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Professor

Department

Plant Sciences
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Research Profiles

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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 investigates two pathosystems, grey leaf spot disease in maize and bacterial wilt in the model plant Arabidopsis. We implement a range of approaches from whole plant phenotyping to genomics to investigate these systems.

 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 in the MPPI research programme.

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Book Chapters
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).
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Publication
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. 10.1186/s12870-017-1137-9
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. 10.1038/s41598-017-09617-z
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. 10.1094/MPMI-03-17-0054-R
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. 10.1111/tpj.13419
Reitmann A, Berger DK, Van den Berg. (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. 10.1007/s10658-016-0993-8
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. 10.1094/PHYTO-02-16-0084-FI
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. 10.1007/s10658-016-0970-2
Daru B, Berger DK, Van Wyk AE. (2016) Opportunities for unlocking the potential of genomics for African trees. New Phytologist 210:772-778. 10.1111/nph.13826
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. 10.3389/fpls.2016.00191 PDF
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. 10.1016/j.pmpp.2015.05.011 PDF
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. 10.3389/fmicb.2016.01953
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. 10.1186/s12870-015-0499-0 PDF
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. 10.1111/nph.13152
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. 10.1186/1471-2156-15-60
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. 10.1094/MPMI-07-12-0188-R
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. 10.3389/fpls.2013.00043
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. 10.1007/s00122-011-1759-5
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. 10.1007/s10658-011-9920-1
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. 10.1186/1471-2229-11-173
Coetzer N, Myburg AA, Berger DK. (2011) Maize microarray annotation database. Plant Methods 7(31) 10.1186/1746-4811-7-31
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. 10.1186/1753-6561-5-S7-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. 10.1111/j.1439-0329.2010.00642.x
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. 10.1016/j.sajb.2010.02.087
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. 10.1186/1746-4811-6-10
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. 10.1007/s10658-010-9676-z
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. 10.1016/j.sajb.2010.02.087
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. 10.1007/s10658-009-9443-1
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. PDF
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. 10.1111/j.1469-8137.2008.02517.x
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. 10.1111/j.1364-3703.2007.00389.x PDF
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. 10.1007/s00122-004-1759-9 PDF
Van den Berg N, Crampton BG, 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. PDF
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.