Pearl Millet

FABI News

News Archive

17 Sep 2025

SASSB Conference 2025 held at FABI

The South African Society for Systematic Biologists Conference 2025 was recently held at FABI at the University of Pretoria.

10 Sep 2025

13 FABIans capped at the UP Spring Graduation

Congratulations to the 13 FABIans that were capped at the UP Spring Graduation.

9 Sep 2025

The KPP team gets ready for the new Kiwifruit season

Members of the KPP were in the field to set up trials for the upcoming season.

8 Sep 2025

A double celebration for Caitlin!

Congratulations to Caitlin Gevers the successful completion of her PhD and being capped at the UP Spring Graduation.

5 Sep 2025

SACTA colleagues visit FABI

FABI recently welcomed senior managers of SACTA to the Institute

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FABI Events

22 September 08h30

Monday Morning Meeting

25 September 08h30

Student Seminars

29 September 08h30

Monday Morning Meeting

02 October 08h30

Student Seminars

FABI in a nutshell

Research Features

Archive

New publication explores the chemodiversity of Penicillium isolated from alpine and arctic environments, including ten new species.

Review emphasizes the importance of understanding the genetics of sex determination for effective genetic pest management in insects.

Eleven new Penicillium and Talaromyces species discovered in South African culture collections.

A new study reveals the presence of Mycotoxins in Eastern Cape maize in South Africa.

Eurotiales update: FABIans Prof. Cobus Visagie and Dr Neriman Yilmaz and their collaborators have published a review of recently described Eurotiales species, including the economically important Aspergillus, Penicillium, Paecilomyces and Talaromyces.

Da Vinci's Yeast: FABIans Prof. Cobus Visagie, Dr Neriman Yilmaz, and their collaborators have recently described and named a newly discovered yeast species of the famous Italian painter, draughtsman, engineer, scientist, theorist, sculptor, and architect Leonardo da Vinci.

The potential economic impact of the PSHB invasion in South Africa has been calculated to be a massive R275 billion over the next ten years, if nothing is done to stop the spread of this invasive beetle. Researchers from FABI collaborated with Stellenbosch University ecologists and economists to model the unmitigated economic impact of this invasion.

A recently published paper in the journal Current Forestry Reports documents a collaboration between an international team of forest pathologists and invasion scientists. Led by Dr Trudy Paap, the authors present a framework for conceptualizing and managing invasive forest pathogens.

A recently published review article by Dr Andi Wilson in a special issue of the journal 'Microbiology & Molecular Biology Reviews' provides details of the genes that are essential to the sexual cycle in filamentous Ascomycete fungi and further describes their functions in a variety of model and non-model species.

Penicillium section Canescentia re-evaluated and five new species described from the fynbos biome in South Africa.

In November 2019, the DSI-NRF Centre of Excellence for Invasion Biology hosted a workshop on ‘Frameworks used in Invasion Science’. The workshop led to a NeoBiota special issue on this theme, and includes a review by FABI researchers and international colleagues, exploring frameworks in the context of forest pathology.

A doctoral study in FABI confirms for the first time the presence of Xylosandrus crassiusculus, a polyphagous ambrosia beetle and its fungal symbiont, Ambroseilla roeperi, in three provinces in South Africa. The authors warn that this beetle species could be a threat to native and plantation trees.

A review on invasive gall-forming wasps that threaten non-native Eucalyptus plantations by researchers in the TPCP appears in Agricultural and Forest Entomology. They profile several species of likely Australian origin that have established on non-native Eucalyptus plantations globally and discuss various challenges to their management.

A study in the TPCP confirms the identity of seven novel fungal species associated with Dendroctonus valens, the red turpentine beetle. The study follows on surveys on the fungal associates of the beetle in China and North America. Results from this work appear in Persoonia.

A postdoctoral study in the TPCP describes two novel Huntiella species in the African clade, bringing the number of known species in the genus to 31. Though closely related, the two species display different mating systems. Outcomes from this study appear in the journal MycoKeys.

A review of the invasion history and global management strategies of Eucalyptus snout beetles in the Gonipterus scutellatus species complex by researchers in the TPCP appears in the Journal of Pest Science.

In a collaborative venture with Dr Jos Houbraken (Westerdijk Fungal Biodiversity Institute, the Netherlands), Prof. Cobus M Visagie, Dr Neriman Yilmaz (both from FABI) and others have recently completed and published a major study updating the taxonomy of the Eurotiales.

A study in the Forest Molecular Genetics (FMG) Programme at FABI interrogates the benefits of implementing genomic selection for growth and wood quality traits in an established Eucalyptus grandis breeding programme in South Africa. Outcomes from this study appear in an article.

The first study on alternative weed and cultivated hosts of Spongospora subterraneaf. sp. subterranea (Sss), in southern Africa identifies two species as ideal trap crops for rotation with potatoes. The study also introduces three new families to the known hosts of Sss in the region.

A consortium of microbiologists from around the globe, FABI included, is pushing for an overhaul in how scientific names are assigned to uncultivated bacteria and archaea. Despite their ecological, agricultural and medical importance, these organisms traditionally have not been recognized by the international body governing the nomenclature of prokaryotes.

Professor Cobus Visagie is a researcher in the Applied Mycology group at FABI. One of the group’s research goals is to discover fungal diversity in South Africa, and Cobus’ research is strongly focussed on the economically important genera Aspergillus, Penicillium and Talaromyces.

Postdoctoral research by Dr Norman Muzhinji in the Potato Pathology Programme at the Forestry and Agricultural Biotechnology Institute (FABI) sheds light on the genetic structure and diversity of Spongospora subterranea f. sp. subterranea in four potato-growing regions in South Africa, providing valuable insights on its management.

An MSc study by Kira Lynn in the RGE-FABI Tree Health Programme at the University of Pretoria has described a new Fusarium species, Fusarium rekanum sp. nov., associated with Euwallacea perbrevis, an ambrosia beetle species infesting Acacia crassicarpa plantations in Riau, Indonesia.

FABI postdoctoral Fellow Dr Andi Wilson has established a CRISPR-Cas9-based genome editing protocol for use in Huntiella omanensis, a tree-inhabiting fungus belonging to the Ceratocystidaceae family.

Research undertaken as part of a PhD study by Molly Malefo at the University of Pretoria’s Department of Plant and Soil Sciences and Forestry and Agricultural Biotechnology Institute sheds more light on the role of protease inhibitors in plants under drought stress.

The South African National Biodiversity Institute (SANBI) has funded a postdoctoral research project dedicated to monitoring plant health in botanical gardens and arboreta across South Africa. Two postdoctoral Fellows at the University of Pretoria’s Forestry and Agricultural Biotechnology Institute have held these fellowships.

The first comprehensive study mapping the distribution and genetic diversity of invasive Eucalyptus insect pests in sub-Saharan Africa confirms the presence of five major foliage-feeding species in 14 countries. The results of this study have implications on the quarantine, future research and management of these pests on the continent and beyond.

Dr Joey Hulbert broke new ground when he became the first candidate at the Forestry and Agricultural Biotechnology Institute to complete a PhD study incorporating citizen science. Citizen science is an approach that involves members of the public as active participants in scientific research.

FABI technology unravels the genetics behind fungal genome evolution The RIPper is a bioinformatics tool for the for quantifying genome-wide RIP mutations in fungal genomes. The strength of this software lies in the automation of laborious techniques to study the mutation process called Repeat-Induced Point mutations (RIP). The RIPper applies these technique

With the increased availability in genome data, inferences regarding evolutionary relationships among taxa can now be performed on a genome-wide scale. But it is widely accepted that not all parts of such massive datasets support the same evolutionary hypothesis. Because of this, a group of researchers at FABI recently investigated the effect of this.

The use of genome data to characterize species and elucidate relationships, particularly between problematic taxa, has become routine practice in bacteria. Recently, researchers from FABI joined in an international effort to describe two novel genera and characterize these within the larger context of the important bacterial group Burkholderia.

A PhD student in FABI, Runlei Chang, has discovered and described 19 new fungal species from China as part of the research for his thesis. These fungi are all associated with conifer-infesting bark beetles and their mites and belong to well-known genera such as Ophiostoma and Leptographium.

Two research papers from FABI were selected as cover stories in two consecutive issues of the international journal, Plant Pathology. The journal is published by Wiley for the British Society of Plant Pathology.

Plastids play an integral role in wood formation, and yet they are routinely ignored in the study of xylogenesis in forest trees. Desre Pinard and Dr Eshchar Mizrachi have published a review highlighting the unique biology of plastids in wood, suggesting that a new type of plastid, the xylopast, exists.

Approaches for characterizing metabolic potential from genomic sequences have previously been predicted to be useful in the description of bacterial taxa. Dr Marike Palmer, has recently employed these approaches for identifying biological processes contributing to the divergence of bacteria with a variety of lifestyles.

Comparative genomics is shaping our notion of what fungal species are. Based on current data, these unique evolutionary units are separated from one another by boundaries that are porous under certain conditions. This affects our expectations regarding their population biology and evolution, and our strategies for recognizing and controlling them.

The Polyphagous Shot Hole Borer is an ambrosia beetle native to Southeast Asia. In 2017 this pest was detected in South Africa. Its presence has since been confirmed in all provinces except Limpopo. The beetle has a symbiotic relationship with the fungus Fusarium euwallaceae, which causes branch die-back and death of susceptible trees.

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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).

Workshops & Symposia

Archive

Joint IUFRO meeting of IUFRO WP 7.03.13 and 7.03.16: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

Joint IUFRO meeting: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

New Publications

Joubert M, van den Berg N, Theron J, Swart V. (2025) Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms: implications for pathogenesis in avocado sunblotch disease. Archives of Virology 170(10):205. 10.1007/s00705-025-06360-z

Mavima L, Steenkamp ET, Beukes CW, Palmer M, De Meyer SE, James EK, Venter SN, Coetzee MPA. (2025) Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia. Molecular Phylogenetics and Evolution 213:108447. 10.1016/j.ympev.2025.108447

Pham NQ, Liu FF, Duong TA, Wingfield BD, Chen SF, Wingfield MJ. (2025) Genetic diversity of Calonectria reteaudii isolates from infected Eucalyptus leaves and associated soils indicates a phyllosphere origin of the pathogen. Forest Pathology 55:e70037. 10.1111/efp.70037

Schröder ML, Hurley BP, Wingfield MJ, Slippers B, Garnas JR. (2025) Thermal limitations to the biological control of Gonipterus sp. n. 2 (Coleoptera: Curculionidae) in South African Eucalyptus plantations. Agricultural and Forest Entomology 10.1111/afe.70002

Lynn KMT, Wingfield MJ, Tarigan M, Durán A, Santos SA, Nel WJ, Barnes I. (2025) Investigating bark, ambrosia and nitidulid beetle (Coleoptera: Scolytinae and Nitidulidae) communities and their potential role in the movement of Ceratocystis manginecans in commercial forestry plantations in Riau, Indonesia. Agricultural and Forest Entomology 10.1111/afe.12698

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