Chemical manipulation and mechanisms of weed seed persistance, dormancy release and germination

Lead Research Organisation: Royal Holloway, University of London
Department Name: Biological Sciences

Abstract

An undeniable and expensive problem of any agricultural practice is the adaptation of weeds to these agricultural systems. This problem is further amplified by climate change, weeds adapt very quickly to environmental change including heat stress. The sustainable intensification of food production necessary to feed the world's growing population will only be achievable if crop harvest losses can be minimised. About 10% of crop production is currently lost to weeds and this loss would be far greater without the use of herbicides. However, the continued effectiveness of herbicide technology is threatened by the rapid advance of weed biotypes that are resistant to herbicides. Resistant weeds are now a problem across most chemical classes of herbicide and also across all the major cropping regions. Thus weed control represents a major concern for global food security, especially given that no new herbicide modes of action have been commercialized since the 1980s. New weed control tools are urgently required especially in the UK where EU/UK regulations have caused shrinkage in our 'crop protection toolbox' ("Healthy Harvest" initiative, UK National Farmers Union). Investment in crop protection in Europe has fallen from 33.3% of worldwide investment in the 1980s to 7.7% today. There is an urgent need for the development of new active substances which are effective and environmentally safe for the production of healthy food. This is also important for food quality and for preventing further food price rises which have recently affected UK consumers more than those in the mainland Europe.
The problem of effective weed control is most severe in annual field crop systems and with annual weeds which emerge at the same time as the crop seedlings. These problem weeds owe their success, at least in part, to the formation of large and persistent soil seed banks. The premise of the current application is that novel and effective weed control tools might be found in compounds that either 1) promote the coordinated germination of weed seeds in the soil bank and/or 2) in 'seedicides' that kill weed seeds at the ungerminated or a very early germination stage. In the former case, germination-promoting compounds might be applied prior to conventional herbicides (or alternative non-chemical strategies) to achieve more effective control of the total weed seed population while 'seedicides' might be applied after crops have emerged in order to limit late weed emergence. Currently, while some germination stimulants are known, none are commercial and neither do any commercial herbicides deliberately target seed-specific processes. All classical herbicides target processes of growing weed seedlings. Thus there is considerable potential for novel weed control solutions through engaging a deeper understanding of the processes of weed seed germination, survival and persistence.
This project establishes a collaboration between the Seed Biology Group of Prof G Leubner at Royal Holloway University of London and Weed Control Research Biology at Syngenta's International Research Centre Jealott's Hill. We plan to investigate the described issues with several representative problem weeds by first modelling their germination responses to a wide range in ambient temperatures, and then by choosing key temperatures to investigate the underlying hormonal changes and molecular mechanisms without and with the application of compounds known to break dormancy and induce germination of seeds. The obtained knowledge will be used to select compound libraries and screen for novel chemicals which have the potential to either promote the coordinated germination of weed seeds and/or to act as 'seedicides'. This will potentially identify novel modes of action instrumental for downstream research to fill our 'crop protection toolbox' with novel chemicals. Our project will generate knowledge to guide the development of novel strategies to control weeds by depleting the seed bank.

Technical Summary

The overall aim of this project is to gain a deeper understanding of the fundamental mechanisms of chemically-manipulated persistence, dormancy release and germination of weed seeds imbibed at key temperatures under lab conditions. The objectives and deliverables of this project are achieved in a collaboration between the Seed Biology Group of Prof G Leubner at Royal Holloway University of London and Syngenta Weed Control at Jealott's Hill International Research Centre. We will conduct cross-species weed seed dormancy and germination thermal-time modelling as affected by selected known dormancy release and germination stimulant (DR/GS) chemicals. This will deliver the quantitative physiological framework for the subsequent comparative hormone and transcriptome profiling to elucidate molecular mechanisms of DR/GS chemicals for different weed species at key temperatures and times during seed imbibition. From the phylotranscriptomics we will select differentially expressed genes and derive candidates for conserved and seed-specific target mechanisms. Together with published knowledge this will serve to select target-catalogue based compound libraries by utilising computional chemistry. Using Syngenta's expertise in high-throughput screening we will screen compound libraries to provide novel DR/GS chemicals for weed seed research. Further to this, we will also conduct screens to chemically manipulate weed seed persistence to study the molecular mechanisms underlying suicidal germination and to identify specific targets affecting seed longevity, aging and death. The mechanisms of two potential 'seedicides' will be analysed on the hormonal and transcriptome (RNAseq, qRT-PCR) level in distinct weed species. Our project has the potential to identify novel modes of action and to generate knowledge to guide the development of novel strategies to control weeds by depleting the seed bank.

Planned Impact

The UK has a highly successful agricultural industry which also exports food, but the UK is not self-sufficient in food production (www.foodsecurity.ac.uk). Therefore many domestic and international factors affect food production, prices, security and quality. This became for example evident during the 2008 world food price spike and the subsequent food price rises have affected UK consumers more than those in the mainland Europe. Furthermore, the reliance of imported food through trading is becoming increasingly unstable as a food security strategy, as we witness unforeseen destabilisation in developing markets such as Eastern Europe. Among the major threats to food production are in-crop weed competition and heat stress which cause severe harvest losses and have the highest negative impact on the sustainable intensification of food production (reports including Living with Environmental Change and The Royal Society Reaping the Benefits). Problem weeds owe their success and rapid adapation to climate change, at least in part, to the formation of large and persistent soil seed banks. This problem is further amplified by herbicide-resistant weeds (e.g. Busi et al. Evolutionary Applications 6:1218-21, 2013) which compromise classical weed management strategies and are most severe for annual weeds in annual field crop systems. A deeper understanding of germination/dormancy of weed seeds has been identified as a key area within Syngenta, specifically in relation to challenges of weed management which are a focus at Syngenta's Jealott's Hill International Research Centre. Our research will establish a collaboration of mutual benefit which will expand the expertise and research possibilities of both partners. Farmer and consumer will benefit from novel and safe herbicides for mitigating problem weeds for the production of healthy food.
Identifying new tools for weed control is especially critical for the UK as crop production levels and regulations cause shrinking of our 'crop protection toolbox' ("Healthy Harvest" initiative of the UK National Farmers Union). UK farmers therefore become less competitive against imported food produced to lower standards. The number of herbicide resistant weed species is growing in all regions of crop production, whilst the rate of introduction of new herbicidal products has declined. Indeed the last introduction of a novel mode of action was in the 1980's. The central scientific objective of our project is pre-competitive research to provide fundamentally novel and comprehensive insight into the mechanisms of chemically manipulated persistence, dormancy release and germination of weed seeds in response to distinct ambient temperatures including heat stress. Manipulation of weed seed behaviour will open up new opportunities for robust weed control strategies, without relying on the need to identify and register new herbicides. Identification of new herbicides is extremely difficult due to unique regulatory requirements in the EU which is discouraging investment in this space. Lack of new tools and deregistrations is eroding the competitiveness of UK/EU agriculture versus other major agricultural regions. New technologies to manipulate the weed population via the seed bank would be a significant supplementary approach to maintaining/increasing crop production, and extension of the weed control strategies available to UK/EU farmers. This project will also train research staff at the interface of fundamental seed biology and applied research into herbicides in weed control and thereby produce experts required for the UK job market in weed research and management. Regulators and government bodies will also benefit from evidence-based knowledge about herbicides in weed seed management. Clearly this research has impact on mitigating a major current threat for food production, and therefore enhances food quality, harvest quantity and the competitiveness of the UK bioeconomy.
 
Description The overall aim of this project "Chemical manipulation and mechanisms of weed seed persistence, dormancy release and germination" was to gain a deeper understanding of the fundamental mechanisms of chemically-manipulated persistence, dormancy release and germination of weed seeds imbibed at key temperatures under lab conditions. This was achieved with selected phylogenetically and "ecologically" distinct annual weed species by comparative (species and chemical compounds) physiological modelling of the conditions, comparative analysis of the associated endogenous hormonal changes and the use of transcriptomics. Key focus areas were:
Weed seed dormancy is released by karrikins and smoke-water.
Description of key physiological and morphological properties of distinct weed seeds.
The allelochemical Myrigalone A is a current focus and transcriptome and hormone analyses.
Publications are currently produced.
Exploitation Route Publication and by a Syngenta-funded follow-up project.
Sectors Agriculture, Food and Drink,Chemicals,Education,Environment

 
Description The research award announcement attracted further funding: 1) An associated BBSRC DTP PhD student scholarship 2015. The student passed the first-year Master with distinction and is now working on PhD level. 2) In addition a project on karrikin-effects on black-grass (£10k). Karrikin and smoke-water used to induce weed germination. This has triggered some public interest based on press releases. 3) Interest by the Royal Horticultural Society (RHS) to collaborate on the topic (Dr Alistair Griffiths, RHS Garden Wisley) of weed management in horticulture and public spaces. A collaboration application to NERC for a PhD iCASE scholarship in their 2016 competition was rejected without review because (a) they don't fund interdisciplinary work and (b) because weeds and environmentally-friendly weed management methods are not in their remit (which is very surprising). 4) The project also triggered that I became consultant and collaborator to the company Azotic Technologies (Nottingham, UK). 5) An associated BBSRC DTP PhD student scholarship 2017 (NPIF). 6) A BBSRC DTP studentship on Myrigalone A in collaboration with Syngenta and the biomedical research group of Prof Robin Williams at RHUL. 7) A follow-up 2-year project on weed management researchrch with a postdoc directly funded by Syngenta. 8) A teaching collaboration has been established which includes a day trip of a new Plant Biochemistry course to visit Syngenta Jealott's Hill International Research Centre
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Chemicals,Education,Environment
Impact Types Societal,Economic

 
Description BBSRC DTP CASE Studentship with Syngenta - PhD student Georges Heslop-Harrison (as Co-Supervisor). Characterising and Identifying the Molecular Mechanisms of Myrigalone A
Amount £109,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2022
 
Description BBSRC DTP CASE Studentship with Syngenta in the NPIF (National Productivity Investment Fund) funding scheme - PhD student Eddison Loades. Mechanisms of weed seed persistence and development of novel weed management tools.
Amount £136,000 (GBP)
Funding ID BB/R505730/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description BBSRC DTP Studentship with Syngenta - WeedSeeds - Thomas Holloway. Epigenetic and hormonal mechanisms of seed adaptation to changing ambient temperatures as targets for secure weed management tools.
Amount £109,000 (GBP)
Funding ID BB/R505730/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description Fire-adapted seed traits in Cerrado species
Amount £79,007 (GBP)
Funding ID NE/T004851/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2020
 
Description Imbibitional Seed Ingression Project with Gd
Amount £50,000 (GBP)
Organisation Azotic Technologies 
Sector Private
Country United Kingdom
Start 08/2016 
End 06/2017
 
Description Novel strategies for weed control: The potential of germination stimulants for 'flush and control'
Amount £235,000 (GBP)
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 12/2018 
End 02/2021
 
Title Biological samples of seeds for hormone, transcriptome and RT-qPCR 
Description Biological samples of seeds for hormone, transcriptome and RT-qPCR 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact Improved seed hormone and transcriptome analyses as described in various of our publications 
 
Title Weed seed transcriptomes 
Description Will be eventually available in connection with publications. Requires Syngenta approval. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Improves weed management research 
 
Description Chemical manipulation and mechanisms of weed seed persistence 
Organisation Syngenta International AG
Department Syngenta Ltd (Bracknell)
Country United Kingdom 
Sector Private 
PI Contribution WP1. Cross-species weed seed dormancy and germination thermal-time modelling as affected by selected Dormancy Release / Germination Stimulant (DR/GS) chemicals including fluridone, karrikins and gibberellins (GA). - Thermal-time modelling currently ongoing in our lab. - Morphological (microscopy) seed characterisation and identification of visible criteria for germination ongoing. - Effects of treatments with DR/GS chemicals (karrikins, gibberellins, fluridone) ongoing. Other WPs are future tasks depend on the outcomes of WP1, everything on time: WP2. Comparative hormone and transcriptome analysis to elucidate molecular mechanisms of DS/GS chemicals of different weed species at different seed imbibition temperatures. WP3. Utilising target-catalogue based compound libraries to characterise and refine novel targets by chemical manipulation and provide novel DR/GS chemicals for weed seed research. WP4. Chemical manipulation of weed seed persistence to study the molecular mechanisms underlying suicidal germination and to identify specific targets affecting seed longevity. Progress is as described in list of outputs/outcomes.
Collaborator Contribution WP1. Cross-species weed seed dormancy and germination thermal-time modelling as affected by selected Dormancy Release / Germination Stimulant (DR/GS) chemicals including fluridone, karrikins and gibberellins (GA). - Weed species and seed batches contributed. - Propagation of seed batches discussed and decided. - Karrikin and smoke water contributed. Other WPs are future tasks depend on the outcomes of WP1, everything on time: WP2. Comparative hormone and transcriptome analysis to elucidate molecular mechanisms of DS/GS chemicals of different weed species at different seed imbibition temperatures. - Hormone analysis discussed between partners and establishing analytics initiated. WP3. Utilising target-catalogue based compound libraries to characterise and refine novel targets by chemical manipulation and provide novel DR/GS chemicals for weed seed research. - Compound groups started to be discussed with Syngenta chemists. WP4. Chemical manipulation of weed seed persistence to study the molecular mechanisms underlying suicidal germination and to identify specific targets affecting seed longevity. Progress is as described in list of outputs/outcomes.
Impact This collaboration is multi-disciplinary with us at RHUL working on molecular seed physiology, while Syngenta is weed biology control research and chemicals. A recent mid-term report summarises the progress made. The overall aim of this project is to gain a deeper understanding of the fundamental mechanisms of chemically-manipulated persistence, dormancy release and germination of weed seeds imbibed at key temperatures under lab conditions. This will be achieved with selected phylogenetically and "ecologically" distinct annual weed species by comparative (species and chemical compounds) physiological modelling of the conditions, comparative analysis of the associated endogenous hormonal changes and the use of transcriptomics. Approximately 20 weed species were selected across the phylogenetic clades for testing their germination. Basic temperature response in weed seed germination was monitored using Grant 2-dimentional thermogradient table. Myrigalone A (MyA) is a rare C-methylated dihydrochalcone flavonoid from Myrica gale fruits (bog myrtle) known as allelochemical which affects competing plants or herbivores. Hormones and transcriptomes are currently being analysed. Publications are listed in the respective section.
Start Year 2015
 
Description Food Security and Sustainability 
Organisation Royal Holloway, University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution Interdisciplinary collaboration with Dr Ivica Petrikova, lecturer in food security in the PIR department.
Collaborator Contribution Interdisciplinary collaboration with Dr Ivica Petrikova, lecturer in food security in the PIR department.
Impact Interdisciplinary: Biology, Biomaterial Engineering, Politics and International Relations
Start Year 2018
 
Description Fruit Evolution and Adaptation to Mediterranean Habitats in Raphanus (Brassicaceae) 
Organisation University of Osnabrück
Department School of Biology/Chemistry Osnabrück
Country Germany 
Sector Academic/University 
PI Contribution Collaboration between Dr Tins Steinbrecher, myself and the lead of this project Prof Klaus Mummenhoff (University of Osnabrück, Germany). This is a trinational collaboration funding project between Prof Klaus Mummenhoff (University of Osnabrück, Germany), O. Barazan (Agricultural Research Organization, Israel), Jotham Ziffer-Berger (Hebrew University of Jerusalem, Israel), Thameen Hijawi (Al Quds University, Palestinian Authority), Nasser Samara (Association for Integrated Rural Development, Palestinian Authority)
Collaborator Contribution Collaboration between Dr Tins Steinbrecher, myself and the lead of this project Prof Klaus Mummenhoff (University of Osnabrück, Germany). This is a trinational collaboration funding project between Prof Klaus Mummenhoff (University of Osnabrück, Germany), O. Barazan (Agricultural Research Organization, Israel), Jotham Ziffer-Berger (Hebrew University of Jerusalem, Israel), Thameen Hijawi (Al Quds University, Palestinian Authority), Nasser Samara (Association for Integrated Rural Development, Palestinian Authority)
Impact Interdisciplinary collaboration
Start Year 2017
 
Description Seed hormone profiling 
Organisation Palacky University
Country Czech Republic 
Sector Academic/University 
PI Contribution Preparation of seed samples for hormone profiling.
Collaborator Contribution Hormone profiling analytics conducted and results received. Placements for PhD students and postdocs.
Impact Publications and ongoing future work for publications.
Start Year 2007
 
Description Weed and crop seed research collaboration with Ethiopia 
Organisation Debre Berhan University
Country Ethiopia 
Sector Academic/University 
PI Contribution Research collaboration on weed management and on crop seed technologies. Establishing network for GCRF collaboration applications.
Collaborator Contribution Research collaboration on weed management and on crop seed technologies. Establishing network for GCRF collaboration applications.
Impact Manuscript submitted on Lepidium draba weed science.
Start Year 2018
 
Description Fascination of Plants Day 2017 
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 Seed germination setup with different crop seeds to inspire the children about plant science and gardening. Exhibition of seed diversity in structures, sizes, shapes and colours and a seed-plant quiz for the same purpose.
Year(s) Of Engagement Activity 2017,2018
 
Description Interview with German Radio (Michael Stang, Deutschlandfunk) related to SEB Annual Meeting July 2016 Brighton, appeared on German radio (Forschung Aktuell): http://www.deutschlandfunk.de/forschung-aktuell.675.de.html 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview with German Radio (Michael Stang, Deutschlandfunk) related to SEB Annual Meeting July 2016 Brighton, appeared on German radio (Forschung Aktuell): http://www.deutschlandfunk.de/forschung-aktuell.675.de.html
Year(s) Of Engagement Activity 2016
 
Description Interview with UK journalist Jonathan Smith related to SEB Annual Meeting July 2016 Brighton: "Smoking out blackgrass seeds" - http://www.eurekalert.org/emb_releases/2016-07/sfeb-sob070116.php, also in Science Daily https://www.sciencedaily.com/releases/2016/07/160706091510.htm and The Farming Forum https://thefarmingforum.co.uk/index.php?threads/smoking-out-blackgrass-seeds.127862/ 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview with UK journalist Jonathan Smith related to SEB Annual Meeting July 2016 Brighton: "Smoking out blackgrass seeds" - http://www.eurekalert.org/emb_releases/2016-07/sfeb-sob070116.php,
also in Science Daily https://www.sciencedaily.com/releases/2016/07/160706091510.htm and
The Farming Forum https://thefarmingforum.co.uk/index.php?threads/smoking-out-blackgrass-seeds.127862/

Text related to interview July 2016 Brighton: "Researchers find smokewater combats problem weeds" appeared 07/07/2016 on RHUL website: https://www.royalholloway.ac.uk/biologicalsciences/news/newsarticles/researchers-find-smokewater-combats-problem-weeds.aspx
Year(s) Of Engagement Activity 2016
URL http://www.eurekalert.org/emb_releases/2016-07/sfeb-sob070116.php
 
Description Science Open Day at Royal Holloway University of London 
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 Seed germination setup with different crop seeds to inspire the children about plant science and gardening. Exhibition of seed diversity in structures, sizes, shapes and colours and a seed-plant quiz for the same purpose.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
URL http://www.rhul.ac.uk
 
Description The Seed Biology Place - www.seedbiology.eu 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our research, teaching and outreach website "The Seed Biology Place" - www.seedbiology.eu is internationally acknowledged and one of the most visited seed biology websites. It provides up-to-date information about seed dormancy and germination and the research of our group, as well as informs on seed anatomy, technology (seed industry), seed evolution and current topics in molecular seed biology and biotechnology. It is recommended by NetWatch of the Science Magazine (Science 313: 595, 2006) and by WebAlert (Current Opinion in Plant Biology 5: 371, 2002) as an information resource for research and teaching. The website has >900 visits / month and is usually among the top-10 hits in seed-related Goggle searches.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018
URL http://www.seedbiology.eu