United States: Harnessing next-generation sequencing technologies for eco-evolutionary studies of herbicide resistance and weed biology

Lead Research Organisation: Rothamsted Research
Department Name: Biointeractions and Crop Protection

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

10 25 50
 
Description GCRF Impact Accelerator Award
Amount £10,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2017 
End 03/2017
 
Description GCRF Impact Accelerator Award
Amount £46,430 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2017 
End 03/2017
 
Description GCRF Impact Accelerator Award (17/18)
Amount £10,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2018 
End 01/2018
 
Description Black grass genome consortium 
Organisation Bayer
Country Germany 
Sector Private 
PI Contribution In December 2018, we finalised an agreement with Bayer Crop Science and Clemson University to collaborate towards the generation of a high-quality reference genome for the major agricultural weed, Alopecurus myosuroides (blackgrass). Rothamsted is contributing plant material for sequencing and re-sequencing and is making a contribution towards sequencing costs. Once sequence data is available, Rothamsted scientists will contribute towards the analysis of data and the publication of outputs in peer-reviewed journals.
Collaborator Contribution Clemson University is contributing bioinformatics expertise and time and will lead on the assembly and annotation of a reference genome. Bayer Crop Science are contributing biological material, expertise and consumables costs for sequencing. All parties will work together on data analysis and production of published outputs.
Impact No current outputs.
Start Year 2018
 
Description Black grass genome consortium 
Organisation Clemson University
Country United States 
Sector Academic/University 
PI Contribution In December 2018, we finalised an agreement with Bayer Crop Science and Clemson University to collaborate towards the generation of a high-quality reference genome for the major agricultural weed, Alopecurus myosuroides (blackgrass). Rothamsted is contributing plant material for sequencing and re-sequencing and is making a contribution towards sequencing costs. Once sequence data is available, Rothamsted scientists will contribute towards the analysis of data and the publication of outputs in peer-reviewed journals.
Collaborator Contribution Clemson University is contributing bioinformatics expertise and time and will lead on the assembly and annotation of a reference genome. Bayer Crop Science are contributing biological material, expertise and consumables costs for sequencing. All parties will work together on data analysis and production of published outputs.
Impact No current outputs.
Start Year 2018
 
Description Understanding invasion routes for glyphosate resistant Amaranthus palmeri into South America 
Organisation Federal University of Rio Grande do Sul
Country Brazil 
Sector Academic/University 
PI Contribution This new collaboration was funded by a GCRF Impact Accelerator Award made to Rothamsted Research. The collaboration was led by my team, in collaboration with the partners above and Dr Todd Gaines at Colorado State University. We established and shared protocols for the collection of South American Amaranthus palmeri populations and arranged for RAD-Seq reduced coverage genome sequencing. This data is being analysed at Rothamsted with a view to determining the introduction routes of this species into South America.
Collaborator Contribution Partners collected local plant material from agricultural fields in Brazil, Argentina and Uruguay. Plant material was shipped to the Federal University of Rio Grande do Sul for DNA extraction and shipping to a sequencing provider in the USA.
Impact Work in progress
Start Year 2017
 
Description Understanding invasion routes for glyphosate resistant Amaranthus palmeri into South America 
Organisation INIA Uruguay
Country Uruguay 
Sector Academic/University 
PI Contribution This new collaboration was funded by a GCRF Impact Accelerator Award made to Rothamsted Research. The collaboration was led by my team, in collaboration with the partners above and Dr Todd Gaines at Colorado State University. We established and shared protocols for the collection of South American Amaranthus palmeri populations and arranged for RAD-Seq reduced coverage genome sequencing. This data is being analysed at Rothamsted with a view to determining the introduction routes of this species into South America.
Collaborator Contribution Partners collected local plant material from agricultural fields in Brazil, Argentina and Uruguay. Plant material was shipped to the Federal University of Rio Grande do Sul for DNA extraction and shipping to a sequencing provider in the USA.
Impact Work in progress
Start Year 2017
 
Description Understanding invasion routes for glyphosate resistant Amaranthus palmeri into South America 
Organisation University of Buenos Aires
Country Argentina 
Sector Academic/University 
PI Contribution This new collaboration was funded by a GCRF Impact Accelerator Award made to Rothamsted Research. The collaboration was led by my team, in collaboration with the partners above and Dr Todd Gaines at Colorado State University. We established and shared protocols for the collection of South American Amaranthus palmeri populations and arranged for RAD-Seq reduced coverage genome sequencing. This data is being analysed at Rothamsted with a view to determining the introduction routes of this species into South America.
Collaborator Contribution Partners collected local plant material from agricultural fields in Brazil, Argentina and Uruguay. Plant material was shipped to the Federal University of Rio Grande do Sul for DNA extraction and shipping to a sequencing provider in the USA.
Impact Work in progress
Start Year 2017
 
Description Bridging the gap between weed genomics and herbicide resistance management 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Paul Neve organised and chaired the workshop. A resulting paper with Neve and Gaines as joint corresponding authors was submitted and is in review. The workshop was part of ongoing efforts to promote an international community effort towards an international weed genomics consortium with Neve and Gaines as key contributors
Year(s) Of Engagement Activity 2017
 
Description Department seminar (Colorado State University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Paul Neve presented a department seminar to the Bioagricultural Sciences & Pest Management Department at Colorado State University.

Title "Evolution at large: Eco-evolutionary approaches to understand herbicide resistance from gene to landscape"
Year(s) Of Engagement Activity 2016
 
Description Department seminar: Colorado State University "Evolution at large; the blackgrass epidemic from field to gene" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Presented above titled talk as part of departmental seminar series at Colorado State University
Year(s) Of Engagement Activity 2018
 
Description Global Herbicide Resistance Challenge conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talks and poster were given by a number of the BGRI team (Comont, Onkokesung, Neve, Hull, Crook). Neve organised a workshop on weed genomics for weed management. This workshop and other related follow on activities has led to the establishment of an international weed genomics consortium, including well-advanced plans to generate a reference genome for black-grass.
Year(s) Of Engagement Activity 2017
 
Description International Weed Genomics Consortium: follow-up meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Paul Neve co-organised a meeting of the International Weed Genomics Consortium at the Weed Science Society of America annual meeting. At this meeting further steps were taken towards the establishment of a coordinating committee for this global efforts towards generating genomic resources for the world's most important weed species.
Year(s) Of Engagement Activity 2018
 
Description Invited annual David Staniforth Lecture, Iowa State University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Paul Neve was invited to this annual, memorial lecture entitled "Weed science: running to stand still?"
Year(s) Of Engagement Activity 2017
 
Description London Evolutionary Research Network conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The London Evolutionary Research Network is run by a collective of postgraduate students and early career scientists working at universities and institutions in and around London. During December 2016, the LERN organised their 2016 conference around the theme 'Applying evolutionary principles to medicine and agriculture' I was an invited keynote speaker and presented a 45 minute talk entitled 'Running to stand still': the evolution of resistance to pesticides and drugs in agriculture and medicine. The talk was attended by about 60 PhD students, postdoctoral scientists and researchers.

The conference provided the opportunity for early career researchers, working in the sometimes disparate fields of medicine and agriculture to come together and share perspectives on the evolutionary challenges and solutions relating to efforts towards securing global food security, human healthcare and bioscience for health
Year(s) Of Engagement Activity 2016
URL https://londonevolution.org/lern2016/
 
Description Mountain West Integrated Pest management Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Paul Neve made a presentation on weed management, herbicide resistance and the pesticide regulatory environment in the UK and EU.

The audience which consisted of industry reps, weed management practitioners and regulators asked a number of questions following the presentation and there was a broader discussion about herbicide resistance problems and the regulatory environment, contrasting the situation in the EU with that in the USA.
Year(s) Of Engagement Activity 2016
 
Description Optimising herbicide use to reduce selection for resistance 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Paul Neve gave a lecture to postgraduate students on the weed ecology and management course at Colorado State University.
Year(s) Of Engagement Activity 2016
 
Description Rothamsted Festival of Ideas 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact In addition to talks and presentations from SCP staff, the work from this programme was presented and discussed with the public over four days at 7 different stalls:

1. Tree of Trade-offs: Balancing the pros and cons, what would you like the future of British agriculture to look like? • More food, greener pastures • healthy diets, cheap produce • profitable farming Explore the issues, and hang a leaf on our tree of trade-offs to air your view.
2. Gene Hunters: THE ASSEMBLATHON: two minutes to build a genome, and one that resists disease and provides bigger and better crops. ENTER THE MATRIX: discover how networks of knowledge provide clues about unknown genes, and explore pathways between data. PHYLO: match DNA blocks correctly for the top score, as scientists use matching gene sequences to identify species.
3. Scents and Sensibility: Organisms use chemical signals to communicate with each other. • crop and livestock pests produce scents • learn how we decode these signals • develop new ways to control pests • and apply that knowledge in the field Natural scents can reduce our reliance on synthetic pesticides.
4. Air Detectives: Find out what is in the air around you... and come and see if you are able to match the image to the name. • spores in the air cause plant disease • see how we capture those spores • be amazed by our new automatic trap Enjoy a brief history of "aerobiology", and how Rothamsted helped to develop the field.
5. Combating the Super Pests: An evolutionary arms race is pitting us against the organisms that threaten our food crops. • insects, pathogens and weeds • they all adapt to evade our control • hear how we are tackling resistance Discover more about the super-pests that threaten global food security
6. Cereal Killers: Find out how fungi infect plants, and watch them taking over through our binocular microscope. • infect a plant with your favourite killer • test your knowledge against our quiz • and enjoy a tasty edible fungi as a prize Learn about the difference between good and bad fungi, and the role of bacteria.
7. Insect Friends with benefits: Bees and ladybirds are heroes but many other insects also pollinate crops and eat pests. • flights in the "bumble-arium" • lasers to detect friend or foe It's not all about field margins; gather ideas to benefit insects in your garden.
Year(s) Of Engagement Activity 2018
URL https://www.rothamsted.ac.uk/sites/default/files/2018%20Rothamsted%20Festival%20Evaluation%20Report%...
 
Description Todd Gaines - glyphosate resistance in the USA 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Todd Gaines (CSU partner lab) presented at a black-grass management workshop at Rothamsted Research. Todd discussed the widespread evolution of resistance to the herbicide glyphosate that has occurred, and continues to occur in the USA. This international perspective provided a salient example to attending representatives from industry and regulatory authorities of the risks of glyphosate resistance, a growing area of concern in the UK.
Year(s) Of Engagement Activity 2016
 
Description Todd Gaines research seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Todd Gaines from the partnering lab at Colorado State University presented a 45 minute research seminar on latest research in herbicide resistance mechanisms and weed genomics. The presentation was made as part of the regular pesticide resistance series at Rothamsted Research.
Year(s) Of Engagement Activity 2016