A draft sequence of the barley genome

Lead Research Organisation: The James Hutton Institute
Department Name: Cell & Molecular Sciences

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

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 ~Euro57.5 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 3,800 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 to 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, with the US food and drug administration recently allowing 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

10 25 50
 
Description We constructed an integrated physical genetic and functional sequence assembly of the 5.1Gb barley genome as a highly enabling informational resource for genetics and breeding in this species. We developed technologies that will be essential for understanding how the barley genome can tell us about the adaptive consequences of migration and spread, and the genes that control the traits important for breeding improvement. We established a methodology (POPSEQ) that has now been used to help develop a similar resource for the more challenging wheat genome. In the final year of the award we developed a physical map based sequence and incorporated an optical map and HiC map. We also exome capture sequenced 500 barley cultivars that is being used for various genetic analyses.

The integration of BAC based sequence, otical map, POPSEQ and Hi-C data has provided the data to generate a new assembly of the barley genome based on physical mapping data and now displayed as Pseudomolecules. The data can be found here: http://plants.ensembl.org/Hordeum_vulgare/Info/Index OR http://mips.helmholtz-muenchen.de/plant/barley/ OR http://apex.ipk-gatersleben.de/apex/f?p=284:10:::::: A raft of papers describing the output of the work were produced in 2017 and reported as publication outputs
Exploitation Route As a reference genome, the whole field of barley (and other triticeae) genetics and breeding will benefit from the resources developed. We also characterised a wide range of elite germplasm using a technology developed alongside the genome sequence and using that data (called exome capture). The diversity data should be highly valuable for the more applied research communities as it reveals considerable potential vulnerabilities in the barley genome through a lack of allelic diversity over enormous tracts encompassing the pericentromeric regions.
Sectors Agriculture, Food and Drink,Energy,Environment,Healthcare

URL http://mips.helmholtz-muenchen.de/plant/barley/
 
Description The findings are being used by the global triticeae (wheat, barley, rye) research and breeding communities to help identify genes underlying phenotypic traits and to develop genetic markers for use in crop improvement. The resource is providing a platform to look at broader genetic diversity within the species, how genetic variation is partitioned in physical and genetic terms and how barley compares to its close relatives. The exome sequences have provided the information to make a new 50K SNP chip for community use and the SNP diversity data a powerful genetic platform for trait dissection and gene isolation using genetic approaches. The 50K SNP chip has been used to genotype all accessions in the JHI seed store and forms a valuable management tool for genetic resources. Outputs of using the 50K platform on 1000 diverse genotypes has been compared to GbS data which reveals platform complementarity but general concordance between patterns of observed molecular diversity.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Energy,Environment,Healthcare
Impact Types Economic

 
Title 50K SNP chip 
Description We developed a 50K SNP chip using illumina technology for use by the entire barley genetics and breeding communities. A publication describing the resource has been uploaded to the publication outputs. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact The platform has had widespread uptake in the barley genetics and breeding communities with in the region of 20,000 assays (genotypes) already collected through research in the public domain. The extent of usage in the commercial sector is - we believe- considerable but accessing the specific numbers impossible. 
URL https://ics.hutton.ac.uk/50k
 
Title POPSEQ 
Description A method for high density ordering of WGS sequence contigs along genomes of simple or complex genomes 
Type Of Material Improvements to research infrastructure 
Year Produced 2015 
Provided To Others? Yes  
Impact Genetically ordered barley, wheat (and other) genome assemblies 
URL http://jgi.doe.gov/doe-jgi-science-highlights-popseq-for-plant-genome-assembly/
 
Title Barley ENSEMBL 
Description EMSEMBL browser of genome data 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact Supports the entire plant genetics and breeding research communities 
URL http://plants.ensembl.org/Hordeum_vulgare/Info/Index
 
Title BarleyGenes 
Description Barley gene expression database based on RNA-seq data 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact Used for candidate gene identification and tissue specific gene expression analysis. 
URL https://ics.hutton.ac.uk/barleyGenes/
 
Description Barley Pan Genome 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution Provide a reference quality sequence of the cultivar Golden Promise
Collaborator Contribution Reference Quality sequences of other barley genotypes (consortium effort)
Impact No outcomes yet
Start Year 2017
 
Description Barley Yield associated Networks (BARN) 
Organisation IPK Gatersleben
Country Germany 
Sector Private 
PI Contribution BARN is an ERA CAPS collaborative award with three partners. We will provide a Reference Transcript dataset and RNA seq information from 2 tissues from 200 barley cultivars. We will jointly analyse the resulting data
Collaborator Contribution Each has common and specific tasks. The Reference Transcript dataset and RNA seq information will be used to interrogate expression in a further 2 tissues from 200 barley cultivars. We will also survey sequence all 200 lines and build cultivar specific RTD's to assist analysis. The partners will jointly analyse the resulting data
Impact Too early
Start Year 2018
 
Description Barley Yield associated Networks (BARN) 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution BARN is an ERA CAPS collaborative award with three partners. We will provide a Reference Transcript dataset and RNA seq information from 2 tissues from 200 barley cultivars. We will jointly analyse the resulting data
Collaborator Contribution Each has common and specific tasks. The Reference Transcript dataset and RNA seq information will be used to interrogate expression in a further 2 tissues from 200 barley cultivars. We will also survey sequence all 200 lines and build cultivar specific RTD's to assist analysis. The partners will jointly analyse the resulting data
Impact Too early
Start Year 2018
 
Description Recombination in wheat and barley 
Organisation University of Adelaide
Department School of Agriculture, Food and Wine
Country Australia 
Sector Academic/University 
PI Contribution I was a Co-Investigator on a successful ARC discovery grant on meiosis and recombination in wheat and barley with Prof. Peter Langridge. The award will use resources generated in my research program for mutual benefit. It was developed largely through the funding awarded for an Australia partnering award which has seen multiple visits in each direction over the past 4 years.
Collaborator Contribution The partners will receive ALL of the funding save some money for travel to meetings throughout the project. The partners will provide lab, consumables funding and all administrative resources required to execute the project objectives. The funding allows the University of Adelaide to employ a PDRA and technician for three years.
Impact Still too early. Project only started a few months ago.
Start Year 2017
 
Description BBC Scotland 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview with BBC Scotland about Barley Research
Year(s) Of Engagement Activity 2015
 
Description Cereals in Practice 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Cereals in Practice is an annual event held jointly with SRUC and attracts mainly the farming community throughout Scotland and NE England. Annual attendance is around the 200-300 mark but varies according to the weather as its an outdoor event. Showcases current research outputs and new varieties.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
 
Description Eucarpia Cereals Section 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact • Eucarpia Cereals Section Conference, Werningerode, June 2014 (session organiser and chair
Year(s) Of Engagement Activity 2014
 
Description Fascination of Plants and Family Fun Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact EPSO's Fascination of Plants day in Dundee is combined with an event called Family fun day that we run annually at the Botanic Gardens. It has a wide range of events - including plant sales from 'friends of the gardens', displays, activities, games, educational events (e.g. the genetics garden) and other activities.
Year(s) Of Engagement Activity 2013,2014,2015,2016
 
Description ITMI 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact • International Triticeae Mapping Initiative Conference Fargo, June 2012(session organiser and chair)
Year(s) Of Engagement Activity 2012
 
Description Landward 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview on BBC Landward program about new breeding technologies in relation to barley and potatoes
Year(s) Of Engagement Activity 2015
 
Description PAG 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact • Plant and Animal Genome, Triticeae Workshop, Speaker, San Diego January 2015
Year(s) Of Engagement Activity 2015
 
Description Plant Genetics and Breeding Technologies, Vienna 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact • Molecular Mapping and marker assisted selection Vienna, Feb 2012 (session organiser, speaker, chair)
• Plant Genetics and Breeding Technologies, Vienna, Feb 2013 (session organiser, speaker and chair)
Year(s) Of Engagement Activity 2012,2013
 
Description Public engagement 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Open day at the botanic gardenss with displays, activities, demonstrations etc.
Year(s) Of Engagement Activity 2014,2015,2016
 
Description Rank Prize Symposium II 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact • Rank Prize symposium, Grasmere, 18-21 May 2015 (organiser, speaker and session chair)
Year(s) Of Engagement Activity 2015