Genomics-assisted breeding for fatty acid content and composition in perennial ryegrass (Lolium perenne L.)

The central objective of this proposal is to improve the fatty acid (FA) content of perennial ryegrass by applying state-of-the-art genomics tools and resources and high throughput phenotyping methodologies and to quantify the impact of modified FA content on animal production, supply of beneficial omega-3 FA to the animal and greenhouse gas emissions (GHG). The project addresses some of the major challenges facing UK agriculture in a world that is undergoing climate change. The UK's climate favours grassland-based livestock production which is charged with the challenging target of increasing production whilst reducing inputs at a range of levels. Such sustainable intensification is increasingly relevant to the future of livestock agriculture. This proposal addresses sustainable agricultural production at the interface of three BBSRC strategic priority areas: crop science, livestock production and healthy and safe food. It is of high strategic relevance, specifically in understanding and exploiting the genomics for enhanced nutritional composition of pasture grasses (crop science). It will also increase the efficiency and sustainability of animal production, including minimising negative environmental impacts, such as emissions of greenhouse gases (livestock production) and investigates the potential of novel nutrient supplies from plants (healthy and safe food).
Fats and oils are an important component of livestock diets, contributing a significant input of energy into the productive requirements of animals that consume them. Beyond delivering basic energy requirements for meat and milk production, FAs, and more importantly the FA profile of lipids in livestock feed can influence rumen function and the quality of animal products used for human food. We have identified a significant opportunity in relation to improving total FA content, in particular the polyunsaturated FA (PUFA) fraction, which will enable the next generation of IBERS high performance ryegrass varieties to provide benefits to UK agriculture and the environment, by potentially reducing enteric methane emissions and increasing ruminant production. It will also potentially result in human health benefits with more forage-derived PUFA being present in meat and milk. The project will combine the expertise of plant geneticists and breeders with ruminant nutritionists in an integrated multidisciplinary project. It will develop the genetic tools and resources to enable efficient selection for FA content and composition. Phenotyping plant material for FA content is however time consuming and costly. This project will therefore also develop high throughput techniques that will complement the advanced genetic approaches. The effect of modified grass FA content and composition on methane emissions, omega-3 absorption and growth of ruminants will be studied in vitro and in vivo. The project will use the results in combination with genomic selection approaches now being applied to the IBERS grass breeding programme to speed up the development of new perennial ryegrass varieties and their uptake by the livestock sector. Grass breeding programmes at IBERS have a track record of innovation and of delivery in terms of quality improvements, particularly in relation to cell wall biochemistry and the development of high water soluble carbohydrate (WSC) grasses which are well adapted to the UK and have a good agronomic performance.
This proposal is being submitted through the BBSRC stand-alone LINK scheme. The project will benefit from the involvement of the only UK-owned forage grass and legume seed production and wholesale company (Germinal Holdings) and HCC representing a large part of the UK ruminant livestock sector, allowing for identification and review of key targets by the industrial partners and uptake and delivery of the outcomes of this project.

Grass lipids contain approximately twice as much energy as carbohydrates and protein per unit of weight, thus representing a potential target for genetic improvement. There is also emerging evidence that fatty acids (FA) can potentially have mitigating effects on methane emissions produced by ruminants from enteric fermentation. This project will develop genomics and high throughput phenotyping methods to increase the speed and precision of improving lipid content in perennial ryegrass.
We will use a combination of QTL mapping and genome wide association studies (GWAS) to identify and validate SNP markers or haplotypes associated with FA constituents in ryegrass forage in biparental populations and an ecotype panel. The SNP panel will consist of approximately 4000 markers developed using next generation sequencing technology. Genome wide selection will be used in the ryegrass breeding populations to develop prediction models for FA constituents. Significant markers identified in the GWAS and QTL analyses will improve the benefits of the SNP panel. These marker assisted technologies will be implemented to generate improved populations with enhanced FA content while maintaining overall merit for other important agronomic and quality traits. Phenotyping will be carried out using FT-IR, GC-MS, Raman spectroscopy and field NIRS and validated using the genetic resources (including the new experimental populations) described above. The impact of modified FA content and composition will be analysed in vitro using gas production techniques and in vivo in zero-grazing trials to enable the effects on animal production and potential effect on methane emissions to be quantified. Advanced germplasm with enhanced FA composition will be developed and tested for submissions to National List trials.

The major beneficiaries of this research will be:
Plant breeding community: Information on the genetic control of FA content and genomically and phenomically characterised germplasm will be available for trait dissection and breeding. Development of high throughput cost-effective phenotyping techniques will enhance trait selection for FA composition in plant breeding programmes.

Livestock sector: This work will also have a significant economic and environmental impact on ruminant production. Advanced germplasm will be developed into potential new ryegrass varieties which will have the enhanced FA composition that will deliver environmental and economic benefits to sustainable livestock production systems. The outputs of this project, to increase the supply of energy from lipids in pastoral systems, are targeted and relevant at various levels of the food chain from the farmer producer, to the retailer and the consumer.
In particular, the improved ability to (1) feed ruminants under high forage input systems, (2) predict nutrient supply and (3) to manipulate production response will lead to improvements in agricultural efficiency both in terms of use of natural resources and in farm profitability. This will contribute to a reduced reliance on imported feeds, to provide energy, which is especially prudent following the recent and on-going problems in the livestock industry. Improved knowledge of the interrelationships between growth of an animal and subsequent effect on eating quality (for juiciness and tenderness linked to FA profiles) will improve the quality of the product, which is of benefit to the producer and the consumer.

The research will also contribute towards a greater supply and subsequent absorption of beneficial omega-3 to the animal. This will potentially have significant health benefits to the animal and has been shown to improve fertility. Protected omega-3 products are becoming more popular in the dairy industry to reduce calving interval. The ability to feed pasture with greater levels of omega-3 will have a significant cost saving not only in terms of reducing omega-3 supplementation but also the benefits of greater fertility. As a consequence of the elevated levels of omega-3 the farmer will produce healthier food in terms of a leaner product which will contain lower quantities of saturated fatty acids and increased content of specific beneficial compounds (i.e. n-3 PUFA linolenic acid) in meat and milk. The role of meat and milk as a vehicle to deliver beneficial fatty acids through to humans is very important and has been marketed by numerous supermarkets over the last few years in developing niche products.

Society: There will be direct environmental benefits from this project to wider society. The ruminant sector is a significant contributor to UK greenhouse gas emissions, as approximately 65% of the methane emitted from the UK is generated as a result of agricultural activities and of that approximately 85% comes from livestock enteric sources. There is good evidence that methane arising from enteric fermentation in the digestive system of ruminants can be reduced by changes in fatty acid content and composition. It has been calculated that methane emissions from ruminants (in g/kg of dry matter consumed) could be reduced by 5.6% for each 1% of supplemental fat. This project will show how using perennial ryegrass with altered FA composition can also impact on production efficiency. As forage fed animals produce meat and milk with a fatty acid composition more favourable to human health than concentrate fed animals, there is also a clear societal benefit that will be derived from this research.