Projects on biocide resistance in pests, weeds and vectors

Understanding adaptive evolution to herbicides in ryegrass

Intense pesticide and herbicide pressures have resulted in the evolution of resistance in multiples pests, insect vectors and weeds. Resistance is both a huge socio-economic issue limiting our capacity to control disease and sustain food production and the most obvious example of adaptive evolution, occuring within a human life-span. As resistance spreads, herbicides lose their efficacy and struggle to control weeds. This can reduce crop productivity and can represent a costly loss for farmers. Resistance is essentially a genetic response, it is best investigated at the genome level. Resistance is increasingly found to be endowed by multiple genes, which warrants to renew the set of tools available in weed research to incorporate recent advances in phenomics and genomics. We are aiming to identify all the mutations confering resistance using genome-wide association mapping and use these association to predict levels of resistance in any uncharacterised population of ryegrass based on genomic information

Ryegrass infestation along the margins of a wheat paddock in Victoria
Our lab develops new tools to diagnostic herbicide resistance combining computer vision, genome sequencing technology and machine learning in collaboration with the GRDC and funded by the Department of Agriculture, Water and the Environment. With enough weed populations characterised, we will be able to test the most likely model of resistance emergence, between multiple local mutations and a few resistance hotspots that help mutations diffuse through gene flow. This program will deliver a landscape-scale understanding of herbicide resistance evolution in ryegrass (Lolium rigidum Gaud.), the most nocious weed in Australia and many Mediterranean regions.

The multiple evolutionary scales of herbicide resistance evolution

Exploring the potential of gene drives to control pest and invasive species

Australia has been and is vulnerable to biological invasion and resistance to control agents is a growing problem. Gene drives are emerging as powerful tools to transform the way we think population control. A gene drive is a selfish genetic element capable of self-replication and able to edit a specific allele and replace it with itself. Through this method, progeny of a gene drive individual will always inherit a copy of the gene drive, as will their progeny. After a number of generations, the gene drive may fixate. This could typically help to make currently ineffective herbicides useful again, by reintroducing a susceptibility allele in lieu of a resistance one.

Ryegrass infesting wheat (Photo: Ben Camm)

To reintroduce susceptilibty, we need to be able to change the allele frequencies at the population scale. However, release of synthetic gene drives requires careful initial risk assessment. In collaboration with CSIRO, we contribute to building a risk assessment platform through the modelling of gene drive evolution using experimental genomic data. This way we can increase the specificity of the analysis to simulate case studies as close as possible to what would happen for the release of a gene drive in the real world.

Lolium rigidum reference genome assembly

Download genome Genome browser

Lolium rigidum genome statistics. Left panel: Assembly statistics, and right panel: features of the Lolium rigidum genome (each tick is ×100Mb). Top right panel - lane a: GC content heatmap of mean GC content per 2.35Mb window (ranging from 42% to 47%); lane b: distribution of Copia long terminal repeat (LTR) retrotransposon family; lane c: distribution of Gypsy LTR retrotransposon family. Bottom right panel: chord diagram shows the syntenic relationships within the top 5 orthogroups with the most paralogs in the genome , where the colours match the colours of the chromosome most of the paralogs per orthogroup are located.

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