Control of seed size and yield by vernalisation

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics

Abstract

A major problem with UK winter oilseed rape (WOSR) cultivation is the large inter-annual fluctuation in on-farm yields, varying from around 3.0 to 3.9 tonnes per hectare. Weather and climate are known to be critical factors in this yield instability, and climate change may be a factor in the current 'yield plateau' in UK agriculture. For this reason breeding and selection of new varieties suited to changing environments is widely appreciated to be a key long-term goal for UK agriculture. Targeting this effort requires an understanding of the precise biological mechanisms through which weather variation influences yield on farms. It is here that this proposal breaks new ground.
In the UK and Northern Europe high yielding so-called 'winter' crops are distinguished from spring crops by their requirement for a period of prolonged winter cold before flowering, a process known as vernalisation. While the effect of vernalisation on flowering has been known for many years, here we show for the first time that vernalisation has a further major role in the control of seed size. We show that seeds from more strongly vernalised plants are around 30% larger than seeds from more weakly vernalised plants, and this size increase comes without any penalty in fruit or seed number. These effects are large enough to account for a substantial fraction of the 30% inter-annual variation in yield observed on farms in the UK. In addition, we provide new evidence that winter cold during a very precise 23-day period is highly correlated to UK rapeseed yields, suggesting that on a landscape scale vernalisation may be important for WOSR crop yield performance.
The molecular mechanism underlying the vernalisation process is understood in detail. A key transcription factor gene, FLOWERING LOCUS C (FLC), is highly expressed before winter and is gradually silenced during the experience of cold weather by the accumulation of repressive chromatin marks. FLC expression in leaves and the shoot apical meristem controls flowering, but FLC is also strongly expressed in seeds where it has previously been implicated in seed vigour. Seed size on the other hand is controlled primarily by the expansion of the seed coat that occurs after fertilisation, creating the space into which the embryo and endosperm grow. Our preliminary study shows that in rapeseed both FLC and a second gene AUXIN RESPONSE FACTOR 2 (ARF2), a known seed size regulator in Arabidopsis, can both be genetically linked to the control of seed size by vernalisation. Furthermore, online genomic scale datasets show that ARF2 is likely a direct target of FLC.
In this proposal we will elucidate the mechanism by which vernalisation controls seed size and examine the importance of this process in on-farm yield variation in WOSR. Our preliminary analysis has revealed a very strong candidate for this mechanism and our experimental programme is designed to investigate this in detail. Using the JIC experimental farm we will test whether winter cold affects WOSR yield by affecting seed size, and how the key molecular events of vernalisation and seed development unfold in a real field scenario. By taking lines carrying genetic variation at FLC and ARF2 loci through to maturity we will directly test whether temperature in early December affects rapeseed yield parameters through a mechanism involving these two genes.
One goal is to identify new combinations of of FLC and ARF2 that maintain large seed size despite only weak vernalisation. Markers for these alleles can then be used by breeders to select new varieties with a more robust yield performance, ameliorating an important negative effect of warmer winters on UK agricultural performance.

Technical Summary

A key goal of breeders is to develop varieties with high yields both in National List trials and on-farms which perform dependably despite variation in seasonal weather patterns. The data presented here show that high UK WOSR yield is driven by increased exposure to winter cold, and demonstrate for the first time that in addition to the well-known regulation of flowering, vernalisation also has a major impact on seed size. We observed that this effect is large, with vernalisation producing more than a 50% gain in TGW in some lines. This conclusion that vernalisation also influences seed size is further supported by a QTL study which implicates FLC and ARF2 in the mechanism, two transcription factors known to be central to vernalisation and seed size control respectively.
The aim of this proposal is to determine the molecular mechanism by which vernalisation affects seed size and consequently WOSR yield, and to test the significance of this biological process for UK on-farm WOSR yields. We will achieve this by artificial manipulation of temperature in field trial plots to examine effects on yield, and by analysing the molecular events leading to vernalisation and seed size variation in the field. Allelic variation at FLC and ARF2 in rapeseed and Arabidopsis will be used to test genetically for a role of these genes in seed size control by vernalisation. Finally ChIP and transient gene expression approaches will be used in rapeseed to determine the effects of BnFLC manipulation on ARF2 gene expression. The results of this work will have implications for winter crop yields during an era when climate change will lead to both warmer winters, and to more inter-annual variation in winter temperatures. Understanding the biological mechanisms underlying year-on-year variation in yield could lead to early prediction of yield facilitate breeding of new varieties that are better suited to the challenge of climate variability in the 21st century.

Planned Impact

The UK rapeseed harvest is worth an average (last 5 years) of £815 million per year. With yield varying by up to 30% each year, this corresponds to a annual value of up to £260 million which could be subject mainly to varation in weather and climate.
The impacts from this work can be divided primarily into two distinct areas:
The first is impact on breeding: this project will yield haplotypes of WOSR which via allelic variation at FLC and ARF2 loci are likely to have enhanced Thousand Grain Weight under a wider range of vernalisation intensities. We will design markers for these haplotypes, and the high copy number of FLC and ARF2 in WOSR suggests that there is likely value in stacking haplotypes to increase effect size. Our aim will be to gather positive alleles together in a single background to expedite use in breeding programmes, i.e. to produce optimised pre-breeding germplasm (see pathways to impact). Using the ecotilling data we will be able to assign each variety a haplotype set for FLC and ARF2 loci. We will make this data accessible via the JIC Brassica webpages so breeders can see which useful haplotypes may already be present in their populations and which they are missing.
The second is yield prediction: with a simple linear model in hand we were able to make some yield predictions for the 2015/16 season by Christmas 2015. December 2015 temperatures averaged 8C, 4C higher than normal, and the model predicts that 2016 harvest yields should be 0.5-0.6 t ha-1 lower than average (which is 3.6tha-1; i.e. on farm yields should be3.0-3.1 tha-1). The final value according to AHDB was 3.0-3.2 tha-1 which is in line with our simple estimates. The work in Objective 5 will improve our predictive abilities still further. This ability to predict yields could be useful for farmers for planning, or to know when to sell the rapeseed crop to the futures market. It could also help planning in supply chains. To aid with yield prediction, we will produce a website widgewhich will predict yields and advertise this prominently (see pathways to impact).

Publications

10 25 50
 
Description Oilseed rape yields vary by around 25-30% between growing seasons in the UK, leading to large uncertainties in farm income and supply chain capacity. This is known as yield instability. We have begun to explain the causes of yield instability, focussing on how temperature variation at specific times of year affects yield, and correlated this with the developmental progression of the crop, suing knowledge derived from working on plant reproductive development in Arabidopsis. To do this we have developed new technologies for warming crops in the field at specific times of year to monitor effects on crop development and yield.

In the UK we primarily grow winter oilseed rape, which is sown in August and harvested the following July, and is known to require a period of cold to promote flowering, along with other major crops, known as vernalisation. We found that warm Octobers and Cold Decembers were strongly associated with high yields, and that vernalisation occurs in October in the field. This funding was a surprise because the field believed previously that vernalisation happens in winter. Thus we now know that warm Octobers promote high yields by prolonging the vegetative growth phase in October.

We also found that in November the oilseed rape plants start to make flowers, even though the flowers do not open in the field until the following April. A second major finding is that during this phase of early flower development the crop benefits from the experience of low temperatures, with low temperatures promoting earlier flowering and higher yields. We are continuing the project to understand the underlying molecular mechanisms.
Exploitation Route The knowledge here is very useful for breeding more resilient crops, for instance for breeding crops that are resistant to the effects of changing climates. For instance, now we know why warm autumn/winter temperatures cause low yields we can target specific genes in predictive breeding programmes. We can also improve predictions for how climate change is going to affect yields, and in this way help the supply chain to prepare better for future climates.
Sectors Agriculture, Food and Drink

 
Description We showed a large UK agronomy company how to predict which rapeseed varieties will perform well for farmers using statistical models. We shared unpublished data in repsonse to a further request. The company will use the information to tell their agronomists which varieties to recommend to farmers. We have presented findings at Industry shows such as The CropTec Show and held discussions with farmers on how to pick more resilient varieties from the recommended lists. We have engaged with major oilseed rape breeders and explained to them the challenges of growing oilseed rape in the UK climate.
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description PhD studentship
Amount £90,000 (GBP)
Organisation University of East Anglia 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2022
 
Description Collaboration with Elsoms Seeds 
Organisation Elsoms Seeds
Country United Kingdom 
Sector Private 
PI Contribution We provided data and materials to Elsoms for the purposes of constructing populations with the purpose of generating pre-breeding materials for oilseed rape.
Collaborator Contribution Our partners at Elsoms seeds generated a Doubled Hapoild population for us, using methods not available at JIC.
Impact The work is ongoing so there are nop outputs yet.
Start Year 2019
 
Description field trials analysis 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution We contributed data and expertise on oilseed rape recommended list trials analysis
Collaborator Contribution They are providing fine scale past meteorological data to correlate with crop data such as yield.
Impact This is multi-disciplnary between plant science and meteorology.
Start Year 2018
 
Description Annual rapeseed and brassica vegetable stakeholder meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The meeting disseminated progress on the BRAVO project and invoited industry to provide strategic direction to our research project.
Year(s) Of Engagement Activity 2018
 
Description Interview on BBC farming today. 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact To follow our publication of a paper on how weather affects oilseed rape yields, we sis a radio segment from the John Innes Centre plant growth facility on how we investigate crop responses to our changing environment.
Year(s) Of Engagement Activity 2019
 
Description Media interview video to promote work to croptec show delegates 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact dd
Year(s) Of Engagement Activity 2019
 
Description Meeting with Elsoms seeds 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact To related project progress and explore participation in spin out projects
Year(s) Of Engagement Activity 2018
 
Description Presentation at The Croptec Show 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact I gave a presentation on our work on weather effects on oilseed rape yields for two days. The audience was farmers, agronomists, breeders, seed distributors and other agricultural supply chain participants.
Year(s) Of Engagement Activity 2019
URL https://www.croptecshow.com/
 
Description Press release on how warming weather is affecting yields of oilseed rape 
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 This press release accompanying a paper in Current Biology was picked up widely by the international press including the Daily Telegraph which publicised the new methods we are using.
Year(s) Of Engagement Activity 2019
URL https://www.telegraph.co.uk/science/2019/12/05/climate-change-couldboost-british-crops-pioneering-fi...
 
Description meeting with hutchinsons seeds 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact I met with hutchinsons seeds to discuss yield prediction in oilseed rape. We transferred knowledge on how to use statistical methods to identify the most reliable yielding rapseed varieties on the market in the UK. Hutchinson will use the information to help decide which varieties their agronomists recommend to farmers.
Year(s) Of Engagement Activity 2017