IMPROMALT: Improving winter malting barley quality and developing an understanding of the interactions of introgressions with genetic background

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

Maltsters, brewers and distillers are concerned about the long-term sustainability of the barley crop. Seasonal problems in many parts of Europe resulted in a restricted malting barley supply that has only just been alleviated by an above average harvest in Argentina. Within the UK, drought conditions resulted in reduced barley crop quality, i.e. higher protein samples, particularly in Eastern England, where much English malting barley is sourced. Under predicted climate change scenarios, such drought conditions are likely to become more frequent and will affect the spring crop much more than the winter crop, which can escape the worst effects of summer drought through a much earlier maturity. Whilst winter barley might therefore provide a more consistent supply, the proportion bought by English maltsters has declined by over 25% over the past 20 years. This decline is due to the reduced quality level of the winter crop compared to the spring so that distillers can produce 16 more litres of raw spirit per tonne of malt on average from the latter. For an industry predicted to use 600,000t of barley from the 2012 harvest, this is a highly significant difference in production efficiency.

All current UK winter barley malting varieties have been derived from Maris Otter, first recommended in 1965. Maris Otter combined the spring malting quality attributes of an older variety, Proctor, with the winter habit of Pioneer. Proctor was the major spring malting variety in the UK for many years but the introduction of Triumph was a quantum leap forward for the spring crop in terms of both quality and yield. In a previous project, we have analysed DNA fingerprints of UK spring and winter barley malting cultivars to identify genetic differences between the two crops that are associated with malting quality. Whilst plant breeders have previously tried to introgress spring quality attributes into winter barley, they have relied on chance events to assemble the right genes, which is an impossible task when the crops differ at thousands of genes. But we now have the knowledge and tools to conduct the introgression of spring attributes into winter barley in a highly targeted manner to test the hypothesis that their introduction will improve winter malting quality. The germplasm emerging from this proposal will then be used by the plant breeding partners of the project in further rounds of crossing and selection to develop improved winter malting quality cultivars that approached the spring quality levels but in a suitable agronomic background for contemporary farming practise and would thus re-generate interest in using winter barley for malting for use in brewing and distilling. As indicated in the previous paragraph, greater use of the winter crop is likely to provide a more consistent supply of malting barley in the future. As malting supplies are becoming tighter due to a variety of market factors, a switch to the higher yielding winter crop would also mean that the effects of competition for land for more profitable crops would have a less pronounced effect upon malting barley supply. As six row barley varieties tend to have a higher yield than two row, a longer term aim is to develop six row malting types that would further decrease the land area required to secure a malting barley supply.

Technical Summary

We will augment existing genotypic and phenotypic information upon elite UK barley varieties to refine key malting quality QTL to more tightly defined intervals. We will then utilise the resources of the UK barley breeding industry to conduct a targeted introgression programme to develop pre-competitive germplasm that combines the top malting attributes of spring barley varieties into winter varieties to improve the sustainability of UK malting barley in the threats of climate change and land competition through the earlier maturity and greater yield of the winter crop. We will utilise the genetic resources developed in this proposal to fine map the QTL and generate a candidate gene list that we will then explore through phenotypic, expression and sequence analyses to identify the likely causal polymorphism in the main candidate for a target. In the process, we will develop QTL near-isogenic pairs, the most tightly defined of which we will use in a time-course experiment to sample the transcriptome at daily stages following imbibition in the malting process.. We will combine RNA-Seq analysis with alignment against the genomic and transcript assemblies being developed for barley, taking account of information being developed under the recently funded barley genome sequencing project (BB/I00663X/1), to align regions of SNP diversity against the genome to identify the gene. The project will not only provide germplasm that will ultimately help sustain the production of a product that contributes over £2.4 billion annually to the exchequer and accounts for 23% of all UK exports in the Food and Drink sector but also provide knowledge and resources to derive a fuller understanding of the action and interaction of genes to provide good malting quality.

Planned Impact

The major beneficiaries of this research will be:
The plant breeding community. Initially this will be restricted to the Consortium members, who will be able to access the germplasm and markers to gain a competitive edge in developing new varieties that will increase their royalty earning potential. This will spread to other plant breeders worldwide through either the use of the improved winter varieties in their own crossing programmes and/or the eventual public release of the markers and protocols for selecting improved varieties.
The farming community. Increased usage on winter malting barley would extend the market opportunities for growers and enable them also to spread their harvest load with an earlier maturing crop. Under predicted climate change scenarios, the drought escape mechanism provided by the early maturity of winter barley means that the crop is less susceptible to large fluctuations in grain protein content so that farmers will be more likely to secure a planned-for malting premium.
Maltsters, brewers and distillers. This end user sector will benefit as the development of improved winter barley cultivars means that it has a wider pool of material to select from and, within limits, can effectively switch from one crop type to the other to take account of seasonal variations differentially affecting the overall quality of one, such as the Eastern region barley crop of 2011. Currently, all winter barley malting varieties produce epiheterodendrin and are thus unsuitable for the distilling market. The introgression of the epiheterodendrin null character into the winter barley crop means that the crop can then be considered for use in the distilling industry, opening further market opportunities for Scottish farmers as well as improving the long term sustainability of the industry.
Society. The distilling sector alone contributes over £2.5 billion to the exchequer annually and so contributes strongly to the overall benefit of UK society. In addition, te industry employs around 10,000 directly and 40-50,000 indirectly. The brewing industry contributes over £3 billion to the exchequer annually and accounts for approximately 600,000 direct and indirect employment so the sustainability of the malting, brewing and distilling sector contributes massively to the UK economy.

Publications

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Jones H (2015) Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Scutari M (2013) Improving the efficiency of genomic selection. in Statistical applications in genetics and molecular biology

 
Description It is possible to predict the yield of new entries within the UK National List for spring and winter barley from genetic marker data which has been trained against yield data in the previous five years of national and recommended list trials. In addition, I found that prediction is uneven across years; for c. 20% of years, prediction accuracy is not signfiicantly different from zero. These failures of prediction are also highly associated with years where direct phenotypic prediction of yield from previous years also fails. The cause appears to be climate variability: all these years exhibited at least one extreme climate variable (e.g. temperature, rainfall) at a sensitive time for the plants growth. As a result, the relative performance of varieties was very different in these years.
Exploitation Route It may prove possible to redesign the national and recommended list processes for barley to save money, to save time and to increase accuracy of assessment.
The results may encourage more incoporation of climate data into genomic prediction algorithms, and possibly different ways of presenting prediction data (with variable predictions based on different environmental scenarios)
Sectors Agriculture, Food and Drink

 
Description Simulations have been used to confirm that the breeding strategy adopted by my collaborators and the James Hutton and among European barley breeders is efficient. Simulations were used to compare the power of proposed phenotyping experiments to detect the effect of multiple introgressions from the backcrossing programmes
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Workshop on implementation of genomic selection in the CGIAR breeding programmes
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Title DiPR: Differentially Penalized Regression 
Description A simple method of independently weighting two or more sets of variables in ridge regression, while using standard ridge regression software. Useful in genomic prediction models with separate classes of genetic markers, and for incorporating different sets of predictors eg plant metabolites and genetic markers. 
Type Of Material Data analysis technique 
Year Produced 2015 
Provided To Others? Yes  
Impact Is being tested in various genomic selection projects. 
URL http://bmcgenet.biomedcentral.com/articles/10.1186/s12863-015-0169-0
 
Title Diferentially Penalized Regression (DiPR) 
Description A simple method of using existing software for ridge regression to independently penalized two sets of predictors. THis is never less accurate than using either set alone or both sets pooled and treated as one. Applications are predicting traits from a combination of genetic markers and metabolites or predicting hybrid performance from co-dominant markers, fitting separate additive an dominance effects at each. Can be used in genomic selection and association mapping. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact Prediction of wheat yields and other agronomic traits from seed metabolites and genetic markers. Combining known markers for QTL with background markers in genomic selection / prediction in an optimal manner. Used in two publications: Ward J, Rakszegi M, Bedo S, Shewry PR, Mackay I (2015) Differentially penalized regression to predict agronomic traits from metabolites and markers. BMC Genetics 16:19 Bentley AR, Scutari M, Gosman N, Faure S, Bedford F, Howell P, Cockram J, Rose GA, Barber T, Irigoyen J, Horsnell R, Pumfrey C, Winnie E, Schacht J, Beauchêne K, Praud S, Greenland A, Balding D, Mackay I J (2014) Applying association mapping and genomic selection to the dissection of key traits in elite European wheat. Theoretical and Applied Genetics, 127:2619-2633 
URL http://www.niab.com/pages/id/326/Resources
 
Description Camb. Plant Sci epidemiology groups 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact A seminar to the two epidemiology groups in the University of Cambridge Plant Sciences Department. To introduce to the methods and approaches of trait mapping and genomic selection in crops, highlighting some overlaps with epidemiological methodology.
Year(s) Of Engagement Activity 2016
 
Description JHI offsite meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Gave talk to James Hutton Institute scientific staff at their annual off-site workshop in Dunkeld on genomic selection and how it can be implemented in small breeding programmes.
Year(s) Of Engagement Activity 2016
 
Description Landmark artucle on GS 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I wrote an article on genomic selection "Genomic selection and the quantitative geneticists' revenge" for the NIAB members quarterly journal: LandMark Bulletin. This described the potential of genomic selection in plant breeding in lay terms.
Year(s) Of Engagement Activity 2016
 
Description QMPB 
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 NIAB run a two week intensive course in Quantitative Methods for Plant Breeding, covering relevant aspects of statistics, quantitative genuetics and population genetics. There are 25 participants every year. To date, no-one has said they would not recommend the course to others. The course has also been put on in Australia, France, India (once at ICRISAT and once at the Punjab Agricultural University) and Malaysia. We update it every year to disseminate developments and methods resulting from out own research work in MAGIC, genomic selection, association mapping and plant breeding strategy. It has resulted in a global set of new contacts, some of which have resulted in successful collaborations.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012,2013,2014,2015,2016
URL http://www.niab.com/pages/id/360/quantitative_methods_in_plant_breeding
 
Description Talk at Plant and Animal Genome International Conference in San Diego, 12 January 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk in Climate Change Section of Plant and Animal genome Conference, tha major annual Academic Forum for Agircultural Genetics Research.Discussion of my findings at teh conference opened up possibiities of future collaborations on incoporating environmental variables into genomic prediction analyses.
Year(s) Of Engagement Activity 2019
URL https://www.intlpag.org/2019/
 
Description Talk to NIAB Genetics and Breeding group 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Internal talk at NIAB to members of Genetics and Breding group
Year(s) Of Engagement Activity 2019