Avocado Research Programme

Research Areas

ARP Research

Avocado Branch Canker

Avocado branch canker is a fungal disease that affects avocado trees, caused by various species within the Botryosphaeriaceae family. It typically manifests as lesions or cankers on the tree's branches, often leading to dieback of affected branches and a decline in tree health. The disease can result in significant economic losses for avocado growers due to reduced yield and tree mortality. These species are associated with disease symptoms such as leaf spot, stem or trunk canker, dieback, and fruit rot. Initial symptoms may include the formation of small, sunken lesions on the branches, which gradually enlarge and become necrotic. Cankers may girdle branches, leading to dieback. Infected trees may exhibit wilting, leaf drop, and overall decline in vigor. Cankers associated with species from the Botryosphaeriaceae family are necrotic with a friable bark that often has a whitish hard exudate, when the canker is cut open, it is discoloured (reddish brown). The cankers are characterized by V-shaped discoloration towards xylem tissues. Factors Contributing to Disease Development: Environmental factors such as high humidity, rainfall, and wounds from pruning or mechanical damage can predispose avocado trees to infection. Additionally, stress factors like drought or nutrient deficiencies may exacerbate the severity of the disease. Management strategies for avocado branch canker typically involve cultural practices to promote tree health and minimize stress, such as proper irrigation and fertilization. Additionally, pruning practices to remove infected branches can help reduce disease spread. Overall, avocado branch canker poses a significant challenge to avocado growers, requiring proactive management strategies to mitigate its impact on orchard productivity and tree health. Ongoing research into disease epidemiology, host-pathogen interactions, and integrated pest management approaches is essential for effective disease control in avocado cultivation. The ARP aims to: Identify Botryosphaeriaceae species associated with branch canker and die-back on avocado trees in South African orchards and nurseries. Find the most prevalent Botryosphaeriaceae species in South African avocado nurseries and orchards. Evaluate the pathogenicity of the Botryosphaeriaceae species against commercial-grown avocado varieties in South Africa. Evaluate the impact of drought stress on avocado branch canker symptom development. ARP Team Members Makhosazana (Khosi) Ngema Heike Möller Images from left to right: 1-3. Wedge shape discoloration caused by Botryosphaeria species.

Avocado Flowering Dynamics

Research into the flowering dynamics and molecular regulation of heterodichogamy in avocado trees holds significant importance for both agricultural practice and scientific understanding. Avocado is a valuable crop worldwide, with increasing demand driven by its nutritional value. However, optimizing fruit yield and quality proves challenging because of the unique reproductive strategy of avocado trees. With Type A and B trees flowering at different times of the day promoting cross-pollination becomes crucial. Understanding the genetic mechanisms underlying the timing of flower maturation is crucial for efficient pollination and fruit set, directly impacting yield and profitability for avocado growers. By elucidating the key genes involved in heterodichogamy and their regulatory pathways, this research can inform targeted breeding efforts to enhance pollination success and fruit production in avocado orchards. Moreover, unravelling the molecular intricacies of flower development in avocado contributes to broader scientific knowledge in plant biology and reproductive biology. Avocado exhibits a specialized form of heterodichogamy, a reproductive strategy that sets it apart from many other plant species. Insight gained from this research can advance our understanding of how plants coordinate flowering and reproductive timing. Additionally, identifying molecular markers associated with flower type and heterodichogamy facilitates the development of screening tools for growers to accurately classify avocado trees and optimize orchard management strategies. Therefore, the research aims to identify differentially expressed genes between Type A and B avocado trees and to develop a putative model for heterodichogamy in avocado using differentially expressed genes from an RNA-seq experiment, with the goal of developing a screening tool for the identification of Type A and B avocado trees. This research bridges fundamental and applied science, offering practical solutions for sustainable avocado production while enriching our understanding of plant reproductive biology. ARP Team Members Johane Cilliers

Avocado Sunblotch Viroid

Avocado sunblotch is a disease caused by avocado sunblotch viroid (ASBVd) – a circular single-stranded RNA molecule in the family Avsunviroidae which is only about 250 nucleotides in length. Despite its tiny size, and the fact that this viroid is not classified as a living organism, the presence of ASBVd in an avocado host can lead to the appearance of severe symptoms such as the formation of coloured, sunken lesions on avocado fruit, discoloured streaks on young stems, and discolouration and malformation of leaves. Although the appearance of these symptoms will not usually lead to death of a healthy avocado tree, fruit symptoms will impact market value of the fruit, and asymptomatic trees may have significantly reduced yield when compared to their uninfected counterparts. While previous research on ASBVd has been largely focused on mapping its distribution, refining detection techniques and monitoring the physiological effect of infection on avocado trees and fruit, there is as yet no definitive evidence to explain how the viroid causes disease at the molecular level. Current research within the ARP aims to elucidate molecular mechanisms of avocado sunblotch disease by investigating host responses to viroid infection, as well as the viroid variants associated with chlorotic symptoms in avocado hosts. By expanding our understanding of how ASBVd causes host symptoms at the molecular level we will pave the way for future research which will aid South African avocado growers in combatting this disease. *Read more about avocado sunblotch viroid on our Fact sheet here . ARP Team Members Melissa Joubert : Investigating molecular mechanisms for disease caused by avocado sunblotch viroid (ASBVd). Images from left to right: 1 . Typical fruit symptoms caused by ASBVd infection include the formation of yellow, sunken lesions on avocado. 2 . ASBVd infection may cause bleaching symptoms in avocado leaves, characterised by yellowing of leaf tissues near or along the leaf midvein. 3 . PhD candidate Melissa Joubert sampling avocado tissues with sunblotch symptoms. Symptomatic tissues may be restricted to only one part of an infected tree, while the rest of the tree remains free of chlorotic symptoms.

Avocado Omics

The advent of next-generation sequencing (NGS) technologies has revolutionised research capacity and its broad applicability over the past decade. These technologies have directly impacted researchers’ ability to understand host-pathogen interactions, holistically, and on a molecular scale. Recently, the avocado industry has begun to unravel some of the underlying mysteries that pertain to prevalent avocado pests and diseases; the Avocado Research Programme (ARP) has been highly influential in this space. As a founding member of the Avocado Genome Consortium - an international collaborative effort which was established in 2016 - the ARP has directly contributed to the development of a high quality, chromosome-level reference genome assembly for Persea americana (avocado). The Avocado Genome Consortium has used this new reference genome to re-sequence more than 10 additional cultivars and rootstocks as part of an ongoing project, with plans to increase this number soon. Provided with this data, researchers will be able to accelerate the arduous process of selecting rootstocks and cultivars with desirable traits. 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 a dual RNA-sequencing experiment - involving both susceptible and partially resistant avocado rootstocks challenged with Phytophthora cinnamomi - was also used to identify avocado defence targets and discovery of pathogen effectors involved in disease development. The data from this work has been published across several research articles and will be used to further our understanding of the avocado- P. cinnamomi interaction. The researchers involved are: David Kuhn, USDA, Florida Patricia Manosalva, UCR, California Noëlani van den Berg, 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

Ambrosia Beetles

An ambrosia beetle, commonly known as Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae), is considered to be a pest, due to its ability to damage trees by acting as a vector for a pathogenic fungi. Fusarium euwallaceae , the fungal symbiont of the PSHB, is inoculated into the tree by the beetle. Eventually, the fungal symbiont prevents the transport of water and nutrients by invading the xylem, that leads to Fusarium dieback and the eventual death of the host tree. This pest-pathogen complex has emerged as an invasive pest in Israel and the United States of America (California), causing severe damage and significant economic losses to agricultural, ornamental and urban trees, especially to their avocado industries. This pest-pathogen complex was detected in South Africa damaging Platanus x acerifolia (London Plane) trees in the National Botanical Gardens, KwaZulu-Natal. Recently, it was detected on a backyard tree and in a commercial avocado orchard. Control management strategies for this pest complex are limited due to inefficient trapping mechanisms, lack of biocontrol measures and inefficient fungicides. The use of resistant/tolerant trees could serve as a potential control strategy. Current research within the Avocado Research Programme (ARP) 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 Images from left to right: 1 . Xylosandrus crassiusculus fungal symbiont Ambrosiella roeperi in culture. 2 . Internal symptoms of PSHB infestation as beetles establish a network of galleries. 3 . PSHB interception traps used in orchards.

White Root Rot

Dematophora necatrix (previously Rosellinia necatrix Berl. ex Prill.) is an ascomycete pathogen that targets a multitude of different plant hosts in various tropical and temperate regions. As the causal agent of white root rot (WRR) it has caused significant economic losses within the agricultural and forestry industries, including apple, citrus and avocado. Symptoms and the presence of D. necatrix were confirmed in a commercial avocado orchard in the Limpopo Province (South Africa) in 2016. Since then, it has been detected in Mpumalanga, Western Cape and Kwa-Zulu Natal. Control options for WRR are imperfect due to the pathogen’s hardy resting structures, deep soil penetration, and resistance to common fungicides. However, various approaches have been used to manage D. necatrix infection, alone or in combination, which includes; (i) cultural practices, such as the removal of diseased plant material; (ii) the use of uninfected and/ or D. necatrix resistant/ tolerant plant material; (iii) physical practices, such as soil solarization; (iv) the use of chemical control agents, such as, fluazinam; (v) the use of biological control agents, including, plant growth-promoting rhizobacteria and Trichoderma .; (vi) and lastly, periodic testing for the presence of the pathogen in soil using baiting and PCR-based detection techniques. Currently, research in the ARP is aimed at understanding D. necatrix population diversity within South Africa and the rhizosphere microbial communities in avocado trees infected with D. necatrix . As well as, to develop an effective management strategy for D. necatrix in avocado orchards using chemical control and biological control agents. Additionally, the ARP is investigating the potential of CRISPR-Cas9 genome editing technology in D. necatrix targeting putative pathogenicity genes, which will be used for functional analysis. * Read more about Dematophora necatrix on our Fact sheet here . ARP Team Members Phinda Magagula: The detection and management of Dematophora necatrix in avocado orchards. Tsakane Miyambo : Investigating the genetic diversity, population structure and virulence of Dematophora necatrix in South Africa. Raven Wienk : Investigating the Persea americana - Dematophora necatrix - Trichoderma interaction. Dr Molly Malefo : CRISPR/Cas9 ribonucleoprotein (RNP)-based genome editing in D. necatrix. Images from left to right: 1 . D. necatrix on semi-selective media. 2 . D. necatrix infected soil material in an orchard. 3 . White mycelial fans of D. necatrix at the crown of an infected tree.

Phytophthora Root Rot

Phytophthora root rot (PRR) is the most severe and damaging disease in avocado plantations in South Africa. The causal agent of PRR is the notorious oomycete, Phytophthora cinnamomi ( Pc ). This pathogen has an extensive host range making it an economically important plant pathogen. The pathogen is a heterothallic species that can reproduce by sexual or asexual means. Furthermore, Pc is hemibiotrophic, meaning it has an initial biotrophic stage prior to switching to the nectrophic stage at later stages of infection. 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. Research within the ARP has provided some insight into the biology, population diversity and the molecular basis for the Pc -avocado interaction. The sequencing of the genome of a South African Pc isolate and the availability of RNA sequencing data from a Pc -avocado infection trial has allowed the group to delve further into understanding how the pathogen is able to manipulate and suppress plant immunity during infection. Current work in the ARP involves identifying and functionally characterising effector genes which are known to play roles during infection. The group is currently on three groups of effectors; the NLPs, RxLRs and Crinklers; and the aim is to determine how these effectors contribute to the pathogenicity of this pathogen and the strategies by which they are able to manipulate or suppress plant immunity to establish infection. * Read more about Phytophthora cinnamomi on our Fact sheet here . ARP Team Members Katelyn Baird : Characterising the role of Phytophthora cinnamomi NLP proteins in plant cell infection. Ncobile Kunene : Elucidating the role of Phytophthora cinnamomi RxLR effector genes during Persea americana infection. Kayla Midgley : Characterising the role of Phytophthora cinnamomi CRN effector proteins in host plant cell death. Susanna Anbu : Expression profiling of Nep-like protein (NLP) effector genes during infection in avocado.

Avocado Defence

Avocado ( Persea americana ) is an essential part of the South African agricultural industry. Most avocado orchards are located in Limpopo and Mpumalanga. Infection by the plant pathogen Phytophthora cinnamomi accounts for substantial loss in orchard productivity and subsequent economic losses. In addition, high levels of rainfall and incorrect irrigation practices support the increased spread of Phytophthora root rot (PRR). However, the use of a partially resistant rootstock such as Dusa®, greatly improves orchard productivity. Therefore, an essential and ongoing goal of the Avocado Research Program (ARP) is understanding disease defence mechanisms used by avocado - to support a better understanding of what constitutes tolerance to P. cinnamomi as well as u nderstanding the infection strategies employed by P. cinnamomi to cause disease in avocado. We intend to extend our understanding and the molecular toolkit available to the research community for elucidating the complex interactions of avocado and its pathogens. ARP Team Members Susanna Anbu : Functional characterization of candidate Persea americana nucleotide-binding leucine rich repeat ( PaNLR ) genes during P. cinnamomi infection. Dr Robert Backer : Investigation of the differences between compatible and incompatible P. americana (Mill.) - Phytophthora cinnamomi interactions over time: A study focused on 0.12 ZAR-dependent signalling and related pathways. Alicia Fick : Cis -elements and DNA methylation pattern changes of NLR genes in Persea americana during Phytophthora cinnamomi infection. Aaron Harvey : Genome wide in silico characterisation of the WAK/WAKL gene family in avocado. Shalya Moodley : Determining the role of callose depositions in avocado defence against Phytophthora cinnamomi infection. Images from left to right: 1 . Root symptoms on avocado rootstocks after P. cinnamomi infection (Engelbretcht et al . 2013). 2 . Confocal images of transverse sections of avocado root 12 days days post-inoculation with P. cinnamomi . Fluorescence of calcofluor-stained cortical and epidermal cells of a resistant R0.06 root - Blue fluorescence of P. cinnamomi hyphae (H) and cells containing callose (CA) (van den Berg et al . 2018). 3 . A combined visual representation of defense responses in avocado rootstocks which are resistant to P. cinnamomi (van den Berg et al . 2021).