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Ecophysiological and molecular mechanisms of weed seed bank persistence


Project Description

Weeds are a major threat to modern agriculture. For example, blackgrass is considered the most destructive cereal weed in European agriculture. The overall aim of this project is to gain insight into fundamental mechanisms of weed adaptation to provide sustainable solutions for weed management. To address this challenge with an interdisciplinary approach, the supervisory team is from Royal Holloway University of London's Seed Science group (Prof Gerhard Leubner and Dr Kazumi Nakabayashi) and Syngenta's Weed Control Research unit (Dr Chun Liu and Anne Seville) at Syngenta's Jeallot's Hill International Research Centre (Bracknell, UK). Seed dormancy in agricultural weeds is the key factor regulating weed emergence patterns in the field. Together with seed viability and persistence, it affects the behaviour of the weed seed bank, which is of vital importance to designing effective weed control strategies.

Blackgrass (Alopecurus myosuroides) is propagated solely by seed. Release of the seed dormancy results in two peaks of seedling emergence during the growing season: a major peak in autumn and a minor peak in spring, affecting the establishment of winter and spring cereals respectively. This phenomenon is well described in field experiments that provide an agro-ecological description of blackgrass seedling emergence, however the ecophysiological and molecular mechanisms underpinning the enforcement and release of seed dormancy, viability and persistence in blackgrass and other important weeds remain largely unknown. This project aims to investigate these mechanisms for informing the development of more effective emergence models and control strategies. We have established that temperature has an important role in the dormancy release and with identified candidate genes involved in this process using an RNAseq approach (Holloway et al. 2020, in prep.), the proposed interdisciplinary project would build on this work.

This Industrial CASE PhD student project will conduct comparative ecophysiological analysis of blackgrass seed lots of interest using population-based hydrothermal-time modelling of dormancy, responses to abiotic stresses and chemicals. The student will analyse dormancy cycling by lab simulation and burial experiments combined with RT-qPCR analysis of gene expression. This will identify dominant abiotic factors and chemicals which can alter dormancy in weed seeds. Quantitative analysis of selected blackgrass seed lot longevity/viability as affected by maternal temperatures. The student will conduct seed ageing assays to quantify the reduction in vigour (speed) and viability (death), identify molecular markers for longevity (RT-qPCR and RNAseq), and investigate the hormonal and epigenetic mechanisms. In the field two annual blackgrass emergence peaks are the result of phenotypic plasticity in response to maternal environmental conditions such as vernalisation. The ecophysiological and molecular analysis of this and transfer of identified molecular mechanisms and quantitative ecophysiological parameters to the modelling of weed seed banks in arable fields. This will provide a data package which can be readily used in the parameterisation of existing weed population models and in the design of weed management strategies to generate impact from the research conducted.

For training and support the student will be integrated into the Seed Science group of Prof Gerhard Leubner (lead supervisor) and Dr Kazumi Nakabayashi (co-supervisor) at RHUL. Their group has >10 postdocs, PhD and technician researchers who will provide further expert support in multidisciplinary methods such as biomechanical engineering, 3D imaging, transcriptome, microscopy and biochemistry. Interdisciplinary team work in a research environment representing a critical mass is providing the research excellence and superb training opportunities. Regular meetings with the RHUL and Syngenta supervisors support the project development.

CASE placement

The student will spend at least 3 months at Syngenta, supervised by Dr Chun Liu and Anne Seville. They will receive an induction to the company which will give them a feel for how a commercial company operates. During the placement, the student will discuss the experimental design, data analysis and how the results contribute to weed management strategies from a practical point of view. Dr Chun Liu will introduce the principles of mathematical modelling, model types, trade-off between complexity and uncertainly, appropriate approaches for descriptive models vs. predictive models, how the data generated by the student can be used to parameterise the existing weed population models, and how model simulations can point to knowledge gaps and future directions for more fundamental research.

BBSRC Priority Area: Agriculture and Food Security, Collaboration with the UK's Industry

Applications

Applications must be complete, including both references, by 24th January 2020

Funding Notes

Fully funded place including home (UK) tuition fees and a tax-free stipend in the region of £17,009. Students from the EU are welcome to submit an application for funding, any offers will be subject to BBSRC approval and criteria.

References

• The Seed Biology Place - www.seedbiology.eu
• Finch-Savage WE, Leubner-Metzger G (2006). Seed dormancy and the control of germination. Tansley review: New Phytologist 171: 501-523 - Highly cited review (>>1000-times)
• Mohammed S, Turečková V, Tarkowská D, Strnad M, Mummenhoff K, Leubner-Metzger G (2019). Pericarp-mediated chemical dormancy controls the fruit germination of the invasive hoary cress weed (Lepidium draba), but not of hairy whitetop (Lepidium appelianum). Weed Science - https://doi.org/10.1017/wsc.2019.33
• Arshad W*, Sperber K*, Steinbrecher T, Nichols B., Jansen VAA, Leubner-Metzger G*, Mumenhoff K* (2019). Dispersal biophysics and adaptive significance of dimorphic diaspores in the annual Aethionema arabicum (Brassicaceae). New Phytologist 221: 1434–1446 - *shared first or corresponding/senior authors.
• Sperber K*, Steinbrecher T*, Graeber K, Scherer G, Clausing S, Wiegand N, Hourston JE, Kurre R, Leubner-Metzger G*, Mummenhoff K* (2017). Fruit fracture biomechanics and the release of Lepidium didymum pericarp-imposed mechanical dormancy by fungi. Nature Communications 8:1868, *shared first or corresponding/senior authors.
• Scheler C, Weitbrecht K, Pearce SP, Hamstead A, Büttner-Mainik A, Lee KJD, Voegele A, Oracz K, Dekkers BJW, Wang X, Wood ATA, Bentsink L, King JR, Knox JP, Holdsworth MJ, Müller K, Leubner-Metzger G (2015) Promotion of testa rupture during garden cress germination involves seed com-partment-specific expression and activity of pectin methylesterases. Plant Physiology 167:200-215
• Graeber K, Linkies A, Steinbrecher T, Mummenhoff K, Tarkowská D, Turečková V, Ignatz M, Sperber K, Voegele A, de Jong H, Urbanová T, Strnad T, Leubner-Metzger G (2014). DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination. Proceedings of the National Academy of Sciences of the USA 111:E3571–E3580, doi: 10.1073/pnas.1403851111

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