Genomics Enhanced Wheat Breeding: Using sequencing technologies for trait dissection, marker assisted selection and genomic selection in wheat.

Bread wheat accounts for a fifth of the world's food, is the main source of protein in developing countries and is second only to rice as a source of calories in those consumers' diets. It is the most widely grown arable crop in the UK, where it is grown on around 1.8 million hectares per year.

UK breeders and farmers have been highly successful in developing and growing wheat varieties with higher yield potential: over the period 1948 to 2006, average yields in the UK increased from ~3 tonnes per hectare to ~8.0 tonnes. Unfortunately, wheat production increases have not kept pace with increased demand. Furthermore, wheat productivity is threatened by disease, competition for high quality agricultural land, resource limitations, and adverse environmental conditions that dramatically reduce optimal yields. It has been estimated that in Europe productivity needs to double to keep pace with demand and to maintain stable prices.

To help plant breeders improve wheat varieties they have utilised genetics variants, in particular Single Nucleotide Polymorphisms (SNPs), that are linked to known traits such as disease resistance, adaptation to particular environments, bread making quality characteristics and components of yield. Breeders use molecular markers to track linked SNPs as a proxy for these beneficial traits. This has the advantage of screening many thousands of lines quicker, cheaper, and in some cases more accurately than growing in a field to assess the lines conventionally.

Wheat evolved from two naturally occurring separate hybridisation events, each creating a genetic bottleneck. Firstly two wild grasses hybridised to form a relative of pasta wheat. Subsequently a third wild grass hybridised to produce bread wheat. As a result, the total genome size is approximately 16,000 Mb or 35 times the size of the rice genome and 5 times the human genome. The relative lack of diversity in bread wheat has led to breeders and researchers crossing wheat varieties with relatives of wheat to increase genetic diversity and specifically to introduce beneficial traits such as disease resistance. Whilst a large number of SNPs have been identified in bread wheat, these have been identified in relatively few varieties and are not always relevant to the particular germplasm that a breeder is working in. In addition, many of the relatives that have been crossed into wheat have not had specific SNPs identified and represent a 'blind spot' to the breeders.

This project aims to produce DNA sequence data for wheat genes for 280 wheat varieties, using a technology known as exome capture and 'next generation sequencing'. This is a complexity reduction process, which reduces the genome size and will enable us to produce sequence data for a large number of lines. The lines will be selected to contain key relatives that have been crossed into wheat. This data will enable us to identify the regions that we have been blind to, and to more accurately locate genes of interest so we can then breed for them using molecular markers. Ultimately, this will help us to develop varieties that have key traits for farmers, such as virus resistances, that will enable them to use less pesticides and to farm wheat more reliably.

Wheat is the UK's major crop and has the 3rd largest production of any cereal globally. This project has the potential to benefit individuals and organisations worldwide for whom improvement in wheat is important. This ranges from farmers, through millers and bakers, to anyone buying bread in their local supermarket.

The impact of the methods we develop will be seen first by the UK wheat varieties targeted in this project, with delivery of improved RAGT varieties to market in the following few years. This will be closely followed by improvements in the RAGT French and German breeding programmes. Whilst the first beneficiary of this research will be RAGT, over time, all wheat breeders will benefit from these improvements as they are able to cross with any national listed varieties through the plant breeders' exemption to Plant Variety Rights and hence will gain access to beneficial combinations of alleles that are achieved through the research undertaken in this proposal. Ultimately this will lead to genetic improvement in wheat varieties as a whole, which will benefit all farmers and consumers who consume the wheat. To provide a specific example, it is anticipated that sequence information for the Bdv2 BYDV resistance introgression in RGT Wolverine will be used to fine-map the resistance gene and to enable efficient marker-assisted selection. This will assist RAGT to breed more varieties with this gene combined with other beneficial alleles. These varieties will allow farmers to grow wheat with fewer or no insecticide treatments. This will have both an environmental and an economic benefit due to the lower inputs. This benefits consumers both through reduced pesticide residues in food and the societal and environmental benefits of reduced effects of agro-chemicals on wildlife food-chains.

One component of the project is the establishment of bioinformatics pipelines within RAGT. This will be conducted by the fellow working with the ERA bioinformatics service company. This will provide a future platform for the cereal genotyping team to utilise publically available wheat sequence datasets and to integrate them with the datasets produced in the current proposal using the current wheat reference genomes and future genomes assembled at high quality from the 10+ Genome Project. This will impact directly on the RAGT molecular wheat breeding programme and also will provide opportunities for further collaborative research with academics utilising sequencing data.

A further beneficiary will be the research of the academic project partner, Prof. Cristobal Uauy. As part of the project ~20 lines to be nominated by Prof. Uauy will be included in the exome capture and sequencing. The intellectual property of this data will reside with the John Innes Centre (JIC) and can be published freely to provide benefits to the wheat research community as a whole. It is anticipated that the project, and the data generated within it, will lead to further possibilities for research collaborations either bilaterally between RAGT and JIC or as part of wider research collaborations between the plant breeding industry and JIC.

Finally, the fellow will be a beneficiary as it provides a unique opportunity to translate methods that have to date been limited to application in academic research, in which he has considerable expertise, to a practical breeding programme to provide more rapid genetic improvement of varieties. He will benefit from the expertise of Prof. Uauy and his research group in the application of genomic technologies to wheat genetics studies. This will provide him with a combination of both specific research skills and transferable skills that will make him well placed to become a global leader in the field of molecular plant breeding.