Controlling seed coat plasticity for seed quality in industry

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


The European seed market is worth around £5 billion annually. Seed quality summarises the desirable characteristics of seeds sold on the market: they should germinate swiftly and evenly across a broad range of germination conditions, leading to a homogeneous stand of robust seedlings in the minimum length of time. These seedlings should establish a vigourous crop stand. Seed companies produce hybrid seeds in multiple sites globally, each subject to environmental variation between and within sites that can negatively impact seed quality. Across all species temperature variation during seed production is a major driver of variable seed quality, and breeding new varieties with robust seed quality in a range of production environments in now a key strategic goal of seed companies. A core goal of our research is to understand signalling pathways through which environmental variation during seed production affects seed quality traits, such as dormancy, germination and establishment vigour.
Based on our recently published research and preliminary data we show that temperature during seed production has a major affect on seed behaviour through a signalling pathway that operates in the mother plant. This is a major new discovery as previously it has not been clear whether the developing seed itself is sensing the environment, or whether the mother plant senses the environment and somehow passes this information to the progeny seeds. We identify that the well known cold-sensing pathway that regulates tolerance to freezing also controls gene expression and physical properties of the seed coat that are known to be linked to changes in seed behaviour.
The first part of the proposal aims to understand how temperature sensing leads to the plastic development, biochemistry and permeability of the seed coat, and how seed coat properties control seed behaviour. A major focus here is to understand how elements of the cold acclimation pathway and control of phenylpropanoid pathway gene expression known from experiments in vegetative tissues operate in maternal seed coat tissues and the nature of their targets in seeds. This requires intergrating knowledge from genetics molecular signalling and transcriptional control of secondary metabolism in seed coats.
The second key section is to transfer this new knowledge from model to crop species, and for this we have developed a collaboration with Syngenta to assess and improve Brassica seed quality, a species where germination and establishment of seedlings varies according to seed production sites and seasons. We will examine control of seed quality in a panel of Brassica varieties with varying seed quality responses to maturation environmental conditions, and relate these to gene expression and the developmental, physical and biochemical properties of the seed coat. Finally we will delete genes in Brassica that we have shown control the transduction of temperature signals affecting seed quality in Arabidopsis. The goal here is to evaluate this technology for use in product development in seed companies, and collaboration with Syngenta will ensure exploitation of commercially useful germplasm.
A key feature of our new seed technology is that seed quality of seed for sale can be controlled in hybrid seed from the genome of the mother plant rather than the zygote. This means that the properties of the seed sold and the crop seed can be independently controlled: in the future this will be useful in the many instances when high germination propensity of the crop is undesirable, such as to control sprouting in cereals, of fruit quality in glasshouse crops.

Technical Summary

Seed dormancy and germination is often variable between lots due to affects of the seed production environment on the behaviour of the mature seed. Here we provide genetic evidence that HOS1, a gene characterised principally for its role in the control of cold acclimation, has a key role in the control of seed behaviour in response to the seed production temperature, from the genome of the mother plant. Hos1 mutants show dramatic high germination vigour which is insensitive to temperature variation during seed production, and we show that temperature and HOS1 control a hitherto uncharacterised plastic seed coat behaviour that regulates seed coat permeability, operating in part on phenylpropanoid metabolism. We hypothesise that this plastic seed coat development underlies much of the described variation in seed behaviour from lot to lot, and is also important in variable seed quality observed by industry. Our preliminary data demonstrate that temperature signalling during maturation in maternal tissues play a central role in controlling mature seed behaviour.
That the cold acclimation pathway controls phenylpropanoid biosynthesis has been previous described in vegetative tissues. In this proposal we aim to understand how maternal environmental experience and HOS1 control Arabidopsis seed coat development, biochemistry and permeability to affect control of seed behaviour, using a varieties of molecular, genetic and biochemical techniques. Finally we will collaborate with Syngenta to transfer our new knowledge into Brassica crops where seed quality problems are a major limitation, using TILLING to identify Brassica hos1 alleles and deploying biochemical assays to determine how variation in seed coat properties in response to the production environment controls Brassica seed quality. Alleles from TILLING will be phenotyped and could exploited by direct incorporation into product development pipelines.

Planned Impact

Impact for the Seed Industry
Seed companies produce seed for sale all year round, including counter-season production at sites in the southern hemisphere. In order to maintain a constant supply of fresh seeds pollinations are carried out at multiple sites, often with different environmental profiles. While the quality of some varieties is maintained across sites, unpredictable environmental variation can cause deterioration in seed quality in many, through mechanisms that we aim to understand in this research. In order to maintain quality in these lots seed companies can employ a variety of techniques, including priming, coating and screening. Priming adds significant labour costs, screening requires outsourcing or major investment in capital equipment, and coating raises sustainability issues with the accumulation of compounds in soils and ground water. All of these come at a cost, a cost that is passed along the food supply chain. For this reason breeding for consistent high seed quality is now a priority for seed companies which aim to develop new varieties that are insensitive to environmental variation during seed production. This project not only elucidates key mechanistic details of the pathways but also provides new Brassica germplasm through TILLING that can enter directly into private sector product development pipelines. This exploits new BBSRC-funded capacity building in Brassica germplasm development at the John Innes Centre.
During the course of this IPA project Brassica alleles of mutants that lead to environmentally-insensitive high seed quality in the closely-related model species Arabidopsis will be identified and phenotyped for suitability for breeding into elite varieties. The timeline for breeding using modern fast-track techniques is 2-4 years leading to potential new varieties within a short time frame post-project. Because this work would be undertaken in collaboration with a major international plant breeding and seed production company, Syngenta, exploitation of high-performance germplasm is guaranteed. If successful this work will serve as a template for improvement of seed quality traits in other species, including tomato rootstock, other glasshouse crops and cereals.
In this proposal we also aim to develop an assay which will assess seed coat traits and their variation with production environment. These assays will provide a basis for the assessment of multiple crops to determine the effect of the environment during production on seed quality. If we can identify seed coat changes this is very important because it means breeding for maternal genotypes is necessary rather than F1 crop genotype.
Impact for the consumer and on government health priorities
The fruit and vegetable sector is the UK's fastest growing food market, doubling in value between 2005 and 2011. This growth was based in part on European government initiates to improve population health through promoting vegetable consumption. A key barrier to vegetable consumption is cost, and improved seed quality has the potential to reduce costs in the supply chains for two reasons: firstly costs of purchasing seeds of elite high-performance varieties will be reduced which will increase their availability. Secondly improved seed vigour impacts growth and yield throughout the life cycle of a plant, increasing productivity per unit time of growth. These improvements have the potential to lower production costs and make healthy food more affordable for poorer populations. This work could have a direct impact on Brassica seed vigour and serve as a template for further improvement programs.


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Description In this grant we showed that the environment that companies produce seeds in makes a big difference to the quality of the seeds produced and thus their market value. We investigated the biological mechanisms underlying this process and found that the development of the seed coat, the brown tissue surrounding the seed, is very different in different environments. In addition we found that endosperm development is also affected by environmental signalling pathways and we found some genes important for the control of endosperm development and seed dormancy by temperature. A key question is why seed companies seed large variation in seed quality from batch to batch, even when the seed in question is genetically identical. We have been working with companies that receive seed to be processed for sale from a number of locations, and where some locations produce high quality seeds and some show more variable seed quality. We found in this study that the mechanisms governing seed quality variation is highly complex and involve processes in multiple seed tissues. However, our principle finding were that the results can be seen in the altered development or the seed coat and endosperm. Specifically, seeds from lower temperatures were browner and had higher tannin contents and germinated to lower efficiencies. Thus seed coat colour may be a good proxy measure for seed quality. We found that temperature regulates seed coat tannin content and the activity of genes required for tannin synthesis in seeds. Secondly we analysed genes important for temperature regulation of plant development and found that these also affected seed dormancy, but this time via the development of the endosperm. We showed that temperature signalling genes affect ABA synthesis in seeds, an important hormone in the negative regulation of seed germination. These findings can be exploited by companies to predict the performance of seed batches based on seed colour.
Exploitation Route What we show is that the seed coat tissue is responsible for some of the seed quality variation caused by environmental variation during seed production. This is important for seed companies because they are producing seeds of the same variety over and over in different years and different locations for different markets. The companies need reliable seed quality for customer satisfaction and to lower insurance premiums. We show that genetic manipulation of the seed coat could improve the robustness of seed quality, and that seed quality differences could be detrmined by looking at the colour of seeds. This information can be used in industrial seed sorting processes, where colour sorting can be used to extract sub-populations of seeds with high seed quality.. We exchanged this knowledge with Syngenta seeds who used it to improve the qualkity of the seeds they put on the market.
Sectors Agriculture, Food and Drink

Description Collaboration with Syngenta Seeds 
Organisation Syngenta International AG
Country Switzerland 
Sector Private 
PI Contribution Our contribution is to provide novel genetic materials for field trials by syngenta seeds
Collaborator Contribution Their contribution is to conduct field trials and assist and train for seed analysis.
Impact no outputs yet to report
Start Year 2011
Description UNiversity of Geneva collaboration 
Organisation University of Geneva
Country Switzerland 
Sector Academic/University 
PI Contribution We provided a scientific problem that we could not address without external expertise.
Collaborator Contribution Our partner has developed new techniques for conducting epigenomic studies of small tissues in arabidopsis seeds, particularly the endosperm. To briung these techniques into out lab they hosted the postdoctoral researcher in Geneva and taught her how to separate large volumes of endosperm tissues and the protocols for chromatin extraction. they also performed some experiments that were necessary for the publication.
Impact One publication came from the collaboration. doi: 10.1111/tpj.14211
Start Year 2016
Description Presentation at Elsoms Seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presented our research program and data at Elsoms seeds, Spalding

no actual impacts realised to date
Year(s) Of Engagement Activity 2014
Description Presentation at International Seeds Testing Association meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk to the industry trade meeting and took part in a debate on measuring seed properties in the seed industry.
Year(s) Of Engagement Activity 2013