FACCE ERA-NET+ An integrated approach to evaluate and utilise genetic diversity for breeding climate-resilient barley

Lead Research Organisation: University of Dundee
Department Name: School of Life Sciences

Abstract

ClimBar will identify genome regions, genes, and alleles conferring the traits needed to breed resilient barley varieties adapted to the climatic conditions predicted for 2070 in different European environments. Predicted conditions and adaptive plant traits for the northern Mediterranean Basin are also applicable to the southern, non-European side and will be relevant to Stakeholders representing farmers from that region. The phenotypic responses of a tailored barley germplasm diversity set that is relevant to resilience, sustainability, and quality will be determined under anticipated conditions of altered water and nutrients, CO2, and pathogen pressure. The set will include cultivated barley, landraces from key European production regions differing in aridity and pre-figuring climate change effects, and wild barley from the Fertile Crescent, which represents the gene pool from which domestication occurred and also carries resilience adaptations. These responses will be connected to genes and genome regions by Genome Wide Association Studies (GWAS) using extensive sequence variant, epigenome, and transcript abundance datasets, and by ecogeographic analysis. The genetic and genomic data sets will be leveraged from earlier (barley 9K SNP set; exome capture) and ongoing (WHEALBI exome capture) studies, which will serve to define the germplasm included in WP1, and will be complemented by planned ClimBar studies (ChIP, small RNA). Therefore, a very large amount of mostly transcribed sequence information will be available to declare and use polymorphisms with a density of coverage and representativeness of germplasm exceeding all previous efforts in this species. Plant phenotyping will be carried out under field conditions within regions expected to experience differing climate change scenarios, and under controlled greenhouse conditions where detailed physiological phenotypes will be collected. Genes and landraces and CWR associated with environmental conditions will be identified by ecogeographic analysis of genetic diversity. Based on observed plant responses and predicted climate scenarios, proposals for genomic selection (GS) and ideotype models for 2070 will be developed, and relevance to interim conditions assessed. Collaborative interactions with agro-economic modellers as well as climatic modellers will set up to estimate harvests in 2070 and their impact on the agro-economy, based on data collected within ClimBar

Technical Summary

In ClimBar the phenotypic responses of a tailored barley germplasm diversity set that is relevant to resilience, sustainability, and quality will be determined under anticipated conditions of altered water and nutrients, CO2, and pathogen pressure. The set will include cultivated barley, landraces from key European production regions differing in aridity and pre-figuring climate change effects, and wild barley from the Fertile Crescent, which represents the gene pool from which domestication occurred and also carries resilience adaptations. We will use GWAS to connect phenotypic responses to genes and genome regions using extensive sequence variant (exome capture sequencing SNP data), epigenome, and transcript abundance datasets, and by ecogeographic analysis. Thus SNP information from a very large amount of mostly transcribed sequence information will be available and provide a density of coverage and representativeness exceeding all previous efforts in this species. Plant phenotyping will be carried out under field conditions within geographical regions expected to experience differing climate change scenarios, and under controlled greenhouse conditions where detailed physiological phenotypes will be collected. Genes, landraces and Crop Wild Relatives associated with environmental conditions will be identified by ecogeographic analysis of genetic diversity. Based on observed plant responses and predicted climate scenarios, proposals for genomic selection (GS) and ideotype models for 2070 will be developed, and relevance to interim conditions assessed. Collaborative interactions with agro-economic modellers as well as climatic modellers will set up to estimate harvests in 2070 and their impact on the agro-economy.

Planned Impact

One of the biggest changes in exploring the genetics of our crop plants over the last 10 years has been the shift in bottlenecks from genotypic to phenotypic analysis. This fundamental shift, largely driven by some participants in this project who have developed technologies that make the former essentially facile, provides the rationale behind the strategy adopted in ClimBar and generates considerable opportunities that are relevant to Food, Agriculture, Environment and Climate Change science. To maximise impact, ClimBar will focus on addressing the phenotype and, by utilising germplasm collections and advances in genotyping made in existing national and international projects, will deliver to each of the food, feed, beverage, milling, farming IT and biotech sectors. The vehicle by which this will be Achieved will be the plant breeding community. By effective characterization and use of the diversity present in ancient barley landraces and wild relatives, and by exploring predictive plant breeding focused on low inputs and climate change coupled with modelling impacts on production, ClimBar will provide the germplasm, tools and information help deliver climate-proofed cereals tailored to our changing environment

Publications

10 25 50
 
Description We have already learned that certain leaf wax mutants have altered Stomata - the leaf pores that allow plants to breath. We have also seen that some Leaf wax mutants lose water very quickly while others apparently do the opposite. Looking at a collection of over 80 independent mutants has shown us that the genetic control of wax deposition is tissue specific and developmentally controlled. We have initiated a number of material exchanges where the reaction of different mutants will be thoroughly assessed for growth in drought, elevated CO2, high Ozone conditions and their reaction to a number of barley pathogens. We are close to identifying the genetic lesion responsible for a dominant spike wax variant found at relatively high frequency in wild populations from the near east fertile crescent. A paper describing our results is currently in preparation. We have made the observation that several of the wax mutants affect the adherence of the hull to the grain and are developing the hypothesis that allelic variation at one or more of these loci may be involved in the recently emerged problem of skinning that reduces barley quality destined for malting. We have obtained new funding from BBSRC (Sarah McKim and Robbie Waugh) to explore aspects of skinning further and a follow on to CLIMBAR is being discussed.
Exploitation Route We hope to identify genes and markers for plant wax composition that may be important for breeding for adaptation to climate change

In addition - while not directly related to the CLIMBAR grant application objectives we have observed that a small number of the barley waxless mutants exhibit poor hull adherence resulting in a 'skinning' phenotype on harvest. This is a particularly interesting observation because skinning has become a major quality issue with UK barley destined for the malt house for use in brewing. This observation gives an unique route to unravel the genetics of this complex trait. Our hypothesis is that plant wax or cutin defects that are apparent in the waxless mutants are somehow involved in the process of 'cementing' the hull to the developing seeds. This may provide two avenues for further investigation - one in relation to solving the skinning problem and 2. in developing alternative 'semi-naked' (or easily pearled) barleys for the human consumption.
Sectors Agriculture, Food and Drink

 
Description Barley Away Days 
Organisation University of Adelaide
Department School of Agriculture, Food and Wine
Country Australia 
Sector Academic/University 
PI Contribution We Hosted Prof Rachel Burton at our Barley Away Days in Dunkeld (3 day meeting) where she gave a talk about her latest research
Collaborator Contribution Rachel attended the BAD and interacted with students and postdocs. She gave an excellent presentation of current research in her group and judged the poster competition and short talks.
Impact Strengthened relationships with the cell walls group in Adelaide
Start Year 2017
 
Description WHEALBI 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution We Selected 500 wheat and 500 barley genotypes for exome capture sequencing, coordinated data generation, multiplied material and distributed to partners, collected and analysed variant data and wrote publications. Managed 2 WP's.
Collaborator Contribution WHEALBI will combine genomics, genetics and agronomy to improve European wheat and barley production in competitive and sustainable cropping systems. Germplasm representing the species diversity will be selected and characterised in unprecedented detail by next-generation-sequencing. Life history and adaptive traits will be evaluated in both transnational field experiments and a state-of-the-art precision phenotyping platform. Germplasm will be stored in a specialised and accessible bio-repository and associated data in knowledge bases that will represent a valuable legacy to the community. Whole genome association scans will be conducted for several traits, signatures of adaptive selection will be explored, and allele mining of candidate genes will reveal new variation associated with specific phenotypes. Pre-breeding tools and pipelines will be developed to optimize the efficiency of allele transfer from unadapted germplasm into elite breeding lines. New methodologies will explore how to optimally exploit the large amount of new genotypic and phenotypic data available. They will focus on the design of ideotypes with improved yield stability and tolerance to biotic and climatic stresses and provide proof of concept of the efficiency of genome and phenome assisted selection. Ideotypes and reference varieties will be evaluated in innovative cropping systems, particularly organic farming and no-till agriculture, and an economic evaluation of these approaches will be conducted. The results will be disseminated to a broad user community, highlighting the benefits and issues associated with the adoption of what is considered sustainable and environmentally friendly wheat and barley crop production in a European context. WHEALBI aims to help the EU remain a major actor in world small grain cereal production while addressing the pressing global priorities of increasing and stabilising primary production, improving food quality and safety, and reducing environmental impact.
Impact So far two papers are accepted for publication involving our group, one in Nature Genetics, One in the Plant Journal
Start Year 2015
 
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 FACCE-JPI 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact • FACCE-JPI 1st Annual Meeting, Speaker, INRA, Paris, September
Year(s) Of Engagement Activity 2015
 
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 FoP day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Chiara Campoli participated in Fascination of Plants Day/Plant Power Day, Dundee Botanical Garden, 23 May 2015
Year(s) Of Engagement Activity 2015
 
Description Guest lecturer 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Course on "BREEDING SMALL GRAIN CEREAL CROPS IN A CLIMATE CHANGE SCENARIO" ,Zaragoza (Spain), 19-23 February 2018. Approx 30 scientists attended from International agencies, breeding companies and research organisations
Year(s) Of Engagement Activity 2018
 
Description Oranges and lemons 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Open day at the Oranges and Lemons technology park nursery, Dundee, 6th February 2016 representing the university doing DNA extractions
Year(s) Of Engagement Activity 2016
 
Description Poster 1 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Surface Waxes as a Driver of Barley Resilience to Climate Change (Chiara Campoli and Robbie Waugh)
At Plant Waxes 2015; 16-20 June 2015 Ascona, Switzerland
Year(s) Of Engagement Activity 2015
 
Description Poster 2 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Surface Waxes as a Driver of Barley Resilience to Climate Change (Chiara Campoli and Robbie Waugh)
At Plant Biology Europe/EPSO 2016; 26-30 June 2016, Prague, Czech Republic
Year(s) Of Engagement Activity 2016
 
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 Seminar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the PAG conference in San diego in January (given by Chiara Campoli - the PDRA on the CLIMBAR grant)
Year(s) Of Engagement Activity 2018
 
Description Talk 2 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Walking a Waxy Path: Molecular Characterisation of the Barley eceriferum-yy Mutant, Presentation at the Barley Away Days Meeting in Dunkeld 2015
Year(s) Of Engagement Activity 2015
 
Description Talk1 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Walking a Waxy Path: Molecular Characterisation of the Barley eceriferum-yy Mutant
At Barley Genetic Network 2016; 30 November - 1-2 December 2016, Zaragoza, Spain
Year(s) Of Engagement Activity 2016
 
Description Women in Science 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Chiara Campoli participated in Women in Science/Fun Day at the Botanics , 13 March 2016
Year(s) Of Engagement Activity 2016