The diversity and evolution of the gene component of barley peri-centromeric heterochromatin.

Barley is the second most important crop in UK agriculture, underpinning the beer and whisky industries, worth some £20Bn to the UK economy, and the meat and dairy industries as animal feed. Over the past 50 years barley grain yield has more than doubled, mostly due to crop breeding efforts, but yields need to keep increasing at this rate to feed the ever increasing population, against the challenging background of climate change with its associated new pests and diseases, higher prices for fertiliser and pesticides and increasing demands from regulatory bodies for lower levels of chemical treatments. New varieties of cereal crops must be bred to deal with these challenges but in recent years the improvement rate has slowed in the cereals, as conventional breeding has optimised the available genes in the 'genetically narrow' barley cultivars. Wild barley offers an escape from this trap as it contains many beneficial gene variants that could improve cultivated barley if they were transferred across by breeding. This is much more difficult than it sounds because a large fraction of the genes of all cereals are buried in vast amounts of useless DNA and wrapped up so tightly inside the cell nucleus that they hardly ever make new combinations with better properties than their parents. In this project we propose to study these 'trapped genes'. Surprisingly, cereals have much more DNA in them than humans and are correspondingly more difficult to study at the gene level, but recent technical advances in DNA sequencing and fingerprinting have made them accessible. This new knowledge will provide the tools to allow us to search through wild barley varieties for new, potentially useful gene combinations which are currently inaccessible to modern barley breeders, maintaining the improvement in the crop that is needed for the future.

The Triticeae cereals share a well-conserved genome organizational structure of 7 chromosomes and a well-understood synteny correlation with other sequenced cereal genomes. High throughput marker analysis and next generation sequencing has given a clear picture, particularly for barley, of the gene complements and genetic map locations of many of the genes. These data, when compared against fully-sequenced cereal genomes such as rice and brachypodium, reveal a detailed picture of the large-scale structure of the genome which shows that a surprisingly high proportion of barley genes are trapped in low-recombining peri-centromeric heterochromatin (LR-PCH). These genes are virtually inaccessible to both current gene-identification and localisation approaches (e.g. genome walking and association genetics) and crop breeding, because very few haplotypes are available per chromosome in the total UK cultivated gene pool and recombinants within them are extremely rare. The first goal of this research is to gain an understanding of the genes in this restricted genomic compartment, to study their sequence diversity and evolution in the species and to use a comparative genomics approach to learn more about how the large scale processes of genome duplication, gene translocation, gene loss and heterochromatization have moulded the barley genome. This will be achieved by applying next generation sequencing of captured genes both within and external to the LR-PCH and comparing it with corresponding diversity data for other sequenced cereal genomes. Our second goal is to investigate the epigenetic context of the barley genome by isolating and sequencing barley genomic DNA associated with the different methylated H3 histones that potentially affect genomic compartmentalization in cereals. Finally, these two studies will be combined together to learn how the genes of LR-PCH and normal recombining euchromatin relate to chromatin histone H3 modification.

Barley is the model Triticeae cereal and this family together constitutes the major sector of UK agricultural and food chain activity in the UK. Although this is a basic evolutionary genomic sproject, information on the large, relatively inaccessible region of the barley genome to be studied in this project will in the longer term lead to advances in genetics/plant breeding and biotechnology. In this regard the beneficiaries of the project will be commercial sector organisations that breed new varieties and the farmers that grow these new varieties in their fields. Additionally, barley has a considerable extra value to the UK economy because it supports the brewing and a large part of the distilling industries. Four of the seven largest brewers in the world are European, and the total annual government revenue across Europe deriving from this activity is roughly 58 billion euro. Also, cereal straw has a big role in animal nutrition and the second-generation bioenergy sector. Lastly, our discoveries in barley potentially impact upon activity in the other cereal grasses such as forage/turf rye grasses, wheat and rye that are less accessible to genomic studies. The gene sequence data and its embracing genome context information will facilitate the identification of genes and gene networks conferring traits including yield, food and feed quality, abiotic stress tolerance and biotic stress resistance. The gene sequences we will explore provide the raw material for allele mining and genomics-derived crop improvement. The UK brewing sector relies upon regular high quality barley production and this in turn guarantees additional downstream employment in supply, retail, and hospitality sectors. Barley is also an important part of the livestock industry (as feed). It also has potential in health-promoting human nutrition, with high content of beneficial nutrients such as beta glucans, arabinoxylans, sterols and stenols. In this regard, the US FDA recently stated that barley products have a role in reducing the risk of heart disease. Advances in crop genomics flow rapidly into marker-assisted breeding activities in the plant breeding sector and then diffuse outards to the food, feed and drinks industries. The UK has an efficient and successful commercial cereal breeding sector (largely with EU parent companies) and the SCRI in has close and longstanding collaborations with the major European barley breeders. SCRI agreessively engages with this user community via open days and a variety of collaborative activities, many of which have received significant UK and EU funding. Internationally, the International Barley Sequencing Consortium has links with the breeding and brewing sectors. We have broad experience in web-accessible databasing of our experimental outputs and we thus have the necessary ability to ensure that our results can be accessed rapidly and effectively by the broad user community.