Herbicide resistance evolution can be tamed by diversity in irrigated Australian cotton: a multi-species, multi-herbicide modelling approach.

BACKGROUND: Because herbicide resistance evolves in very large populations over periods of many years, modelling is an important tool for investigating the dynamics of the problem. The Diversity model tracks the simultaneous evolution of resistance to multiple herbicides, using multiple genetic pathways, in several weed species at once. Tracking multiple species and simultaneous resistances is an important development in resistance modelling. We used the Diversity model to test weed management strategies for new cropping cotton varieties with multiple herbicide tolerances ('triple-stacked' varieties), in an Australian context. RESULTS: The diversity required for long-term control of three key weeds in Australian cotton goes beyond using three herbicides, especially where there is already a substantial background of existing resistance to one or more of these herbicides. Assuming some glyphosate resistance is already present, simulations showed that glyphosate-resistant summer grass populations reach 20 000 seeds m-2 within 12 years using the triple-stack herbicides (glyphosate, glufosinate and dicamba) and a minimum of other tactics. Adding three pre-emergent modes of action plus cultivation to the system effectively controls glyphosate-resistant grasses for over 30 years. In conditions where resistance genes are as frequent as 1 in 100, however, highly fecund weeds such as Conyza bonariensis are hard to control beyond 15 years even with very highly diverse management. CONCLUSIONS: Stacked herbicide tolerances in new crop varieties offers potential for increased herbicide diversity, but existing glyphosate-resistant weed populations need substantial extra management beyond what a glyphosate/glufosinate/dicamba resistance stack provides. More diverse systems can provide robust management over 30 years in the absence of very high levels of background resistance to other herbicides. © 2018 Society of Chemical Industry.

Complete chloroplast genome of glyphosate resistant Sonchus oleraceus L. from Australia, with notes on the small single copy (SSC) region orientation.

Sonchus oleraceus, common sowthistle, is an asteraceous weed in Australian agricultural systems and has recently developed resistance to glyphosate. We present the complete chloroplast sequence of S. oleracueus reconstructed from Illumina whole genome shotgun sequencing. This is the first complete chloroplast genome available for the genus Sonchus. The complete chloroplast sequence is 151,808 bp long. A Bayesian phylogeny of the chloroplast coding regions of the tribe Cichorieae (Asteraceae) is presented. The S. oleraceus chloroplast genome is deposited at GenBank under accession number MG878405.

Gene expression in response to glyphosate treatment in fleabane (Conyza bonariensis) - glyphosate death response and candidate resistance genes.

BACKGROUND: This study takes a whole-transcriptome approach to assess gene expression changes in response to glyphosate treatment in glyphosate-resistant fleabane. We assessed gene expression changes in both susceptible and resistant lines so that the glyphosate death response could be quantified, and constitutively expressed candidate resistance genes identified. There are three copies of the glyphosate target site (5-enolpyruvylshikimate-3-phosphate; EPSPS) gene in Conyza and because Conyza bonariensis is allohexaploid, there is a baseline nine copies of the gene in any individual. RESULTS: Many genes were differentially expressed in response to glyphosate treatment. Known resistance mutations are present in EPSPS2 but they are present in a glyphosate-susceptible line as well as resistant lines and therefore not sufficient to confer resistance. EPSPS1 is expressed four times more than EPSPS2, further reducing the overall contribution of these mutations. CONCLUSION: We demonstrate that glyphosate resistance in C. bonariensis is not the result of EPSPS mutations or overexpression, but due to a non-target-site mechanism. A large number of genes are affected by glyphosate treatment. We present a list of candidate non-target-site-resistance (NTSR) genes in fleabane for future studies into these mechanisms. © 2017 Society of Chemical Industry.

Complete chloroplast genome sequences of six lines of Echinochloa colona (L.) link.

Barnyard grass (Echinochloa colona, (L.) Link) is the wild relative of barnyard millet (E. frumentacea (Roxb.) Link). This species, widely distributed globally, is an agricultural weed and has developed resistance to several herbicides including glyphosate. This paper presents the complete chloroplast sequences of two haplotypes (139,718 bp & 139,719 bp) sequenced from six lines of E. colona from Australia. The E. colona chloroplast sequence is very similar to that of E. frumentacea (163-169bp =0.12% differences across the genome). The gene content, arrangement, and the inverted repeat structure is the same as in the other species of Echinochloa sequenced to date.

Complete chloroplast genome sequences of two species of Chloris grass, Chloris truncata Sw. and Chloris virgata R.Br.

Chloris truncata (windmill grass) and Chloris virgata (feathertop Rhodes grass) are both weedy grass species that have developed resistance to glyphosate in Australia. This paper describes the complete chloroplast genomes of these two species generated by high throughput shotgun sequencing. The chloroplast genome of C. truncata is 135,584 bp and C. virgata is 134,561 bp; both have a GC content of 38%. The gene content and order followed the conserved pattern observed across the subfamily Chloridoideae.

Complete chloroplast genome of glyphosate resistant Conyza bonariensis (L.) Cronquist from Australia.

Conyza bonariensis, flaxleaf fleabane, is a serious weed in Australian agricultural systems, particularly the north-east cropping system. We present the complete chloroplast sequence of C. bonariensis reconstructed from Illumina whole genome shotgun sequencing. This is the first complete chloroplast genome available for genus Conyza. The complete chloroplast sequence is 153,014 bp long, and has the same gene content and structure as other members of the tribe Astereae. A Bayesian phylogeny of the chloroplast coding regions of 18 representatives of Astereae is presented. The C. bonariensis chloroplast genome is deposited at GenBank under accession number MF276802.

Herbicide resistance modelling: past, present and future.

Computer simulation modelling is an essential aid in building an integrated understanding of how different factors interact to affect the evolutionary and population dynamics of herbicide resistance, and thus in helping to predict and manage how agricultural systems will be affected. In this review, we first discuss why computer simulation modelling is such an important tool and framework for dealing with herbicide resistance. We then explain what questions related to herbicide resistance have been addressed to date using simulation modelling, and discuss the modelling approaches that have been used, focusing first on the earlier, more general approaches, and then on some newer, more innovative approaches. We then consider how these approaches could be further developed in the future, by drawing on modelling techniques that are already employed in other areas, such as individual-based and spatially explicit modelling approaches, as well as the possibility of better representing genetics, competition and economics, and finally the questions and issues of importance to herbicide resistance research and management that could be addressed using these new approaches are discussed. We conclude that it is necessary to proceed with caution when increasing the complexity of models by adding new details, but, with appropriate care, more detailed models will make it possible to integrate more current knowledge in order better to understand, predict and ultimately manage the evolution of herbicide resistance.

Simulating the evolution of glyphosate resistance in grains farming in northern Australia.

BACKGROUND AND AIMS: The evolution of resistance to herbicides is a substantial problem in contemporary agriculture. Solutions to this problem generally consist of the use of practices to control the resistant population once it evolves, and/or to institute preventative measures before populations become resistant. Herbicide resistance evolves in populations over years or decades, so predicting the effectiveness of preventative strategies in particular relies on computational modelling approaches. While models of herbicide resistance already exist, none deals with the complex regional variability in the northern Australian sub-tropical grains farming region. For this reason, a new computer model was developed. METHODS: The model consists of an age- and stage-structured population model of weeds, with an existing crop model used to simulate plant growth and competition, and extensions to the crop model added to simulate seed bank ecology and population genetics factors. Using awnless barnyard grass (Echinochloa colona) as a test case, the model was used to investigate the likely rate of evolution under conditions expected to produce high selection pressure. KEY RESULTS: Simulating continuous summer fallows with glyphosate used as the only means of weed control resulted in predicted resistant weed populations after approx. 15 years. Validation of the model against the paddock history for the first real-world glyphosate-resistant awnless barnyard grass population shows that the model predicted resistance evolution to within a few years of the real situation. CONCLUSIONS: This validation work shows that empirical validation of herbicide resistance models is problematic. However, the model simulates the complexities of sub-tropical grains farming in Australia well, and can be used to investigate, generate and improve glyphosate resistance prevention strategies.