The PSHB –  polyphagous shot hole borer, ambrosia beetle (Coleoptera: Curculeonidae: Scolytinae) is a generalist, insect species, considered to be a pest, due its ability to damage trees by acting as a vector carrying pathogenic fungi. Fungal species are inoculated into reproductive and non-reproductive hosts, causing Fusarium dieback. This invasive beetle and its fungal symbiont, Fusarium euwallaceae (within the Fusarium solani species complex (FSSC)), forms a complex that is internationally notorious for the damage it has caused, especially in Israel and in the United States of America. In these countries, this pest threatens not only urban trees, it is also presenting a major threat to the avocado industries.

In a recent study in South Africa, this ambrosia beetle-fungal complex was detected damaging Platanus x acerifolia (London Plane) trees in the KwaZulu-Natal National Botanical Gardens. Subsequent analysis confirmed the insect to be one of the invasive haplotypes of the PSHB. This is of particular concern to the local avocado industry. Current research within the Avocado Research Programme is therefore aimed at identifying Fusarium spp. isolates sampled from avocado trees to determine the extent of the threat to industry, after which the taxonomy of these isolates will be defined.  We are also in the process of determining the threat on various, commonly growth avocado cultivars through the use of multiple pathogenicity trials.

Read more about Ambrosia beetles and Fusarium dieback on our Fact sheet here

ARP Team Members

Michael du Toit: Assessing the potential threat of Fusarium spp. from the Fusarium solani species complex (FSSC) to avocado, in South Africa


Phytophthora root rot (PRR) is the most severe and damaging disease in avocado plantations in South Africa. The causal agent, Phytophthora cinnamomi, is an oomycete that also causes disease on thousands of other plant species. The pathogen is a heterothallic species that can reproduce by sexual or asexual means. It can persist in soil or infected plant material for extended periods of time, and there is no means to eradicate this oomycete from infected areas once the pathogen has successfully established in soils. Currently, phosphite injections, along with the use of good agricultural practices, are commonly used as methods of control for PRR.

Given the severity of the disease, however, little is known regarding the biology, population diversity, and the molecular basis for the P. cinnamomi - avocado interaction. Current research of ARP therefore focuses on characterizing the genetic diversity and monitoring pathogen populations using microsatellite markers, and using genomics and genetics tools to characterize effectors genes (RxLR and Crinkler) as well as other genes that are known to contribute to the pathogenicity of the oomycete. The sensitivity and effectiveness of phosphite control and its mode of action towards P. cinnamomi is also being investigated.


ARP Team Members

·         Melissa Joubert: Identification and expression analysis of RxLR effector genes in Phytophthora cinnamomi

·         Mohamed Seedat: Identification of CRN effector genes in Phytophthora cinnamomi during avocado root infection

·         Tsakani Miyambo: The identification and characterization of polygalacturonases in Phytophthora cinnamomi

·         Juanita Hanneman: Analysing the effect of phosphite on the morphology and transcriptome of South African Phytophthora cinnamomi strains

·         Juanita Engelbrecht: Population genetics and genomics of Phytophthora cinnamomi

Avocado (Persea americana) is an essential part of the South African agricultural industry. Most avocado orchards are found in high rainfall areas (>1000 mm p.a.) such as in Limpopo and Mpumalanga. High levels of rainfall and incorrect irrigation practices support increased spread of Phytophthora root rot (PRR). The causal agent, Phytophthora cinnamomi, accounts for substantial loss in orchard productivity and subsequent economic losses. However, the use of tolerant rootstock such as Dusa® greatly improves orchard productivity. Thus, an essential and ongoing goal of the Avocado Research Program (ARP) is understanding disease defence mechanisms in avocado to support a better understanding of what constitutes tolerance to P. cinnamomi. We have published several peer reviewed articles to date, each focused on a particular aspect of avocado defence responses (van den Berg et al. ; Mahomed and van den Berg 2011; Engelbrecht and Van den Berg 2013; Reeksting et al. 2014; Backer et al. 2015; Reeksting et al. 2016; Prabhu et al. 2017).


 Understanding disease involves realising the infection strategies employed by pathogens as well as defensive tactics used by the host. Therefore, our current research is focused on unravelling the molecular basis of P. cinnamomi infection response in avocado by label-free relative quantitative proteomics as well as functional characterisation of the NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) protein family through overexpression and subcellular localisation studies. Herewith, we intend to not only extend our understanding but also the molecular toolkit available to the research community for elucidating the complex interactions of avocado and its pathogens.


Backer, R., W. Mahomed, B. J. Reeksting, J. Engelbrecht, E. Ibarra-Laclette et al., 2015 Phylogenetic and expression analysis of the NPR1-like gene family from Persea americana (Mill.). Front Plant Sci 6: 300.

Engelbrecht, J., and N. Van den Berg, 2013 Expression of defence-related genes against Phytophthora cinnamomi in five avocado rootstocks. South African Journal of Science 109: 1-8.

Mahomed, W., and N. van den Berg, 2011 EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi. BMC Plant Biol 11: 167.

Prabhu, S. A., B. Ndlovu, J. Engelbrecht and N. Van den Berg, 2017 Generation of composite Persea americana (Mill.)(avocado) plants: A proof-of-concept-study. PloS one 12: e0185896.

Reeksting, B. J., N. Coetzer, W. Mahomed, J. Engelbrecht and N. van den Berg, 2014 De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PLoS One 9: e86399.

Reeksting, B. J., N. A. Olivier and N. van den Berg, 2016 Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi. BMC Plant Biol 16: 205.

van den Berg, N., J. Christie, T. Aveling and J. Engelbrecht, Callose and β1, 3glucanase inhibit Phytophthora cinnamomi in a tolerant avocado rootstock. Plant Pathology.


ARP Team Members


Ashok Prabhu: Next generation label-free quantitative proteomics approach to understand the avocado-Phytophthora cinnamomi interaction


Robert Backer: Molecular cloning and functional characterisation of NPR1-like genes from Persea americana (Mill.)



Rosellinia necatrix Berl. ex Prill. is an ascomycete pathogen that targets over 400 different plant hosts. Its ability to switch between saprophytic and pathogenic lifestyles allows the occupation of an area for long periods of time. It is the causal agent of white root rot which has resulted in significant economic losses within the agricultural and forestry industries of numerous temperate and tropical countries. Recently, symptoms resembling white root rot were observed in a commercial avocado orchard in the Limpopo Province. These symptoms were determined to be due to R. necatrix infection. The majority of the commercial South African avocado rootstocks were subsequently found to be susceptible to white root rot.

Research within the ARP aims to survey the prevalence, spread and distribution of this pathogen in South African fruit tree orchards. We also aim to assess physiological responses of South African avocado rootstocks to R. necatrix infection, as well as to evaluate potential control techniques for white root rot on avocado. Additionally, candidate pathogenicity-related genes of R. necatrix will be predicted prior to functional characterization of these genes using a CRISPR-Cas9 system. 


Read more about Rosellinia necatrix on our Fact sheet here


ARP Team Members

Jesse Hartley: The Detection and Surveillance of White Root Rot caused by Rosellinia necatrix in South African Avocado Orchards


Phinda Magagula: Physiological response of South African avocado rootstocks to Rosellinia necatrix and its control




Avocado (Persea americana) is a tropical tree species that is a commercially important fruit crop worldwide due to its nutritional value. Avocados belong to the Magnoliidae clade, a basal lineage of the flowering plants. Because Avocados have a long vegetative period (approximately 6 to 8 years) directed crosses are complicated in Avocado breeding. Genome sequence information could thus be highly valuable to breeding programmes, to speed up the selection of cultivars and rootstocks with desirable traits.

The Avocado Genome Consortium was established in 2016 as an international collaborative initiative between researchers interested in avocado genomics, with an aim to sequence and annotate the Avocado genome.

The researchers involved are:

  • David Kuhn, USDA, Florida
  • Patricia Manosalva, UCR, California
  • Noëlani van den Berg, UP, South Africa
  • Sarah Mwangi, UP, South Africa
  • Antonio Javier Matas Arroyo, Departamento de Biología Vegetal, University of Malaga, Spain
  • Aureliano Bombarley Gomez, Virginia Tech Horticulture, USA
  • Randy Ploetz, University of Florida, USA
  • Alan Chambers, University of Florida, USA

The consortium aims to sequence a homozygous avocado and re-sequence two avocado rootstocks, (one from the UCR breeding programme and one from WTS) in order to improve on the quality of the draft genome which is already available. Sequencing and annotation of the Avocado genome is currently underway, and it is anticipated that this will provide important advances in research methodologies and opportunities to study the genetics underpinning complex traits such as disease tolerance and tolerance to abiotic stresses.

As part of the broader objectives of the Avocado Genome Consortium, transcriptomic data has also been generated. This data will be utilized to answer fundamental questions pertaining to the evolutionary biology, gene expression, physiological processes and molecular pathways in avocado. Transcriptomic data from an RNA-sequencing experiment involving avocado challenged with Phytophthora cinnamomi will also aid in the identification of avocado defense targets and discovery of pathogen effectors involved in host-pathogen interactions.

Knowledge of the avocado genome and related genetic diversity will provide important information and a molecular toolbox to facilitate the establishment of more effective breeding programmes, and further research into all aspects of avocado health and defense.


ARP Team Members

Sarah Mwangi: Genomics and transcriptomics of Persea americana (Avocado)