13 ERA-CAPS. Identifying and exploiting genetic variation controlling seed yield and quality in oilseed crops

Lead Research Organisation: John Innes Centre
Department Name: Cell and Develop Biology

Abstract

Oilseed rape is one of the most important UK crops, providing nutritious oil for human consumption and contributing to biodiesel production to meet renewables obligations. Globally it is the third largest source of oils, behind soybean and oil palm, and is the second leading source of nutritious protein meal for livestock rations. Oilseed rape is also a very useful rotation crop grown alternately with wheat. This is used extensively, but problems with weed build-up and increased disease potential may could lead to reduced cultivation of oilseed rape. Therefore higher yielding crops will help with sustainable agricultural practices.
However, the yields of oilseed rape seed has not changed significantly since 1980, and production levels have increased through increasing the growing areas. One of the contributing factors is that the overall form and growth of the plant has not yet been highly adapted for crop yield, compared to wheat or maize for example. The aim of the UK part of this project is to exploit recent advances in oilseed rape genomics and genetic analysis to identify genetic variation that contributes to seed yield and composition and to overall plant form, and use this to identify and understand genes that influence these traits.
The work on understanding gene function will draw on parallel studies carried out by German and French partners in the project that aims to identify genes that control key aspects of seed formation and to assess in detail how genetic variation contributes to seed composition. The genetic analysis work uses a wide variety of oilseed rape relatives that although not directly useful for crop improvement, help to identify genetic variation causing interesting and relevant changes to plant growth and seed formation. The highly precise genetic analyses afforded by genomics helps define genes linked to genetic variation that is associated to traits- in our case seed formation. The functions of these genes can be understand, and eventually used for crop improvement. We will engage with breeding companies to pass on relevant information and advice on how to use it.

Technical Summary

The research plan links research in leading European laboratories in a multidisciplinary network aiming to identify genes and genetic variation controlling seed yield and quality in Arabidopsis, Capsella, Camelina and Brassica napus. The close evolutionary relationships of these plants effectively couples the exceptional depth of knowledge of gene function in Arabidopsis to wider developmental variation found in Capsella with increased understanding and utilization of genetic variation in two crops, oilseed rape and Camelina, a promising low-input crop. The three overall research objectives are summarized.
WP 1 will link extensive knowledge of the control of seed development, reserve accumulation and yield in Arabidopsis and Capsella with associative genetic analysis of yield traits in B. napus to identify the functions of potentially causal genes, mine the association data, and delineate new variation in quality traits using new phenotype screens and RNAseq resources.
WP2 will exploit new genetic variation in a key seed yield trait. Ovule formation sets the number of seeds per fruit, a key yield determinant, and genetic variation in this trait is low in Arabidopsis. A high-effect QTL in Capsella will be used to identify a promising causal gene. Its function will be defined in transgenic Arabidopsis and genetic variation in B. napus will be assessed for contributions to seeds/pod and overall yield.
WP3 focuses on the composition and quality of seed storage products (oil, protein, starch), which are critical determinants of quality. A key objective is to link knowledge of regulatory networks controlling this process to seed storage product levels in Camelina and B. napus. Multi-scale phenotyping of B. napus lines will identify new genetic variation associated with seed storage product levels and quality.

Planned Impact

The outputs of this project include joint research publications, scientific reports and presentations, recombinant DNA, germplasm and DNA sequences. We will make these data available in useful formats as soon as practicable after generation in order to promote new research and to advance the field as quickly as possible. This maximizes the value of research funding and amplifies the impacts of the research. The policy of the partner laboratories is to share data in appropriate standard formats to maximize the utility of the research outputs; for example, germplasm will be made available through stock centres and from individual's labs; sequence data will be submitted to public databases, and publications will be open access, in accordance with our IP strategy.
A key objective of the project's dissemination plan is to identify and capture Intellectual Property (IP) relevant to oilseed rape genetic improvement. We will liaise closely with the respective IP managements of our institutions to identify potential IP generated in each laboratory- for example genetic variation in genes underlying yield and quality traits in oilseed rape that can be used as markers to identify and select desired traits in molecular breeding strategies. The dissemination plan aims to establish links with oilseed rape breeders early in the project to facilitate knowledge transfer in both directions; we will learn breeders' objectives in yield and quality improvement, and we will describe our research objectives and methodologies. The outcomes from this engagement include guidance on trait analysis, potential industrial partnerships and users of IP. Key potential European industrial users include KWS, major European oilseed rape breeders (who were closely involved in setting up the B. napus association genetics project at John Innes Centre), Saaten-Union, Nickersons, Monsanto and BIOGEMMA.
A key objective in our dissemination plan is to engage with academic researchers and promote our integrated approach to seed development and crop improvement, as we think it will help establish closer alignment of basic research with crop improvement. This will be achieved through normal academic outlets such as invitations to speak at meetings, seminars etc. The project will provide excellent opportunities for high-level training of post-docs and PhD students working in associated areas who are interested in learning how to apply work in experimental species to crops. To facilitate this integration, a training workshop will be held in Norwich using the dedicated training suite. This will coincide with the second round of Brassica GWAS analyses, and participants will have the opportunity to see field trials, data collection and learn the computational methods for SNP and GEM association. A training workshop programme will also showcase the wider aspects of the PI's work in genomics, growth control and regulatory network analysis. We aim to seek institutional and other sources of support to help approximately 10 PhD students from less advantaged parts of Europe to participate, and participation from industrial researchers will be encouraged. The PIs will also explore the potential to create an ITN to expand the scope of training and realize the full potential of the project.
The project will establish links with plant breeders and biotechnologists. In the third year a workshop will be organized to promote the outcomes of the project. By then the B. napus GWAS analysis will be robust and genetic variation in functionally characterized contributing to yield and quality of oilseeds identified. This will give industry direct opportunities to understand and use the valuable genetic variation, markers, germplasm and scientific understanding needed to achieve higher crop yields.
 
Description This project has been running for 4 months. This summer we conducted the first phenotypic analyses of a Brassica diversity set of 102 lines grown in a greenhouse. Data has been collected and GWA conducted. several strong associations of genetic variation and gene expression with seed traits have been detected and candidate genes are being studied. Another trial will be replicated next year with new lines to increase variation. UPDATE the project has been completed, and we have submitted a publication that is currently under review in a high impact journal. We show that the HECT E3 ligase UPL3 in Arabidopsis and oilseed rape targets the transcription factor LEC2 for ubiquitylation and degradation. LEC2 initiates and maintains seed maturation and controls the expression of seed lipid biosynthesis genes. Reduced UPL3 expression leads to prolonged seed maturation and elevated seed lipid levels. Field yields are elevated

We are completing revisions to a manuscript to include new data on UPL3 activity. We have initiated work on soybean UPL3 to assess whether ABI3 and LEC2 are substrates in collaboration with Corteva
Exploitation Route Allelic variation in genes influencing yield traits will be characterised and any potential commercial value discussed with PBL for patenting and licensing
Results will be published and presented so that other researchers can contribution to a thorough genetic analysis of growth and yield in Brassica napus. UPDATE: the technology has been patented and licensed for application in soybean

Contract work with Corteva is being carried out. This looks quite promising in being able to substantially increase soybean meal protein content
Sectors Agriculture, Food and Drink

 
Description As the project has only been going for 4 months the findings are at an early stage. The plan is to conduct detailed analyses to identify candidate genes and allelic variation and publish this. If deemed novel and useful the discoveries will be patented and licensed. UPDATE: a publication describing the work has been submitted. A patent has been submitted and updated. The technology has been licensed for application in soybean. The post-doc has gone on to a great position in the USA at the Salk Institute The project is essentially completed. We are addressing reviewers' concerns about a submitted manuscript and this will be completed at the end of March. In summary, we showed that natural variation of a UPL3 gene in oilseed rape caused increased seed size and lipid content by affecting levels of the master transcriptional regulator LEC2.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description ABCEED project 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Academic/University 
PI Contribution We work with these two groups on the mechanisms controlling seed size in Arabidopsis, Capsella and Brassicas. We have used genetic variation influencing seed numbers, seeds per pod and seed size in oilseed rape to identify genetic variation that reduces expression of a gene encoding a HECT-E3 ubiquitin ligase. We have shown that this enzyme ubiquitylates the transcription factor LEC2, a master-regulator of seed lipid and protein deposition
Collaborator Contribution The Versailles group contribute biochemical analyses of seed lipids and a transient expression system for testing transcription factor action. Potsdam work on genetic analyses of ovule size determination
Impact A patent has been applied for
Start Year 2015
 
Description ABCEED project 
Organisation University of Potsdam
Country Germany 
Sector Academic/University 
PI Contribution We work with these two groups on the mechanisms controlling seed size in Arabidopsis, Capsella and Brassicas. We have used genetic variation influencing seed numbers, seeds per pod and seed size in oilseed rape to identify genetic variation that reduces expression of a gene encoding a HECT-E3 ubiquitin ligase. We have shown that this enzyme ubiquitylates the transcription factor LEC2, a master-regulator of seed lipid and protein deposition
Collaborator Contribution The Versailles group contribute biochemical analyses of seed lipids and a transient expression system for testing transcription factor action. Potsdam work on genetic analyses of ovule size determination
Impact A patent has been applied for
Start Year 2015
 
Description Collaboration with Corteva on soybean seed size 
Organisation Corteva Agriscience
Country United States 
Sector Private 
PI Contribution We showed that loss-of-function mutations in the HECT E3 ligase UPL3 leads to substantially increased seed size and lipid yields in Arabidopsis and oilseed rape. The aim of the collaboration with Corteva is to see i UPL3 has the same phenotype in soybean and to explore the mechanisms involved
Collaborator Contribution Cash and clones
Impact none yet
Start Year 2018
 
Description Discussions with Pioneer HiBred on application of UPL3 technology to soybean improvement 
Organisation DuPont
Department DuPont Pioneer
Country United States 
Sector Private 
PI Contribution We patented UPL3 technology for increasing seed size and this technology has been licensed to Corteva for application in soybean. Corteva have funded a 2 year project in the Bevan group that is determining if soybean UPL3 ubiquitylates soybean LEC2, and if there are other transcription factors such as ABI3 that may also be substrates. There is a question over the possible role of LEC2 in soybean seed maturation transcription networks, and we will assess the potential of soybean LEC2 to activate transcription of lipid biosynthetic genes
Collaborator Contribution Cash payments to support research plus DNA clones of LEC2 and ABI3.
Impact The research may lead to improved crop yields by increasing the duration of soybean seed maturation.
Start Year 2018
 
Description ERA-CAPS Identifying and exploiting genetic variation controlling seed yield and quality in oilseed crops 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Academic/University 
PI Contribution We are academic partners in an ERA-CAPs project studying seed size and quality traits in Brassicas
Collaborator Contribution Potsdam provide expertise in genetics while INRa Versailles provides expertise in metabolite measurements and gene regulation
Impact no publications so far but 1 is planned from my group in 2016
Start Year 2013
 
Description ERA-CAPS Identifying and exploiting genetic variation controlling seed yield and quality in oilseed crops 
Organisation University of Potsdam
Country Germany 
Sector Academic/University 
PI Contribution We are academic partners in an ERA-CAPs project studying seed size and quality traits in Brassicas
Collaborator Contribution Potsdam provide expertise in genetics while INRa Versailles provides expertise in metabolite measurements and gene regulation
Impact no publications so far but 1 is planned from my group in 2016
Start Year 2013
 
Title Methods of increasing seed yield 
Description Methods for increasing seed yield by modulating the activities of a HECT E3 ligase 
IP Reference GB1700380.7 
Protection Patent application published
Year Protection Granted 2017
Licensed No
Impact the project is still going on so impacts are not fully realised
 
Description ABCEED 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof Bevan participated in the annual ABCEED meeting in Berlin to discuss progress with the project and plan future work.
Year(s) Of Engagement Activity 2015
 
Description ABCEED consortium meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mike Bevan and his Post Doc Charlotte Miller participated in the ABCEED consortium meeting, held at the University of Potsdam, Germany. The objectives of this meeting were dissemination of results and planning future work.
Year(s) Of Engagement Activity 2015
 
Description Attendance at ERA-CAPs coordination meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Prof Bevan attended the ERA-CAPs coordination meeting in Lisbon for discussions on how to address major challenges to secure future food supplies and a viable bio-economy in Europe.
Year(s) Of Engagement Activity 2015
 
Description ERA-CAPS ABCEED program meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mike Bevan and his Post Doc Charlotte Miller attended the first meeting of ERA-CAPS ABCEED program to discuss progress.
Year(s) Of Engagement Activity 2015