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
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People |
ORCID iD |
| Paul Neve (Principal Investigator) |
Publications
Ravet K
(2018)
The power and potential of genomics in weed biology and management.
in Pest management science
Patterson EL
(2018)
Glyphosate Resistance and EPSPS Gene Duplication: Convergent Evolution in Multiple Plant Species.
in The Journal of heredity
Gaines TA
(2019)
Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance.
in The New phytologist
Gaines TA
(2021)
Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America.
in Molecular ecology
| 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 |