Brassica Rapeseed And Vegetable Optimisation

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

Abstract

Agriculture is facing the crucial challenge of adapting crop productivity to changes in the climate. More variable weather patterns require the development of crops that are able to perform more robustly under a wider range of environmental conditions. At the same time, climate change also provides new opportunities for increasing the length of the UK vegetable growing season and increasing food security by reducing imports of fresh produce during the winter, but this requires breeding new varieties that are able to produce robustly at different times of year.

The BRAVO consortium aims to meet these challenges through close interactions between academia and industry. To achieve this goal, we have brought together world-leading experts in both Arabidopsis and Brassica plant reproduction from research institutes and universities within the UK. As the result of a series of meetings between consortium members and stakeholders from the oilseed rape and vegetable Brassica industries, optimisation of flowering and coordination of developmental transitions in the production of high-quality seeds were identified as important common targets. These transitions that occur during plant reproduction such as to flowering, fertilisation, inflorescence growth, seed production, dispersal, and subsequent seed performance are now known to be managed by environmentally responsive gene networks built on a foundation of common components first described for their ability to control flowering time.

The goal of BRAVO is to provide a mechanistic understanding of the role of flowering time gene networks in the control of Brassica reproductive developmental transitions from vegetative growth through to seed production and seed vigour. Because these networks control environmental responsiveness, this knowledge can be exploited to increase robustness in the performance of oilseed and vegetable Brassicas. A key challenge is how to optimise individual traits when the same flowering time gene network has been optimised by evolution over millions of years for multiple functions, each of which is important for crop performance. In this proposal, we will combine genomics and phenomics technologies with approaches in developmental genetics and mathematical modelling to link genotype to phenotype for master regulators of key transitions during Brassica reproductive development. Through exploitation of available genetic resources, we will reveal the architecture of flowering time gene networks in Brassicas and how they have been modified in the past by plant breeders to cause trait variation, life history variation and climate adaptation. This will allow us to develop a predictive framework for designing strategies to vary specific crop characteristics without harming others, and to generate and test novel genetic variation with potential uses in future trait enhancement.

In parallel we will establish and exploit resources such as a gene expression atlas and targeted gene disruption which will allow the Brassica research and breeding communities to expand knowledge on important biological processes and use the outputs form BRAVO collectively to improve Brassica crop performance.

Long-term improved and sustainable Brassica crop performance can only be achieved through fundamental understanding of biological processes. The composition of the BRAVO consortium allows the combination of excellence in Brassica research with knowledge transfer from the closely related Arabidopsis model species. The project builds on and expands academia-industry interactions through industrial membership on the project's Supervisory Board, industry engagement and practical involvement in case studies, frequent consortium meetings and annual stakeholder events.

We believe this project provides a unique opportunity to align industry priorities with excellent fundamental research programmes in order to help secure the future yield of Brassica crops in the UK and worldwide.

Technical Summary

A fundamental challenge in modern crop science is the exploitation of big genomic data by linking variation in genotype to phenotype. Flowering time pathways are now recognised as master regulators of plant development, and as signal-processing machineries allowing plants to adapt to their environment. These genes affect all major reproductive processes from the timing of flowering, through inflorescence architecture, flower, fruit and seed development and finally seed vigour. The goal of BRAVO is to combine genomic tools, predictive biology and high throughput phenotyping to efficiently link genotype to phenotype across multiple reproductive traits sharing regulatory components from flowering time pathways in Brassica napus and B. oleracea. We hypothesise that investigating each transition as part of an integrated project could target breeding programmes towards loci offering the opportunity for a win-win: that is to positively manipulate more than one trait, and to predict inevitable trade-offs between traits that maximise yield in different environments.

High-throughput phenotyping will be used for association genetics approaches in both B. napus and B. oleracea to identify candidate genes linked to trait variation in variety panels. In parallel, construction and validation of in silico gene networks will be combined with large-scale EcoTILLING to make phenotypic predictions for each of ~200 Brassica varieties based on the ability of alleles to disrupt network architecture and critical outputs for each trait. Candidate genes controlling each trait and their place in the network will be validated in Brassica by exploiting our TILLING and transformation platforms together with our novel CRISPR pipeline at JIC.

Close integration of our research programme with industrial stakeholders will see germplasm with commercial potential taken into field trials, providing a seamless innovation pathway from laboratory to field.

Planned Impact

Oilseed rape is the second most important combinable crop in the UK with an annual market value in excess of £800M with the vegetable Brassica crop worth a further £227M (Food and Agricultural Organisation of the United Nations, FAOSTAT, 2014; Defra statistics, 2014). Varying environmental conditions often result in unpredictable heading, fertility, seed yield and seed quality resulting in estimated losses in excess of £30M per annum through poor establishment, up to £40M from unscheduled harvest and an estimated 20% loss (£160M in 2014) from pod shatter resulting partially from asynchronous development. The commercial seed industry also experiences significant losses through poor seed batch performance thus making production of high-yielding varieties with quality seed both as a commodity and for commercial seed multiplication a key target for the Brassica industry.

This project will address the delivery of more robust oilseed and vegetable Brassicas to combat these losses by targeting five, industry validated, fundamental concerns: (1) uniform and shortened flowering period through more determinate flowering, (2) fertility under changing environments, (3) reduced seed loss through infertility, pod shatter and pre-harvest sprouting, (4) properties of the seed coat for downstream processing and (5) the homogeneity and speed of seed development and germination. A greater understanding of the genetic control underlying these traits in current varieties and identifying allelic variation underlying phenotypic differences will have a large impact on the breeding of improved varieties to suit the UK market and help the oilseed and Brassica industry maintain and enhance its current competitive advantage.

The project targets two major BBSRC Agriculture and Food Security strategic priority areas: Priority 4: Reducing and re-using waste and Priority 5: understanding "genotype X environment = phenotype". The combined expertise of the academic partners together with thedustrial collaborators will develop a strategic pipeline to optimise brassica productivity through understanding of the key developmental transitions and trade-offs during plant growth.

Specific impacts will take the form of:

1. Reducing industry waste and crop losses due to unscheduled harvest and yield and quality reduction through asynchronous pod development by understanding the factors controlling development.
2. Help ensure future crop supply in a changing environment by understanding environmentally sensitive developmental traits and how to genetically mitigate effects in future climate scenarios.
3. The introduction of new knowledge, technologies, tools and capabilities to the private sector to assist in crop breeding and management (i.e. associative transcriptomic pipeline for vegetable Brassicas, gene expression browser for accelerated gene discovery, database of allelic variation to facilitate marker assisted selection, CRISPR technologies). Through direct industry participation, shape further research development to best support industry.
4. Produce valuable new germplasm with desirable traits, associated markers and seeds, and work with project partners to assess their suitability for product development pipelines. Develop mechanisms for delivery and utilisation of outputs to foster continuous opportunity and commercial exploitation in industry.
5. Introduce and train young scientists and researchers in crop genomics and breeding as a career path to ensure quality future researchers in both public and private sector.
Nurture relationships between academia and industry stakeholders across the supply chain, enhancing understanding and interaction between research and industry thus increasing support for future collaboration.

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