetzer N, Gazendam I, Oelofse D, Berger DK. (2010) SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. Plant Methods 6:10.
|Legay G, Marouf E, Berger D, Neuhaus JM, Mauch-Mani B, Slaughter A. (2010) Identification of genes expressed during the compatible interaction of grapevine with Plasmopara viticola through suppression subtractive hybridization (SSH). European Journal of Plant Pathology 129:281-301.
|Solomon OL, Berger DK, Myburg AA. (2010) Diurnal and circadian patterns of gene expression in the developing xylem of Eucalyptus trees. South African Journal of Botany 76:425-439.
|Crampton BG, Hein I, Berger DK. (2009) Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata, in pearl millet (Pennisetum glaucum). Molecular Plant Pathology 10:291-304.
|Meisel B, Korsman J, Kloppers F, Berger DK. (2009) Cercospora zeina is the causal agent of grey leaf spot disease of maize in southern Africa. European Journal of Plant Pathology 124:577-583.
|van den Berg N, Berger DK, Hein I, Birch PRJ, Wingfield MJ, Viljoen A. (2009) Genes up-regulated in tolerant cavendish banana roots in response to Fusarium oxysporum f. sp. cubense infection. Acta Horticulturae 828:273-282.
|Creux NM, Ranik M, Berger DK, Myburg AA. (2008) Comparative analysis of orthologous cellulose synthase promoters from Arabidopsis, Populus and Eucalyptus: evidence of conserved regulatory elements in angiosperms. New Phytologist 179:722-737.
|Law P, Claudel-Renard C, Joubert F, Louw A, Berger D. (2008) MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters. BMC Genomics 9:105.
|Naidoo S, Murray SL, Denby KJ, Berger DK. (2007) Microarray analysis of the Arabidopsis thaliana cir1 (constitutively induced resistance 1) mutant reveals candidate defence response genes against Pseudomonas syringae pv tomato DC3000. South African Journal of Botany 73:412-421.
|van den Berg N, Berger DK, Hein I, Birch PRJ, Wingfield MJ, Viljoen A. (2007) Tolerance in banana to Fusarium wilt is associated with early up-regulation of cell wall-strengthening genes in the roots. Molecular Plant Pathology 8(3):333-341.
|Fouche-Weich J, Berger D, Poussier S, Trigalet-Demery D, Coutinho T. (2006) Molecular identification of some African strains of Ralstonia solanacearum from eucalypt and potato. Journal of General Plant Pathology 72:369-373.
|Oelofse D, Dubery IA, Meyer R, Arendse MS, Gazendam I, Berger DK. (2006) Apple polygalacturonase inhibiting protein1 expressed in transgenic tobacco inhibits polygalacturonases from fungal pathogens of apple and the anthracnose pathogen of lupins. Phytochemistry 67:255-263.
|Lotter HC, Berger DK. (2005) Anthracnose of lupins in South Africa in caused by Colletotrichum lupini var. setosum. Australasian Plant Pathology 34:385-392.
|Naidoo S, Denby KJ, Berger DK. (2005) Microarray experiments: considerations for experimental design. South African Journal of Science 101:347-354.
|Gazendam I, Oelofse D, Berger DK. (2004) High-level expression of apple PGIP1 is not sufficient to protect transgenic potato against Verticillium dahliae. Physiological and Molecular Plant Pathology 65:145-155.
|Lezar S, Myburg AA, Berger DK, Wingfield MJ, Wingfield BD. (2004) Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis. Theoretical and Applied Genetics 109(7):1329-1336.
|Crampton BG, van den Berg N, Hein I, Birch PRJ, Berger DK. (2004) High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis. BioTechniques 37(5):818-824.
|Bhoora R, Berger DK, Wingfield MJ, Wingfield BD. (2003) PCR cloning by genome walking of a complete polygalacturonase-inhibiting protein gene from Eucalyptus grandis. South African Journal of Science 99(9-10):410-412.
|Murray SL, Denby KJ, Berger DK, Loake GJ. (2002) Disease resistance signalling in Arabidopsis: Applications in the study of plant pathology in South Africa. South African Journal of Science 98
|Botha WJ, Serfontein S, Greyling MM, Berger DK. (2001) Detection of Xylophilus ampelinus in grapevine cuttings using a nested polymerase chain reaction. Plant Pathology 50:515-526.
|O'Kennedy MM, Burger JT, Berger DK. (2001) Transformation of elite white maize using the particle inflow gun and detailed analysis of a low-copy integration event. Plant Cell Reports 20:721-730.
|Berger DK, Oelofse D, Arendse MS, du Plessis E, Dubery IA. (2000) Bean polygalacturonase inhibitor protein-1 (PGIP-1) inhibits polygalacturonases from Stenocarpella maydis. Physiological and Molecular Plant Pathology 57:5-14.
|De Villiers SM, Kamo K, Thomson JA, Bornman CH, Berger DK. (2000) Biolistic transformation of Chincherinchee (Ornithogalum) and regeneration of transgenic plants. Physiologia Plantarum 109:450-455.
|Murray SL, Van Vuuren RJ, Berger DK. (1998) Tomato transformation is dependent upon Agrobacterium cell density and acetosyringone levels. Journal of the Southern African Society for Horticultural Sciences 8:60-64.
|Murray SL, Burger JT, Oelofse D, Cress WA, Van Staden J, Berger DK. (1998) Transformation of potato (cv. Late Harvest) with the potato leafroll virus coat protein gene, and molecular analysis of transgenic lines. South African Journal of Science 94:263-268.
|Berger DK, Narberhaus F, Lee HS, Kustu S. (1995) In vitro studies of the domains of the nitrogen fixation regulatory protein NifA. The Journal of Bacteriology 177:191-199.
|Berger DK, Narberhaus F, Kustu S. (1994) The isolated catalytic domain of NifA, a bacterial enhancer-binding protein, activates transcription in vitro: activation is inhibited by NifL. PNAS 91:103-107.
|Kilkenny CA, Berger DK, Rawlings DE. (1994) Isolation of the Thiobacillus ferrooxidans ntrBC genes using a T. ferrooxidans nifH-lacZ fusion. Microbiology 140:2543-2553.
|Lee HS, Berger DK, Kustu S. (1993) Activity of purified NIFA, a transcriptional activator of nitrogen fixation genes. PNAS 90:2266-2270.
|Santero E, Hoover TR, North AK, Berger DK, Porter SC, Kustu S. (1992) Role of integration host factor in stimulating transcription from the sigma 54-dependent nifH promoter. Journal of Molecular Biology 227:602-620.
|Berger DK, Woods DR, Rawlings DE. (1990) Complementation of Escherichia coli sigma 54 (NtrA)-dependent formate hydrogenlyase activity by a cloned Thiobacillus ferrooxidans ntrA gene. Journal of Bacteriology 172:4399-4406.