This project aimed to minimise the adverse impact of glyphosate-resistant weeds on the cotton industry by assessing the prospect that genetic diversity of targeted weed species can be used to predict which species are at highest risk of glyphosate resistance. Through this project, the industry has been able to develop bioinformatics and next generation sequencing skills, which was a capacity gap in understanding herbicide resistance.

Resistance to herbicides can happen by changes to the target gene (target site resistance) or other genetic changes (non-target site resistance, NTSR). Non-Target site resistance is particularly difficult to decipher as it is usually polygenic and can be constitutive, stress-induced, or possibly both. Cross resistance between different herbicide groups is not possible with target site resistance; however, since NTSR is the result of both regulatory processes (signal production, reception, and response) and protective processes of several kinds, they have the potential to interact together and accumulate, and possibly provide resistance across herbicide groups.

This project examined four weed species from cotton growing regions. The only species investigated that had a fixed target site mutation is Feathertop Rhodes grass. Fleabane, barnyard grass and windmill grass all have glyphosate resistance by NTSR mechanisms.

Gene expression analysis was conducted to test for genes that are more highly produced or supressed in resistant barnyard grass and fleabane to explore NTSR mechanisms in these two species. In barnyard grass about 50 genes are differentially expressed in intermediate resistant lines, whereas about 300 are in strong resistant lines. This indicates that NTSR is a polygenic trait in this weed.

In fleabane only five genes were differentially expressed in the resistant lines, and these genes are involved in plant signalling pathways and transporter proteins. It is therefore likely that NTSR in fleabane is controlled by relatively few genes and involves the transport of glyphosate within the plant.

The genomic data generated during this project (UQ1301) will be leveraged in project UQ1501 to

establish the mechanisms of NTSR in cotton-system weeds so that the threat of cross resistance can be assessed as the industry moves to stacked herbicide resistance traits.