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

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.

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.

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.