Irene van Nugteren


Aim: To understand the molecular mechanisms of plant resistance in the cereal pearl millet

 

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a cereal of importance to food security in Africa since the varieties planted are more tolerant to drought stress than other cereals. The main biotic stresses are downy mildew and rust diseases. The aim of the research project is to identify novel mechanisms of defense against stress through studies of the millet transcriptome. Since, very little genome sequence is available for this non-model crop, we chose to construct cDNA libraries from pearl millet using the Suppressive Subtraction Hybridization (SSH) technique. A novel method was developed for screening these SSH cDNA libraries on microarray slides (Van den Berg et al. 2004). This method allows identification of up-regulated genes, as well as determining whether the up-regulated transcripts are rare or abundant in the original treated sample. A complete methods protocol for library construction and description of a software package SSHscreen in R language have been published in a book chapter in 2007 (Berger et al. 2007).

Gene expression profiling of pearl millet treated with a range of defence signaling molecules as well as pathogen infection has been completed by Bridget Crampton at CSIR-Bio/Chemtek, and candidate defence genes are under investigation.

 

 

Microarray Screeing of pearl millet cDNA library. Note: Only 1/12 of Microarray image is shown. Green spots represent genes induced by pathogen elicitors. Orange/red spots represent genes repressed by elicitors.


Collaboration:


This project was initiated as the PhD project of Bridget Crampton, and has been supported by the African Centre for Gene Technologies. Click here for more information. Development of the SSH screening method was done in collaboration with Noelani van den Berg who applied the method to banana, and Dr. Paul Birch and Dr. Ingo Hein of the Scottish Crops Research Institute.


Publications:

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 (2) 291-304

La w PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK (2008) MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters BMC Genomics 9: 105

Berger DK, Crampton B, Hein I, Vos W (2007). Screeing cDNA libraries on glass slide microarrays. In: Microarrays, Second Edition, Volume II Applications and Data Analysis (Editor J.Brampal), Series: Methods in Molecular Biology (Series Editor J.M.Walker), Humana Press, Totowa, New Jersey, USA (www.humanapress.com) ISBN10# 1-58829-944-9, Chapter 12, 177-203.

Van den Berg N, Crampton BC, Birch PRJ, Hein I & Berger DK (2004). High throughput screening of SSH cDNA libraries using DNA microarray analysis. Biotechniques. 37(5): 818-824 (November).

New Publications

Zumaquero A, Martinez-Ferri E, Matas AJ, Reeksting B, Olivier NA, Pliego-Alfaro F, Barcelo A, van den Berg N, Pliego C. (2019) Rosellinia necatrix infection induces differential gene expression between tolerant and susceptible avocado rootstocks. PLoS ONE 14(2):e0212359. 10.1371/journal.pone.0212359
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. 10.1016/j.fgb.2019.01.005
van den Berg N, Mohamed W, Olivier NA, Swart V, Crampton B. (2018) Transcriptome analysis of an incompatible Persea americana-Phytophthora cinnamomi interaction reveals the involvement of SA- and JA-pathways in a successful defense response. PLoS ONE 13(10):e0205705. 10.1371/journal.pone.0205705
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. (2018) First report of maize yellow mosaic virus (MaYMV) on maize (Zea mays) in Tanzania. Journal of Plant Pathology 1:1. 10.1007/s42161-018-0152-5
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. 10.1007/s00239-018-9837-9
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. 10.1016/j.fbr.2017.11.003
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. 10.5598/imafungus.2017.08.02.10
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
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. 10.1038/srep45402 PDF
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 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. 10.1007/s10658-016-0993-8
Human MP, Barnes I, Craven M, Crampton BG. (2016) Lack of population structure and mixed reproduction modes in Exserohilum turcicum from South Africa. Phytopathology 106(11):1386-1392. 10.1094/PHYTO-12-15-0311-R
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