Skip to main content

Host Resistance to Fusarium pathogens


Fusarium head blight and crown rot

Donald Gardiner, Kemal Kazan, Chunji Liu,

Fusarium crown rot (FCR) is a major disease in wheat and barley in Australia. It is an infection of the stem base of cereal plants which causes yield loss and is particularly prevalent in dry seasons. The primary causal agent in Australia is Fusarium pseudograminearum. Resistance or tolerance to this disease is quantitative with no absolute immunity available in current wheat cultivars. Fusarium head blight is a sporadic disease in parts of Australia, but is globally one of the most important disease of wheat and barley. It is primarily caused by Fusarium graminearum but F. pseudograminearum is also known to incite the disease in Australia.

The team based in the Brisbane laboratories investigates the interaction from multiple angles including:
• The identification and mapping of resistance loci for germplasm improvement,
• The understanding the molecular mechanisms of the host response to infection and
• Mechanisms of pathogen virulence.

Fusarium crown rot resistance

Fusarium crown rot (FCR) is becoming a major disease in many parts of the cereal-growing regions worldwide, and effective management of damage from this disease requires breeding and exploiting resistant and tolerant varieties. To facilitate breeding programs, the team aims to identify novel sources of resistance, detect effective QTL, generate diagnostic markers, and develop breeding lines with enhanced resistance by marker-assisted selection. We provide breeding companies with not only sources of novel resistance, but also markers tightly linked to QTL and breeding lines developed by pyramiding resistance loci.

Results from our studies show that both plant height and flowering time have strong interaction with CR resistance, that QTL which reduce yield loss due to CR by more than 15% are not uncommon, and that each of the three loci assessed in barley reduces yield loss through the maintenance of higher proportions of fertile tillers.

Not surprisingly, the most effective loci conferring CR resistance were detected from semi-wild germplasm in both wheat and barley. To overcome the problem that such genotypes do not grow properly, thus being difficult to get meaningful comparison with local varieties under field environments, we routinely develop near isogenic lines (NILs) for the putative QTL detected from them. Using NILs to evaluate the effect of a locus on CR resistance also minimize possible interference of plant height and flowering time. The availability of NILs also facilitate the development of diagnostic markers.


In Western Australia the incidence of and potential for FCR has increased (Hüberli et al., 2015). Yield loss from crown rot infection across common WA barley and wheat varieties are up to 59% for barley and 42% for wheat (Hüberli et al., 2017). The problem has been amplified by stubble retention on which the pathogen can survive between crops, a limited appetite for break crops in management strategies, unpredictable seasonal factors, and a lack of knowledge on the epidemiology of the causal pathogen in WA. In light of this, CSIRO researchers in Perth and Brisbane conducted two systematic surveys of WA wheat growing regions, one in 2008 and one in 2015, detailing the geographical distribution of causal FCR species identity, genotypic diversity, pathogenicity and mycotoxin potential across the WA wheat belt. Joint CSIRO University of Queensland PhD student Mohammed Khudhair has been assessing these populations.

Fusarium pathogenomics

On the pathogen side of the interaction, we use genomic technologies to dissect mechanisms of virulence. Functional studies are undertaken with a particular focus on regulation and biosynthesis of toxins, biosynthesis of plant hormone mimics and mechanisms of degradation of host produced antimicrobial compounds. These fungi are easily cultured in the lab, have small genomes and can be transformed to create mutants or fluorescently tagged isolates. These organisms’ genomes are also very compact with genes, such as those for toxin biosynthesis, present in gene clusters.

We are also using Fusarium graminearum as a model for developing gene drive technology to control fungal pathogens

GFP-tagged Fusarium graminearum growing out of wheat rachis, inside rachis, and inside stem

Fusarium wilt

Louise Thatcher, Donald Gardiner, Karam Singh, Kemal Kazan

Fusarium wilt disease is of global significance, affecting over 100 plant species.  Those of highest agricultural importance in Australia are cotton, banana, tomato, legumes and cucurbits. The disease is caused by members of the F. oxysporum species complex, with pathogenic members causatively defined by their pathogenicity or lineage specific chromosomes, which are encoded with high levels of plasticity.

Using model plant systems (Arabidopsis thaliana, Medicago truncatula) coupled with powerful genetic, genomic, transcriptomic, and bioinformatics approaches, the team has made step changes in our understanding of the molecular dialogue that takes place between pathogen and host. The knowledge gained has been used to remove plant susceptibility genes, to track pathogen evolution and identify weaknesses in the pathogen to be exploited in resistance breeding.

For recent publications on our Fusarium work, please check our reseachers’ bios at the links above.