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Integration of seasonal signals through a two gene mutual repression switch in flower buds

Reference	BB/S003878/1
Principal Investigator / Supervisor	Professor Steven Penfield
Co-Investigators / Co-Supervisors	Dr Xiaoqi Feng, Dr Judith Irwin
Institution	John Innes Centre
Department	Crop Genetics
Funding type	Research
Value (£)	424,870
Status	Completed
Type	Research Grant
Start date	01/03/2019
End date	28/02/2023
Duration	48 months

Abstract

The floral repressor FLC plays a key role in seasonal temperature sensing, modulating its epigenetic state according to past temperature experience. Importantly, temperature controls FLC expression by transcriptional regulation of a group of non-coding antisense RNAs synthesised at the FLC locus, collectively known as COOLAIR. During flowering time regulation a central role of FLC is to inhibit FT expression in leaves, and we have shown that maternal FLC and FT also mediate and control progeny seed dormancy, enabling maternal temperature signals to be passed to progeny. Further investigation of the mechanism by which FLC and FT control seed dormancy has changed the way we think about how seasonal environmental signals are integrated to control plant development. Here we show that FT controls dormancy not by regulation of a downstream target, but by feedback regulation of FLC itself through the COOLAIR promoter. Furthermore, we show that FT can transfer environmental information to COOLAIR, such as photoperiod regulation. Therefore, we propose that instead of acting stepwise to control plant reproductive development, FT and FLC functions are linked into a mutual inhibition switch, with FLC functioning as a store of multiple types of seasonal environmental data, not just temperature. Our aim is to investigate how this feedback regulation between FT and FLC generates and utilises seasonal information. In attempting to locate the tissue in which FLC/FT switching occurs, we provide new data to show that flower buds are also a key site of seasonal sensing in Arabidopsis: this insight more closely aligns our understanding of control of annual plant behaviour with that of trees which also make vernalisation-responsive flower buds. We now aim to understand the significance of environmentally plastic FLC gene expression domains in flowers for dormancy control and the mechanism by which FLC expression switches sex in flowers.

Summary

Plants use the seasonal cues temperature and day-length to time their transition from vegetative to reproductive development. Weather and climate affects plant development primarily by acting on these signalling pathways, and thus this is a highly studied area of plant biology from which a simple paradigm has emerged, especially in the control of time to flowering. Firstly, long term temperature is sensed by the FLC locus, with temperature known to affect FLC mRNA transcription (at least in part through regulation of antisense transcript) and resulting in epigenetic changes to FLC that reflect seasonal progression. In leaves FLC represses the expression of a second key gene FT, which receives a separate signal at its promoter that reflects a measurement of day length. Thus, temperature and day-length information is believed to act additively at the FT promoter to modify plant behaviour. FT is a general phloem-mobile seasonal signal, acting as a transcriptional co-factor in target cells to promote developmental programmes associated with summer. We have been studying the same seasonal sensing pathway in the control of seed dormancy. This is a maternal process through which the mother uses her memory of seasonal information to affect the dormancy characters of her progeny seed. In this way we have previously shown that seasonal information is passed from mother to progeny in plants. The preliminary data we present here show that although FLC and FT are two of the most intensively-studied genes in plants, the above paradigm of stepwise additive integration of seasonal cues at the FT promoter cannot explain our observations on the maternal control of seed dormancy. Specifically, we show using genetics, gene expression analysis and chromatin immunoprecipitation that FLC is a previously unrecognised direct target of FT, and that FT can deliver day-length information to the antisense FLC promoter. Thus we propose a new model for plant seasonal sensing in which FT and FLCboth inhibit each other in a classical two gene mutual inhibition switch, a very similar model to that believed to control cell cycle progression. Such a switch is likely to have non-linear properties, and integrate day-length and temperature information in non-obvious ways to control the effects of weather, seasons, and climate on plant development. The first Objective, split into three parts, aims to discover missing components of the FT/FLC seasonal switch, and how the switch operates in response to seasonal combinations of temperature and photoperiod cues. We focus on the timing and duration of winter temperature cues, and how their sensing and efficacy can be modified by occurring in days with different photoperiods. For instance, temperature cues experienced in longer days might affect the system in a different way to temperature cues experienced in very short winter days. The second part of the proposal deals with identifying the tissue in which the switch occurs to control post-flowering reproductive development. We show striking preliminary evidence that the FT/FLC switch has a dramatic spatial dimension in flowers, with environmental cues and FT causing FLC mRNA expression to switch from the female organ to the male organ. We hypothesise therefore that environmental cues controlling seed dormancy are sensed in developing flower buds, also the time at which development of the first seed structures begins. This is interesting because it aligns our understanding of the behaviour of annual plants much more closely to perennial plants, in which buds are set in summer but are dormant until cold winter conditions break this dormancy and enable bud break in the spring. We will examine the effect of expressing FLC heterologously in the male and female flower organs on bud and seed development and dormancy, and aim to uncover the molecular mechanism that enables FLC expression to switch dramatically between the two flower organs in response to seasonal cues.

Impact Summary

Environmental variation causes major impacts on plant reproductive biology. These include affecting flowering time, seed vigour, and seed yield which is impacted by temperature effects on seed development leading to seed size changes. Because of the diverse effects of seasonal temperature on plants aqnd seeds there are a large number of independent beneficiaries of this research. Impact for Seed companies The European seed market is worth around £5 billion annually. Major seed companies produce seeds for sale at multiple global locations, often under sub-contracts. We now know that lot-to-lot variation in seed quality is largely mediated by environmental temperature effects on seeds. By understanding how these signals act we can help advise seed companies which sites are likely to reliably produce high quality seeds, and whether low quality at specific sites is due to the prevailing climate, rather than for instance differences in agronomic practises. Knowledge of the underlying mechanisms also is enabling us to start to breed for more resilience in seed quality, by smart genetic interventions in seed developmental programmes to limit environmental sensitivity. This is a key component of a related project funded by Syngenta Seeds and the BBSRC Horticulture and Potato Initiative, which aims to improve resilience in seed quality. These impact-driven projects rely completely on the fundamental mechanistic discoveries in model system projects like this, for it is only when we understand the detailed biology underlying plasticity in seed development and behaviour that we can start to understand their effects on the wider economy, and how to enhance or mitigate them as appropriate. More reliable seed quality will result in fewer insurance claims for losses by growers unhappy with their seed quality, and could reduce premiums for seed companies. Breeding for improved control of the timing of crop maturity is an important goal for vegetable breeders, with the potential to increase the year-round availability of locally grown produce and reduce importants. This is especially the case in field vegetables, and there is also an emerging market for short duration vegetable crops for use in urban farming systems and by clean indoor vegetable growers. Impact for famers and growers Because we know that environmental temperature effects control seed size and crop yield via FLC, understanding the basic mechanisms will enable us to breed for crops with more stable and dependable yields. This is important because climate change is resulting in a wider variation in weather patterns in the UK, and higher frequency of more extreme conditions could have large an stochastic effects on the yields of crops if we do not understand how to mitigate the effects. The most effective way to gain this understanding is by combining research in crops with faster moving fundamental biology exploiting the latest tools in model systems, such as described here. In rapeseed where this is effect is strong 30% of the yield is variable from year to year, and our estimate is that up to one half of this variation is due to effects of vernalisation on seed development causing up to £200 million per annum in lost UK farm income (Beeby et al., submitted manuscript). Impact for wider society Breeding for more resilience in plant reproductive systems will be necessary to ensure price stability. This will enable whole supply chains to invest with confidence and pass savings on to consumers.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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