Synchronization of crop seed germination

In order to ensure the survival of their offspring, many organisms employ a bet-hedging strategy whereby they produce a large number of progeny having different behavioural characteristics. This approach ensures that a subset of their progeny survive regardless of unexpected fluctuations in their environment.

Seed germination in plants also follows this bet-hedging strategy. While seeds are resistant to harsh environmental conditions, seedlings are not, and this makes the correct timing of germination critical for the future survival of plants. Plants have evolved noise-generating mechanisms to create variable behaviour within the individual seeds they produce in order to alter the timing of their germination responses to the environment. In this way at least a fraction of their progeny are ensured survival regardless of future climatic conditions.

While this is a powerful adaptive trait for the survival of plants in natural ecological settings, the asynchronous germination of seeds represents an obstacle to agriculture. The vast majority of food production begins with the planting of a seed, and the rapid and uniform establishment of seedlings in the field is key determinant of future yield. Non-uniform germination leaves gaps in the field which increases herbicide use, and asynchronous crop development lowers yield following single-pass mechanical harvesting. Robust and synchronous germination underpins the sale of high quality seed in the £52 billion annual global seed trade. Climate change and variable weather further exacerbates uniformity issues, which continue to persist.

This project seeks to uncover the mechanistic basis of variability generation and bet hedging in model and crop seeds, and to leverage this information to synchronise the germination of seed populations. This will be done together with industrial partner Rijk Zwaan through a mutually beneficial interaction.

We have previously developed a powerful predictive mathematical model that captures the relationships between hormones in seeds which determine when they germinate. Using this model, the preferential use of alternating temperatures to promote seed germination was accurately predicted (Topham et al. 2017, PNAS). This project will extend the use of this model to identify mechanisms that lead to the creation of variable germination-controlling hormone abundance in individual seeds. By identifying how variability in generated within individual seeds, targeted strategies to mitigate these noise-generating mechanisms will be utilized in order to harmonize the hormone content, and in turn germination, of seed populations.

Initial proof of concept studies will be performed in the model species Arabidopsis, and together with Rijk Zwaan this will be extended to the crop species lettuce where agronomically limiting issues in germination synchronization are present. By the conclusion of the project this same germplasm will be modified to have enhanced synchronization in their germination profile.

A second aspect to this project involves the development of a vital high throughput germination monitoring system. The expression of genes in individual seeds can be monitored dynamically, and used to predict the future timing of germination following early events. In this way the variability in seed populations can be quantified, and this system can be used to sort seeds having similar germination characteristics. This represents both a powerful scientific tool and agricultural technology to generate populations with synchronized germination behaviour.

This project will address a key scientific questions relating to variability and bet hedging which also have a direct and powerful relevance to modern food production systems and industry. Following state of the art modelling and biological approaches and an industrial partnership, the development of strategies and germplasm enhancing the synchronization of crop seed germination will be provided.

Variability in populations underpins bet-hedging strategies by producing non-uniform responses across individuals. This serves as an adaptive trait that enables species to survive diverse and unpredictable climatic conditions. While extensive research has provided mechanistic insights into how noisy inputs are filtered to generate robust outputs, much less is known as to how variability is generated and harnessed within individuals.

Bet-hedging mechanisms are utilized by seeds from plants to ensure the survival of their progeny. This is achieved by genetically-encoded noise generating mechanisms that enable seeds to germinate at different times. While this non-uniform behaviour is beneficial in an ecological context, it presents an obstacle in agriculture where uniformity is favoured.

Together with industrial partner Rijk Zwaan, this project will integrate molecular genetics, plant physiology and mathematical modelling to reveal the mechanistic basis of bet hedging in model and crop seeds, and develop germplasm with synchronized germination using rational approaches.

Our mathematical model describing the metabolic interactions between the antagonistically acting germination regulatory hormones abscisic acid (ABA) and gibberellic acid (GA) accurately predicts the ability of alternating temperature inputs to break seed dormancy. This project will leverage this model to uncover how variability in hormone content is generated within the individual seeds of both model and crop species. The identification of these noise-generating mechanisms enables the pursuit of rational synthetic biology approaches to harmonize the concentration of these regulatory molecules. This will lead to the creation of novel crop germplasm with increased synchronization of germination within the lifetime of this project. This will further provide a basis for synchronizing germination in diverse crop species, and the identification of the genetic basis of a bet-hedging mechanism.

Impacts for Society
The need for feed security and robust food production systems during rapid climate change represents one of the grand challenges facing the modern world. This project directly addresses this by developing crop germplasm leading to the more uniform establishment of plants in the field. The yield-limiting effects of climate change manifest themselves at the stage of crop establishment, and mitigating these impacts promises to increase food security.
The absence of plants in the field due to uneven seed germination also enables weeds to grow in gaps where crop canopies are absent. This leads to an increase in herbicide use. By increasing crop establishment uniformity, this project will reduce the application of these chemicals in our environment, benefitting broader society and the environment.
A partnership with seed industry leader Rijk Zwaan will ensure that novel germplasm with increased uniformity is created in a commercially relevant context. Working with this company also ensures that these seeds will ultimately reach the target end user to enhance food security.
This significance of seed quality and outputs of this research project will be shared with the greater public through public outreach events at the Birmingham ThinkTank science museum, and through University of Birmingham Community Days.

Economic impacts
The annual global seed trade is valued at over £52 billion and underpinning this is the sale of high quality seed that germinate synchronously. Enhancing uniformity provides a strategic market advantage. This project will develop rational strategies to improve seed performance in model and crop species, laying a foundation for robust climate change-resistant agriculture.
The enhancement of this key germination property in the crop species lettuce will be addressed in an industrially relevant context in collaboration with industrial partner Rijk Zwaan using their commercially sold lettuce germplasm. This promises to increase the economic potential for both seed sales, and increase the resilience of food production systems.
Our development of a high throughput single seed monitoring method predicting germination performance in individual seeds has been a long term objective of seed industry. This will enable seeds to be sorted on their future germination timing, and ensure the sale of high value seeds having uniform properties.

Training
The PDRA on this project will receive a highly interdisciplinary training involving mathematical modelling, synthetic biology and plant physiology. Working at the interface between experimental and theoretical biology will endow a highly desirable sets of skills to pursue further career opportunities in either academia or industry. Regular interaction with industrial partner Rijk Zwaan will further facilitate the opportunity to understand industrial activity and make relevant contacts.

Academic impact
Variability has been studied extensively at the single cell level, yet less is known about its influences at the whole organism and population levels in multicellular organisms. This makes this proposal of great value from both scientific and agronomic perspectives in light of the need to synchronize the germination of seed populations. Seeds are well suited to examine whole organism variability given the ability to measure large numbers over time and our high-throughput luciferase monitoring system using 96 well plates.
Mathematical approaches applied further enable the genetic basis of bet hedging in different plant species to be examined. The identification of these motifs represents an important step change in our understanding of heterogeneity in populations. This will in turn lead to the development of rational strategies to harmonise variability in populations through the targeted re-engineering of motifs that create noise.