A draft sequence of the barley genome

Lead Research Organisation: Earlham Institute
Department Name: Directorate Office

Abstract

Summary: Barley is the second most important crop in UK agriculture. High quality malting barley (some 30% of the total) underpins the beer and whisky sector in the UK that is worth some £20B to the UK economy with almost £5B flowing directly to the treasury as duty. Lower quality barley grain and by-products of the malting process are a major component of animal feed that underpins the meat and dairy industries and barley straw is a source of nutrition for ruminants, is used for animal bedding in the winter and for frost protection in horticulture. In March 2010 merchants' buying prices for barley straw reached £86 per ton ex-farm, equivalent to the price of the grain. In social terms, barley cultivation and its use in the whisky industry indirectly supports up to 40,000 families in Scotland, largely in rural communities. Over the past 50 years cereal grain yields, including barley, have more than doubled, due largely to the efforts of a small number of commercial organisations that seek to improve the quality, diversity and performance of our key agricultural crops. Recent analyses by the National Institute of Agricultural Botany have shown that over the past 25 years, greater than 90% of this improvement can be attributed to genetics through innovation in plant breeding (as opposed to agricultural practices). Despite this considerable success, with crop yields needing to double again by 2050 in order to feed an estimated 9B population, climate change bringing erratic and potentially devastating weather patterns and the drive for low input sustainable production, the industry is facing challenges unlike any that have gone before. The scientific community agree that to meet these will require a deeper understanding of how different variants (called alleles) of barley's estimated 35,000 genes can be brought together in optimal combinations to increase yield, quality and resilience, and methods that allow plant breeders to improve the rate of genetic gain in crimprovement programs. In this project we propose to generate information on the complete complement of genes in the barley genome (its genetic blueprint) and to start to explore how different versions and combinations of genes have been assembled by breeders over the past 25 years of successful yield improvement. Our hypothesis is that an understanding in genetic terms of how crop production successes of the past were brought about will allow us to predict how to bring about further and faster successes in the future, equipping us to address the key global challenges listed above.

Technical Summary

Technical summary: We propose to conduct an ambitious project that will deliver a draft 2GS assembly of the 5,300 Mbp barley genome with a sequence contig N90 of >5 kb covering the non-repetitive portion of the genome that should capture almost all barley gene sequences in their native genomic context. Deep 2GS RNA sequencing will reveal patterns of expression of all barley genes at tissue and developmental stage levels and facilitate gene building and annotation. We will also investigate genome-wide patterns of alternative mRNA splicing in plants subjected to abiotic stress. We aim to incorporate layers of data generated by the International Barley Sequencing Consortium (IBSC) since 2006, including extensive BAC end sequences, Phase 1 sequence of c. 3,000 BACs, 500,000 ESTs, 25,000 full length cDNAs, small RNA data, low CoT and methyl filtered 2GS data, chromosome arm specific 1.5X 454 data, and a physical map, including anchoring information to the barley genetic map. The project will fully exploit the considerable investment in barley structural genomics already made at a national, European and global level and we will encourage participation in the genome analysis by the international community. We aim to establish an ENSEMBL-based portal to the assembled and integrated data and release this to the community as soon as is practicable. Collaboration with the IBSC contributors will be positively encouraged through early release of data for community-based analyses. To progress the genome sequence towards exploitation by a broad user pool in the UK we will genotypically characterise (by sequencing) a large association mapping panel of elite UK cultivated barley lines to link genes to phenotypes and provide a bridge for exploitation by both breeders and academics.

Planned Impact

Who will benefit from this research? The Triticeae cereals are a dominant component of European agriculture and barley, as a simple diploid, is a model for genomics-assisted molecular breeding. Making the assumption that a draft barley genome sequence will, in the longer term, lead to advances in genetics/plant breeding and biotechnology (which we strongly believe), the immediate beneficiaries of the project will be commercial sector organisations that breed new varieties and the farmers that grow these new varieties in their fields (UK farm gate value >£500M). However, barley has a considerable 'hidden value' beyond the farm gate as it underpins the European brewing (and Scotch whisky) industry which is the largest in the World. Four of the seven largest brewers in the world are European, with their product directly / indirectly generating a total government revenue estimated at ~£57.5 billion annually. Cereal straw has a potentially expanding role in animal nutrition and also in the second-generation bioenergy sector. Considering the grasses as a single genetic system, discoveries in barley will impact directly other members of the Family - including Lolium/Festuca, wheat and rye - that are less amenable to genetic analysis. How will they benefit from this research? A draft barley genome sequence will be a platform for biological discovery, not an end in itself. It will facilitate the identification of genes and gene networks that impact upon traits ranging from yield, quality, and environmental resilience to nutritional value. Functionally characterised gene sequences are a template for allele mining and for biotechnology-based crop improvement strategies. Supporting and enhancing barley production will maintain a vibrant brewing sector where 3800 European breweries provide jobs for >164,000 employees. For each of these, an additional job is generated in retail, two in the supply sectors and more than 12 in the hospitality sector (Total >2.5M). Disruption the supply of high quality UK / European barley would therefore have widespread detrimental social and economic effects. Barley is a key feedstock for the livestock industry and a traditional food on the marginal lands of Europe that are unable to support the growth of wheat or maize. It has great potential as a whole-grain health-promoting food of the future, given its high content of sterols, stenols, arabinoxylans, and beta glucans and the US food and drug administration recently allowed barley products to claim a role in the 'reduction in risk' of coronary heart disease What will be done to ensure that they have the opportunity to benefit from this research? The conduit through which almost all genetic advances in crop production must pass to release their benefits to the broader community is the plant breeding / biotech sector. Translational activities from basic science to application are therefore crucial. The UK boasts one of the most efficient and successful commercial cereal breeding sectors in Europe and the PI maintains long lasting, strong and, importantly, funded collaborations with all of the major barley breeders in Europe. He has proactively engaged this community, including maltsters and distillers, from the outset of structuring this proposal (see attached letters of support) and will continue to do so if it is judged suitable for funding. Internationally, the IBSC also has links to all of the major sectors of the breeding, brewing and academic sectors and a strong identity within the global community. We anticipate that, if supported, our project will lever additional funding from other national agencies, particularly in Germany, the USA, Australia and Japan. The objective of developing an open access portal to the generated information should ensure widespread awareness of the resource. The PI's have the relevant expertise, track record and motivation to ensure that this happens effectively.

Publications

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Bolser DM (2015) Triticeae resources in Ensembl Plants. in Plant & cell physiology

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International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. in Nature

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Mascher M (2013) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. in The Plant journal : for cell and molecular biology

 
Description We have developed a high-throughput, low cost BAC sequencing and assembly pipeline using Illumina sequencing. Using this pipeline we have completed the sequencing for chromosomes 2H and 0H, the UK's contribution to the International Barley Sequencing project. http://barleygenome.org/
We generated gene expression data for 16 samples of the barley cultivar Morex.
We are running a pilot experiment using exome capture to resequence just the gene-coding part of hundreds of barley samples, uncovering the genetic basis for natural diversity.
Exploitation Route Barley is a model for plant genetic research. Large collections of geographically diverse elite varieties, landraces and wild samples are readily available and contains genetic diversity that could counteract the effect of climate change and further enhance dietary fibre in the grain. The primary route for exploitation will be through use of the diversity data by all UK barley breeders to improve crops breeds.
Sectors Agriculture, Food and Drink,Environment

URL http://www.barleygenome.org.uk/
 
Description We have led the development of a gene nomenclature consortium focused on the annotation of Triticeae species (with the sponsorship of the Wheat Initiative)
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Environment
Impact Types Economic,Policy & public services

 
Title Updated genome reference for barley 
Description An updated version of the barley genome reference was generated by the International Barley Sequencing Consortium. This project contributed with sequencing, assembly and data analysis capabilities to this resources. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact The access to this genome reference is open and available via a number of websites. This resource has supported a number of other studies conducted by members of the barley community (e.g. diversity studies). 
URL https://plants.ensembl.org/Hordeum_vulgare/Info/Index
 
Title Annotation of the Barley Genome 
Description The project contributed with data and analysis capability towards the annotation of the barley genome. The collection includes a comprehensive catalogue for the gene coding regions of the barley genome reference. A brief summary of the dataset: Coding genes 39,809; Non coding genes 2,965; Small non coding genes 2,770; Long non coding genes 195; Gene transcripts 251,310 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The gene annotation for barley is an essential resource that will support the development of new approaches for breeding and research projects for the barley community. 
URL https://plants.ensembl.org/Hordeum_vulgare/Info/Index
 
Description Seeds of Discovery - CIMMYT 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution Expertise in data analysis and integration with wheat DNA resources.
Collaborator Contribution DNA material and expertise in statistical analysis. CIMMYT supports an extensive network of collaborators.
Impact We have integrated informatics resources based in the UK to support the analysis of large genomics datasets generated by CIMMYT and other partners. The collaboration is multidisciplinary - it combines expertise in wheat pre-breeding, genomics, bioinformatics and data analysis.
Start Year 2015
 
Description Wheat Information System - Wheat Initiative 
Organisation Wheat Initiative
Country France 
Sector Charity/Non Profit 
PI Contribution I am co-chair of the Wheat Information System, part of the Wheat Initiative. We have develop a consortium to annotate gene names in wheat and related Triticeae species.
Collaborator Contribution We have work with our partners in different organisations that are members of the Wheat Initiative.
Impact A report advocating a gene nomenclature committee for wheat and other Triticeae species (http://www.wheatinitiative.org/sites/default/files/wysiwyg/triticeae_gene_nomenclature_workshop_-_report_.pdf)
Start Year 2011
 
Description Barley genome project publication 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact NIAB News item/press release regarding the barley genome project publication (A chromosome conformation capture ordered sequence of the barley genome, Nature, 27 April 2017.)
Year(s) Of Engagement Activity 2017
URL http://www.niab.com/news_and_events/article/407