BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme

Oilseed rape is commercially viable because a co-product can be exploited (a protein-rich feed for animals) in addition to the primary product (oil). However, many other valuable products could be extracted and exploited commercially, adding value to the crop. This opportunity is particularly important for emerging industrial applications of rapeseed oil (such as thermally-stable oil types produced recently by JIC), where the product must compete on price with mineral oil if it is to be successful commercially and hence adopted sufficiently widely to realize the associated environmental benefits. The serial purification of co-products is termed "bio-refining". Emerging opportunities include tocopherols (vitamin E) and phytosterols (cholesterol lowering compounds) from rapeseed oil, waxes (with aphid-repellent properties and those with medical properties) from pod walls and stems, and functional polysaccharides (including high-value stabilisers, surfactants and barriers) from stems. Although the biosynthetic pathways involved in the synthesis of these compounds are known to some extent from studies conducted in species such as Arabidopsis thaliana, the quantitative control of their accumulation (key to yield of the compounds) is not understood. Such products have not been foci for crop improvement by breeders, so there is no improved germplasm and no molecular markers are available to aid breeding. Similarly, the efficiency with which fertilizer is used by rapeseed is poorly understood, but its optimization is essential for the commercial production of substitutes for mineral oil as fertilizer is both expensive and potentially damaging to the environment.

The approach of associating disease or other traits with DNA sequence variation has become a key tool in human genetics and has also been applied successfully in a few plants. The drawback for most crops is that the traditional approach has been expensive. However, recent advances in sequencing technology and genomics has led to the emergence of a technology termed Associative Transcriptomics, which makes this approach accessible for most crops. In this approach, the search for DNA sequence variation is focussed on gene sequences and variation for gene expression is also exploited; both providing very large sets of potential "markers" for trait variation. The technology has been proven recently using a small genetic diversity panel of Brassica napus (the species that includes oilseed rape as one of its crop types) and is ready for scale-up to a full and widely-used genetic diversity panel, i.e. that termed the ASSYST panel. This approach is ideally suited to the initial genetic analysis of traits for which little is know as it quickly enables the estimation of genetic complexity, the development of hypotheses for the control of traits and produces molecular markers that can be used to assist breeding.

The proposed research aims to exploit Associative Transcriptomics to identify genes associated with the control of a range of bio-refining targets and fertilizer use traits. Data will all be made publicly available. The annotations of genes showing either sequence or expression variation associated with trait variation will be examined. Hypotheses will be developed for both the control of the pathways involved and predictive capabilities of molecular markers arising from the identified relationships between gene sequence and/or expression variation and trait variation. These will be tested by the quantitative analysis of traits following the inter-crossing of different plant lines from the collection and/or the selection and testing of plant lines from a population chemically treated to induce gene sequence variation. Using the knowledge gained, mathematical models will be developed to help industry estimate economic and environmental consequences of the development of optimised new cultivars.

The principal aim of the project is to understand the genetic control, in rapeseed, of the accumulation of compounds representing emerging bio-refining opportunities and fertilizer use efficiency. We will:

1. Establish data models for Brassica transcriptomics and traits. This involves the development of databases and systems enabling the UK Brassica research community to access, analysis and exploit large-scale gene sequence and expression datasets, trait data and marker-trait associations.

2. Determine and make available functional genotypes for Brassica diversity collections. This involves the production of Illumina sequence reads from mRNA extracted from the leaves of each of 600 Brassica accessions (400 B. napus accessions plus 100 accessions of each of B. rapa and B. oleracea), along with the identification and scoring of sequence polymorphisms and quantification of transcript abundance.

3. Improve our understanding of the genetic bases of rapeseed bio-refining traits: tocopherols, phytosterols, waxes and functional polysaccharides, and nutrient use efficiency. This will involve the use of Associative Transcriptomics (a combination of genome-wide association scans, gene expression correlation with trait variation and co-expression network analysis) to identify gene sequence and/or gene expression markers. Hypotheses and markers will be developed for the control of product accumulation. These will be tested by the quantitative analysis of traits following the inter-crossing of plant lines from the collection and/or the selection and testing of plant lines from a "TILLING" population.

4. Develop models for both economic and environmental sustainability of rapeseed. This involves both a cost-benefit analysis for the economic exploitation of co-products from rapeseed and an assessment of the potential environmental impacts, taking into account the potential for improving nutrient use efficiency.

The proposed research is very well aligned with BBSRC's strategic objectives. Rapeseed is the UK's main vegetable oil crop and of importance for food security (BBSRC's research priority 1), both directly in terms of its production of edible oil and use of residual meal (the material left after extraction of oil from seeds) for feed, and indirectly due to its importance in rotation with cereal crops. Rapeseed is grown on a large scale in the UK (~700,000 Ha in 2011/12) and provides enormous opportunities for bioenergy and industrial biotechnology (BBSRC's research priority 2), particularly for providing renewable substitutes for mineral oil (e.g. modified oil composition for lubricants and biofuels derived from waste straw) and as a source of a range of high value compounds via bio-refining.

Beneficiaries:

The immediate beneficiaries of the research will be the industry partners: Cargill, Biogemma, Limagrain, Monsanto, HGCA, CaseIH and ADAS.

Direct beneficiaries, but on a longer time scale, will be the broader rapeseed breeding and farming industries.

Indirect beneficiaries are the broad range of breeders, farmers and processors around the world working with crops on which the technology will act as an exemplar for rapidly addressing the economic and environmental feasibility of bio-refining.

Benefits:

Cargill will have early access to knowledge of the ranges of quantity and types of co-product that can realistically be accumulated in rapeseed.

Rapeseed breeders will have molecular markers and germplasm to underpin the breeding of rapeseed cultivars with enhanced value from co-products and improved fertilizer use efficiency.

Farmers (represented by HGCA) will be able to sell rapeseed from new cultivars for a higher price per tonne and gain a return from residues such as straw and pod walls, as processors will be able to purify and sell on valuable co-products.

Indirect beneficiaries in other crops will benefit in the same ways as their counterparts in the rapeseed industry.

UK economic performance will benefit as the country's agricultural products will have increased value; similarly for global economic performance.

Public health will benefit as the work will underpin the development of new sources of important compounds with benefits such as dietary antioxidants and lowering LDL cholesterol.

There will be environmental benefits. Directly, alleles that result in improved fertilizer utilization efficiency can be introduced into conventional rapeseed for the production of edible oil. Indirectly, rapeseed lines have recently been developed that produce highly thermo-stable oil that could provide a renewable substitute for mineral oil in a range of applicants such as lubricants and hydraulic fluids. Tocopherols and phytosterols could provide a high value co-product to be extracted from rapeseed oil before such industrial applications, improving the economics of producing such oil.
There are industrial applications for co-products. For example tocopherols are attracting increasing interest as thermal stabilisers in melt polymers (e.g. in the production of LLDPE films) and in lubricants intended for a sensitive environment such as food production. Some of the wax molecular compounds are important semiochemical molecules that help reducing aphid foraging on important food crops. Functional polysaccharides include high value stabilisers, surfactants and barriers.