Bilateral NSF/BIO-BBSRC: Unravelling the Grass Leaf

Lead Research Organisation: John Innes Centre
Department Name: Cell and Develop Biology

Abstract

Flowering plants exhibit two major growth strategies. The dicot strategy is for the growing tip of the plant to climb upward by producing an elongating stem below it. Leaf buds are also generated at the growing tip and eventually these grow out from the stem to form fully grown leaves. The monocot strategy is for the growing tip to stay protected at the base of the plant and produce a series of concentric leaves that rise above it. Leaf blades emerge and bend outwards at the top of the concentric cylinder or leaf bases. Only at later stages does the growing tip itself rise upwards through elongation of the stem to produce the flowering structures. This monocot strategy has the advantage of protecting the growing tip at the base of the plant for much of its life history. It enables grasses to survive extensive grazing and is the growth strategy that underlies cereals like wheat, maize and rice.

Despite its ecological and agronomic importance, the monocot strategy is much less well understood than the dicot strategy. In particular, it is unclear how monocot leaf buds grow to form concentric cylinders topped by outwardly bending blades. By using computational modelling we have developed some preliminary hypotheses for how this might work. A key idea is that growth is oriented by a polarity field; analogous to the way a magnetic field can be used to orient directions of navigation. The observed growth and shape changes of the monocot leaf can then be explained by simple changes in the polarity field and pattern of growth rates it orients. The main aim of this proposal is to test and further build upon this model to determine whether the fields and rates of growth it predicts are correct or not. This will be achieved using the maize monocot system which has the advantage of having well developed genetics and associated technologies. By looking at markers that highlight the presumed polarity fields and determining the growth rates in different regions of the leaf we hope to test predictions of the model. Models will also be tested by analysing the mutants in which key transitions of development are disrupted. These studies will be made quantitative by writing computer programs that extract the relevant measures automatically. New computational methods will also be developed and applied to this system so that the processes can be understood at different levels, from cellular to tissue scale.

This type of study, which integrates computational and experimental approaches, should provide a rigorous and quantitative understanding of the mysteries behind the monocot growth strategy. The understanding it generates may also allow us to further modulate the shape and disposition of leaves in crops. The angle at which the leaf blade bends out, for example, depends on growth at the blade junction, and has an important effect on yield because it influences the amount of light that can be harvested for photosynthesis. Knowing how this process works and is controlled by genes may therefore help breeders improve crop performance.

Technical Summary

Through a combination of experimental and modelling approaches we aim to produce a mechanistic model for how the key developmental transitions underlying the monocot strategy are generated and genetically controlled. Hypotheses for key developmental and shape transitions will be tested by visualising maize PIN auxin transporter proteins, which act both as markers for tissue cell polarity and as readouts for auxin-based polarity coordination mechanisms. Further tests will be carried out by following the expression of genes known to affect PIN1 polarity and key developmental switches in maize. We will also introduce Cre-Lox reporters to enable induction and visualisation of clonal markers at various stages, allowing hypotheses about growth patterns to be tested. Both Confocal and Optical Projection Tomography imaging will be used to obtain information from the cellular to whole organ scales. We will apply the above methods to wild type and mutants which affect key transitions and determine whether the results confirm or refute particular hypotheses. We will also use the Cre-Lox system to generate timed clonal sectors for genes such as KN1 and analyse their consequences on polarity and growth. In parallel, computational methods will be developed to extract salient features and parameters from images generated by immunolocalisation, GFP markers, clonal analysis and live tissue tracking. The results will provide quantitative measures for hypothesis testing. In conjunction with the experiments described above, hypotheses for key developmental transitions will be further formulated and modified using the GPT computational framework, which allows tissues to be modelled as 2D sheets that deform in 3D. This framework will also be elaborated to allow cellular level models for polarity coordination to be explored, and models for the formation of volumetric 3D outgrowths, such as ligules, to be incorporated.

Planned Impact

This project will benefit non-academic beneficiaries, in the following ways:

1. Breeders will benefit from knowledge that will facilitate the selection of candidate genes for improving crop growth and yield by conventional or transgenic approaches. The expected time frame for this beneficial impact will be 10 years after the start of the project.

2. Biotech industries will benefit from our work in the long term, through the greater fundamental understanding of processes that underlie tissue properties in plants and animals. This may open up new avenues to exploit and manipulate growing tissues. They will also benefit from the tools developed in the project such as integrating computational methods with bioimaging approaches that may become applicable to their research and development programmes. The time frame for this type of impact is expected to be 10-20 years.

3. The general public and school children will benefit directly from this project through the proposed hands-on training events and through dissemination of latest research findings in an accessible way via media routes like youtube videos and press articles. They will also benefit in the longer term because of the contribution that this project will make to maintaining and developing forward-looking scientific research that provides the foundations of a modern healthy and growing economy.

4. BBSRC will benefit because the project is directly relevant to the research priority Systems Biology and the general area of food security. It will also benefit from the integration of expertise in developmental genetics of monocots from a leading lab in the USA, with computational modelling and image analysis in the UK, enhanced by leverage of funds from NSF.
 
Description A PhD student working on barley development in relation to this award has shown that plant development involves two polarity types: tissue cell (asymmetries within cells are coordinated across tissues) and regional (identities vary spatially across tissues) polarity. Both appear altered in the barley (Hordeum vulgare) Hooded mutant. Overall, the results suggest that key genes trigger different morphogenetic effects through interplay between tissue cell polarity, identity, and growth. We are now developing models to account for the key switches in growth and cell division in cereals, and validating software using Arabidopsis. We have published methods for modelling plant growth in 3D and are preparing papers on modelling of grass leaf growth, and ligule formation.
Exploitation Route Too early to be used at this stage.
Sectors Agriculture, Food and Drink

 
Description We have raised public awareness of the importance of understanding cereal growth and evolution through our website The Inner World of Cereals.
Sector Agriculture, Food and Drink
 
Description Maize leaf development 
Organisation University of California, Berkeley
Country United States 
Sector Academic/University 
PI Contribution We contribute computational modelling of development
Collaborator Contribution The partner is carrying out molecular genetic analysis in maize
Impact We were awarded an NSF/BBSRC grant
Start Year 2014
 
Description Article STEMM Champion: Sam Fox 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Cambridge Norwich Tech Corridor article about Sam Fox (Coen Lab) as a STEMM Champion.
Year(s) Of Engagement Activity 2019
URL https://www.techcorridor.co.uk/articles/tech-corridor-women-in-steam-the-scientists/
 
Description Bringing the 'Self-made Shape' exhibit to 'Science Uncovered 2016' at the Natural history museum 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact An exhibition stand called 'Self-made shape', which communicated research findings on how form and pattern develop in different plants, was created. The stand was very interactive, consisting of a very visual display of carnivorous plants, two computer games, a video, a shrinking plastic activity and a cellophane activity. The stand was exhibited to the general public at the 'Science Uncovered 2016' event at the Natural History Museum, London, on the 30th September 2016, an event that attracted 5,789 visitors.
Year(s) Of Engagement Activity 2016
 
Description Bringing the 'Self-made Shape' exhibit to Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact An exhibition stand called 'Self-made shape', which communicated research findings on how form and pattern develop in different plants, was created. The stand was very interactive, consisting of a very visual display of plants and pottery- combining science and art to explain research findings, two computer games, two videos, a shrinking plastic activity, a cellophane activity and a carnivorous plant section. The stand was exhibited at the first ever Norwich Science Festival (18th-30th October, 2016). The stand was one of two main attractions visited by 1409 students and 109 teachers from 36 high schools during the initial four 'Learning Days' alone, and by many more members of the general public throughout the rest of the festival. Members of the Coen Lab were interviewed about the Self-made Shape exhibit by Anglia News, Mustard TV, BBC Radio Norfolk and the Young Communications Team at the Forum.
Year(s) Of Engagement Activity 2016
URL https://www.jic.ac.uk/news/2016/11/celebrating-norwich-science-festival/
 
Description Bringing the 'Self-made Shape' exhibit to the Royal Society 'Summer Science Exhibition' 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact An exhibition stand called 'Self-made shape', which communicated research findings on how form and pattern develop in different plants, was created. The stand was very interactive, consisting of a very visual display of plants and pottery- combining science and art to explain research findings, two computer games, two videos, a shrinking plastic activity, a cellophane activity and a carnivorous plant section. The stand was exhibited to the general public at the Royal Society Summer Science Exhibition in London for a week (4th-10th July) . The event attracted 14,371 visitors, including 2,697 students, 328 teachers.
Year(s) Of Engagement Activity 2016
URL https://www.youtube.com/watch?v=QGgLfRUhW3Y
 
Description Chelsea Flower Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact 157 000 attendees at the Chelsea Flower Show had the opportunity to Engage with our research at our Silver Award Winning Exhibition at the Chelsea flower show.
Year(s) Of Engagement Activity 2019
URL https://genetics.org.uk/news/centenary-garden-exhibit-at-chelsea-flower-show-2019/
 
Description Created 'Self-made Shape' YouTube video 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This YouTube video explains scientific findings in relation to growth, polarity, form, pattern and the development of different morphologies to a lay audience. The video currently has 1353 views (15.02.17).
Year(s) Of Engagement Activity 2016
URL https://www.youtube.com/watch?v=QGgLfRUhW3Y&t=4s
 
Description Haldane Lecture at the Royal Institution 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Lecture at the Royal Institution. The lecture was recorded and has had 13,000 views on youtube
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=Q4QS62qMImw
 
Description Interview article in school science magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Sam Fox was interviewed for an article in a school magazine on the 7th March 2018. The interview was about her job as a plant scientist and the route educationally she took to get into that role.
Year(s) Of Engagement Activity 2018
 
Description Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Engagement activities with Norwich Science Festival on how genetics influences how plants grow and plant form
Year(s) Of Engagement Activity 2019
 
Description Press release: "How Snapdragons keep their colour: signposting trick reveals evolutionary mechanism" 
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 Media (as a channel to the public)
Results and Impact A press release was completed on the story and released to the John Innes Centre website with a link to collaborators and the paper. The story was also then promoted via the social media platform including Instagram, Twitter and Facebook. To promote the story further distribution platforms including 'Eurekaalert' (for a science specific audience) and 'Vuelio' (for a more general audience) were used. Own contacts were also followed up including local news reporters to ensure the paper and story was well publicised. The press release led to the following articles:

https://www.nytimes.com/2017/11/17/science/snapdragons-colors-genes.html

https://www.edp24.co.uk/news/environment/norwich-scientists-discovery-of-genetic-gymnastics-in-snapdragons-brings-new-insight-into-evolution-1-5294260

https://www.atlasobscura.com/articles/snapdragons-spanish-pyrenees

https://www.sciencedaily.com/releases/2017/11/171116142146.htm
Year(s) Of Engagement Activity 2017
URL https://www.jic.ac.uk/news/how-snapdragons-keep-their-colour-signposting-trick-reveals-evolutionary-...
 
Description Press release: "How Snapdragons keep their colour: signposting trick reveals evolutionary mechanism" 
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 Media (as a channel to the public)
Results and Impact A press release was completed on the story and released to the John Innes Centre website with a link to collaborators and the paper. The story was also then promoted via the social media platform including Instagram, Twitter and Facebook. To promote the story further distribution platforms including 'Eurekaalert' (for a science specific audience) and 'Vuelio' (for a more general audience) were used. Own contacts were also followed up including local news reporters to ensure the paper and story was well publicised.
Year(s) Of Engagement Activity 2017
URL https://www.jic.ac.uk/news/how-snapdragons-keep-their-colour-signposting-trick-reveals-evolutionary-...
 
Description Press release: "Leap forward in understanding plant organ growth" 
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 Media (as a channel to the public)
Results and Impact A press release was completed on the story and released to the John Innes Centre website with a link to collaborators and the paper. The story was also then promoted via the social media platform including Instagram, Twitter and Facebook. To promote the story further distribution platforms including 'Eurekaalert' (for a science specific audience) and 'Vuelio' (for a more general audience) were used. Own contacts were also followed up including local news reporters to ensure the paper and story was well publicised.
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/press-release/new-model-is-a-leap-forward-in-understanding-plant-organ-growth/
 
Description Press release: "Leaves possess a molecular compass" 
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 Media (as a channel to the public)
Results and Impact A press release was completed on the story and released to the John Innes Centre website with a link to collaborators and the paper. The story was also then promoted via the social media platform including Instagram, Twitter and Facebook. To promote the story further distribution platforms including 'Eurekaalert' (for a science specific audience) and 'Vuelio' (for a more general audience) were used. Own contacts were also followed up including local news reporters to ensure the paper and story was well publicised.
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/news/leaves-possess-a-molecular-compass/
 
Description Press release: "Snapdragon enters the genomic age" 
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 Media (as a channel to the public)
Results and Impact A press release was completed on the story and released to the John Innes Centre website with a link to collaborators and the paper. The story was also then promoted via the social media platform including Instagram, Twitter and Facebook. To promote the story further distribution platforms including 'Eurekaalert' (for a science specific audience) and 'Vuelio' (for a more general audience) were used. Own contacts were also followed up including local news reporters to ensure the paper and story was well publicised.
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/press-release/snapdragon-enters-the-genomic-age/
 
Description Science Cafe Public talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Enrico Coen and Scott Boden gave a joint Science Cafe talk entitled 'Cereals and Snapdragons' to the general public in Oct 2018 as a part of the Norwich Science Festival.
Year(s) Of Engagement Activity 2018
 
Description Skype interview with MSc student from Central St Martins University 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Discussions and advice on carnivorous plants, our research and scientific thinking for creation of an installation exploring plants in the environment.
Year(s) Of Engagement Activity 2019
 
Description Smithsonian magazine coverage of modelling work on how plants make leaves 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Coverage of our Science publication on understanding how leaf shape evolved through the study of carnivorous plants.
Year(s) Of Engagement Activity 2020
URL https://www.smithsonianmag.com/science-nature/deciphering-how-plant-genes-drive-weird-wonderful-dive...
 
Description Soapbox Science Norwich Science Festival: how plants shape their leaves 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact On the 27th October 2018 Beccy Horn in the Coen Lab stood on a raised platform in Norwich City Centre and spoke to the genral public about their research that understands how the different shapes of leaves are formed.
Year(s) Of Engagement Activity 2018
 
Description Talk at the Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact On the 24th October 2016 Enrico Coen gave a talk titled: "Why is a Snapdragon like a Fruit-fly?" to the general public at the Norwich Science Festival 2016.
Year(s) Of Engagement Activity 2016
 
Description Taught on a Genetics Society Communicating Science Course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact In April 016 Enrico Coen taught at a Genetics Society Communicating Science Course how to effectively disseminate your research to others.
Year(s) Of Engagement Activity 2016,2017
 
Description Visit to home educated students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Science discussion with home educated school children
Year(s) Of Engagement Activity 2019
 
Description Women of the Future 2017 Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The 3rd Women of the Future Conference took place on Wednesday 29th November 2017. 170 young girls from 17 schools across Norfolk and Suffolk attended the unique event. The event is specifically aimed at Year 10 girls, and aims to raise aspirations, broaden horizons and facilitate engagement with world class scientists and leaders and promote careers in STEMM subjects.

The lack of women in STEMM careers continues to be a real cause for concern for employers.

At the John Innes Centre we are committed to promoting equality and diversity for all our staff and students and in addition recognise the importance of inspiring the next generation of female STEMM professionals.

Having first been launched in 2015, this year's event built on the success of the previous two conferences, giving the participants a great chance to meet and speak with more than 27 female role models and exhibitors from a diverse range of industries.

There was also fascinating line-up of speakers that included science author and presenter Dr Emily Grossman, Senior Advisor for Medical Applications at CERN Dr Manjit Dosanjh, and JIC Research Fellow Dr Philippa Borrill.
Year(s) Of Engagement Activity 2017
URL https://www.jic.ac.uk/blog/women-of-the-future-2017/
 
Description Women of the Future Conference 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The Women of the Future 2018 event took place with 200 girls from yr 10 (14-15 yr olds)

5 GEN female people involved:
-Speakers Jemima Brinton & Mikhaela Neequaye (Jemima is a researcher in crop genetics, Mikhaela is a Phd student in food nutrition). Science Chat on the Sofa with Speakers (Auditorium) -Chaired by Samantha Fox
-Closing Remarks - Samantha Fox
-Meet a professional session: Mikhaela Neequaye, Natalie Wager, Jess Hughes, Penny Hundleby
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/blog/the-story-of-women-of-the-future-2018/
 
Description Year 10 Science Camp 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact We introduced year 10 science students to life as a scientist and working in our labs.
Year(s) Of Engagement Activity 2019
URL https://www.jic.ac.uk/training-careers/work-experience/year-10-science-camp/
 
Description YouTube video created: Evolutionary Genetics of Snapdragons 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 'A Flying Visit to the Antirrhinum Hybrid Zone in the Pyrenees'
Take a tour through the hybrid zone in the Pyrenees where a population of magenta Antirrhinum pseudomajus on the east meets a yellow Antirrhinum striatum population to the west and form a rainbow of hybrid flowers over a 1km stretch. Read about how our study of this region revealed how small RNA helps maintain diversity in the region. The video creates interest and communicates to the general public the research that takes place in the Coen Lab.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=muP7fSn1eaE&feature=youtu.be
 
Description YouTube video: movie explaining the relationship between growth and division in plants 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Sam Fox (Coen Lab) and Ruby O'grady in our communications team created a video explaining the relationship between growth and division in plants after a new model was published. The video had 1587 views from the JIC tweet alone on 13.03.19 and another 250 on the JIC YouTube Channel.
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=bvXBYL7WUDA
 
Description Youth STEMM Award mid-term conference 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 80 students from 8 schools in Norfolk and Suffolk attended the Youth STEMM award mid-term conference on the 26th February 2019. There were 2 talks from John Innes Centre scientists and 10 interactive stands including the Coen Lab, who displayed a range of plants and research, explaining to the students what they do for their job. Feedback from the event indicated that 95% of those that completed a feedback form (53/80) felt the event was informative as it highlighted a range of different STEMM careers out there. 80% said the event had made them inspired to pursue a STEMM related career, or take a STEMM subject at higher education. ""This exhibit has inspired me to take a higher education level in biology or as a job."
Year(s) Of Engagement Activity 2019
 
Description Youth STEMM Mid Term conference 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact On the 6th March 12 schools with 146 students (aged 13-17) participated in the YSA midterm conference at the JIC Conference Centre. The event had a combination of science talks and interactive activities as a part of the STEMM showcase. The Coen lab exhibited their research on evolution, development of shape and form and genetics at the event.
Year(s) Of Engagement Activity 2018