Causes and control of grain skinning in malting barley: Phenotyping and genetic analysis

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

Abstract

The quality of malting barley is of paramount importance, for reasons of food safety, product quality and the competitiveness of the UK cereals industry. Barley grains have an outer coat called a husk. Loss of the husk during harvest or post-harvest is called grain skinning. This undesirable condition has very serious consequences for farming and food sectors that depend on UK malting barley. Primarily, grain skinning is a serious problem in the malting process. However, its financial implications extend across the whole supply chain. Breeders invest about £2M in bringing a new barley variety to market, this spend is wasted if farmers and the malting industry no longer approve its use. Even low levels of skinning mean than loss of barley quality or malt production amounts to several £ million.

If in a batch of barley there are grains without husks, the malting process becomes very uneven as these grains will take up water and begin to grow (germinate) more rapidly than grains with firmly adhering husks. Sometimes, grains without husks sustain damage that prevents them from starting to grow (germination). This can give rise to mould growth. In grains with a loosely adhering husk, germination during malting tends to be more vigorous than in grains with a tightly adhering husk. This leads to handling problems and to greater malting losses. In brewing, the husk plays a vital role in filtration of the liquid that is produced from mixing the malted barley with hot water in the brewing vessel. Malting barley is, therefore, rejected by maltsters if it contains an undue proportion of skinned grains, with either no husk or an incomplete husk.

Weather conditions such as wet and dry spells during summer months appear to have a strong influence on skinning. However, so does the genetic make-up of different plant types (varieties). This means that an understanding of how a plant's genetic make-up influences grain skinning will increase the likelihood of breeding new barley vieties without this undesirable condition. Differential growth the husk and the underlying grain, or poor quality of the "glue" that bonds them together are likely causes of skinning.

Crop breeding supported by high quality science will help to solve this problem, as it will underpin the development of new barley varieties, with improved husk adhesion properties, and thus provide more reliable grain and processing quality for the UK cereals supply chain. Identification of plant screening and genetic tests will enable susceptible barley varieties to be eliminated before they are recommended for use by farmers and the malting industry. This will provide greater security for the UK barley supply chain and a more efficient development pipeline for the plant breeding of new varieties. An added benefit to farming is the promotion of more efficient use of inputs, as these will not be wasted on poor quality or rejected crops.

The aim of this project is to understand how differences in grain development, and their genetic controls, give rise to skinning. The outcome is for new varieties to be bred without this undesirable condition. The key areas towards application of this research are: (1) Understanding how weaknesses in husk and grain growth cause skinning; (2) Establish procedures to screen-out weak varieties, based on their grain characteristics (phenotyping), that give rise to skinning; (3) Identify the location of genes that influence or determine skinning; this means relating genetic locations to grain characteristics which lead to resistant and susceptible varieties; (4) Work towards the development of genetic (molecular) markers to identify 'good' and 'poor' varieties and thus eliminate weak varieties from being grown on farm and (5) The uptake of plant screening and genetic tests by crop breeders.

Technical Summary

Skinning, or poor husk adhesion, is a failure of cuticular material from the outer grain layer (pericarp) to adhere to the inner epidermis of the husk (palea or lemma). The causal hypothesis is differential tissue development; especially variation in the amount and/or quality of wax-lipid deposited on these surfaces from early grain development, and involve synthesis of cuticular material. Other traits e.g. husk thickness will also be measured.

Up to 300 spring barley genotypes will be phenotyped for differential expression of skinning. Barley germplasm and genotypic data in the 'Association Genetics of Elite UK Barley' project allows a genome wide association genetic analysis to detect QTL for skinning. This will identify a sub-set of susceptible/resistant varieties for structural analysis of grain development using LM and TEM.

Grains from the sub-set will be sampled post-anthesis for RNA extraction and transcriptomic analyses, using a newly developed high-density barley microarray based on the Agilent platform. This represents 50,000 gene models from the current barley genome assembly. Additional novel sequences from extensive in-house 2GS transcriptome resources may also be considered.

Transcriptional differences should be expressed as differences in either type and/or amount of wax being deposited between the pericarp and husk. These tissues will be sampled to extract wax for characterisation. Transcriptomic data will be combined with biochemical and structural data to identify genes that are up/down regulated and associated with wax differences. Those that co-locate with QTL detected in the association analysis will be re-sequenced to detect possible causal polymorphisms.

Validation will be conducted in an independent pool of genotypes, including some known to be susceptible or resistant to skinning. These lines will be phenotyped and genotyped to ascertain whether or not individual SNP polymorphisms are associated with phenotypic differences.

Planned Impact

Skinning is a grain spoilage condition of much concern to the UK malting barley supply chain. It can result in widespread loss of the UK malting barley crop, which then becomes suitable only for animal feed. Grain skinning causes significant handling and processing problems for maltsters, brewers and distillers, resulting in lengthy delays and large financial costs. Malt produced from skinned grain is of inferior quality and value. Skinning also reduces malt yield per tonne of grain. A modest 1% loss of malt yield across the malting sector would cost £4M to maltsters alone.

Maltsters assess skinning at intake. In some seasons, it is present in more than 20% of samples, resulting in a significant number of rejections. Even a low national rejection rate of 10,000t per annum (or 0.5% of the UK maltsters average intake) represents a net loss to the industry of about £1.8M. Breeders have made good progress in improving grain quality, but skinning remains a concern. Breeders will invest to £2M in bringing a new variety to market. A malting barley variety encountering a skinning problem will rapidly lose market share, resulting in failure to re-coup the breeders' investment.

Outcomes for supply-chain beneficiaries will be:
1) The UK malting industry, brewers and distillers will make significant savings in handling and processing costs by using a more reliable supply of quality grain.
2) Farmers will be able to grow more robust varieties, ensuring that skinning does not affect their malting premium of £30-£50 per tonne of grain. Without this research, farmers may need to accept losses of £1200 to £2000 for each typical 40t load, together with the associated transport costs.
3) Breeding of a new barley variety takes 8-10 years with an annual investment in excess of £200k to commercialise. Therefore, it is important for breeders to be able to meet future market specifications. Failure of a variety at the large-scale multiplication stage means a loss of up to &D investment. This research presents breeders with the best opportunity to eliminate risk that skinning poses to their businesses, and the supply chain.
4) Policy-makers will be reassured with good progress in reducing a serious grain spoilage condition, with improved supply protection. Key policy stakeholders are: Defra, RESAS, Fera, SASA, NFU/NFUS and industry bodies: MAGB, HGCA and BSPB.
5) The general public can be reassured that the public funding, with stakeholder backing through CIRC, is being well spent on protecting UK industry.
6) Other crop/cereal sectors will benefit from adopting the innovative research methods and strong implementation strategy employed in this project. The PI's have a strong track record in science and knowledge transfer, especially to the cereals industry.

After consultation with the CIRC Steering Group, SAC and JHI will implement knowledge exchange with the beneficiaries listed above (see Pathways to Impact). Our strong links to the supply chain gives us confidence to deliver the outputs for wealth creation across all sectors. We will utilise our existing links with barley breeders, and testing authorities, to transfer our findings so that selection for lines resistant to skinning can be conducted early in the breeding cycle, and at the official testing stage. Specific and measured outputs on the route to commercial outcomes will be:
1) New grain skinning protocols presented to industry in Year 1.
2) Opportunities for the malting industry to evaluate grain types with their own barley and micro-malting tests, end of Year 2.
3) Phenotyping and genotyping methods presented to breeders, Years 2 or 3.
4) Delivery of micro-array and QTL studies to inform breeders' own selections, Year 3.
5) Validation of phenotypes and genotypes with breeders own material , Year 3.
6) Industry-wide dissemination of a full package of target traits, in-field and glasshouse screening tests and potential diagnostic markers, Year 4.

Publications

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Thomas WTB (2019) Barley Methods & Protocols

 
Description The JHI component of this work has been to integrate the phenotyping carried out by SRUC with genotypic data, and to generate transcriptome and wax composition analysis from selected barley lines grown under controlled environments. Genomic regions affecting different measures of grain skinning have been identified and our findings have been updated to include some alternative measures together with a new integrated barley genetic map. Regions where 3 or more measures of grain skinning were co-located were detected on barley chromosomes 1H, 2H (2 separate regions), 6H, and 7H. Only one of the significant effects was consistent across all four environments in which skinning was measured. Thirty of the remaining 33 effects were only significant in one or two of the four environments but were consistent when significant in more than one. The other three significant associations were inconsistent in that a copy of a gene inherited from one parent significantly increased a measure of skinning in one environment but significantly reduced it in another. We chose a panel of 5 lines that had a high level of skinning and another panel of 5 that had a low level and assayed the relative expression levels of a known set of 60,000 gene probes under conditions to promote skinning and a control environment. The same set of lines has also been analysed for wax composition as wax has been implicated in the adherence of the husk to the grain so known genes in the wax biosynthetic pathway could affect grain skinning. Combining all three data sets has provided a set of candidate genes that can be used to develop a list of DNA markers to select for reduced levels of skinning in the future and we hope to validate these findings before the end of the project.
Exploitation Route The markers that we develop will be used by breeders and testing authorities to select varieties that have significantly improved resistance to skinning for the benefit of the malting, brewing and distilling industry.
Sectors Agriculture, Food and Drink

URL http://www.barleyhub.org/projects/circ-skinning/
 
Description See report by PI from lead organisation
 
Description Barley Breeding whats hot and whats not 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Survey of international researchers to identify future barley R&D priorities
Year(s) Of Engagement Activity 2019
 
Description Barley Information Portal 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Barley Information Portal (www.barleyhub.org) and associated facebook page has been developed to promote barley and UK barley research to the wider world. There are specific pages for defined research projects but also some general information pages that ultimately will provide a 'one-stop shop' for people trying to find useful facts about barley, including information gathered during the course of various research projects.
Year(s) Of Engagement Activity 2015,2016
URL http://www.barleyhub.org
 
Description CIRC Dissemination Events 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation of BBSRC Crop Improvement Research Club Projects to club members for comment and feedback
Year(s) Of Engagement Activity 2012,2013,2015
 
Description Cereals 2018 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Manned a stand at Cereals to present JHI barley related research work and the International Barley Hub to a wide audience
Year(s) Of Engagement Activity 2018
 
Description Defra Research Advisory Group, Rothamsted 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Meeting to integrate the Defra Genetic Improvement Networks and integrate with other crop research
Year(s) Of Engagement Activity 2018
 
Description Diageo vist 
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 Industry/Business
Results and Impact Talk about potential exchanges of staff between IBH and Diageo
Year(s) Of Engagement Activity 2018
 
Description IBH & APGC Project Board Meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Develop business case for IBH and APGC
Year(s) Of Engagement Activity 2019
 
Description IBH Advisory Group meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Reviewing ongoing research activity under IBH soft-start and making future plans
Year(s) Of Engagement Activity 2018
 
Description IBH Industry Advisory Group Meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Review research from IBH soft-start and identify future priorities
Year(s) Of Engagement Activity 2018
 
Description IBH Industry Strategy Groupo meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Discuss research strategy for IBH and how to develop it
Year(s) Of Engagement Activity 2019
 
Description IBH Research & Innovation meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Discussion of ongoing research from IBH soft-start
Year(s) Of Engagement Activity 2018
 
Description Institute of Brwing & Distilling Scottish section visit 
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 Industry/Business
Results and Impact Present barley research and IBH to an industrial group
Year(s) Of Engagement Activity 2018
 
Description Lecture to Nottingham MSc in Brewing course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Invited lecture on barley genetics and breeding
Year(s) Of Engagement Activity 2018
 
Description Lectures to Nottingham Raw Materials in Brewing MSc course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation of barley and its importance to the UK malting, brewing and distilling industries to postgraduate students
Year(s) Of Engagement Activity 2019
 
Description MAGB Technical Symposium 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation to staff of MAGB member companies learning about raw materials
Year(s) Of Engagement Activity 2017
 
Description Meeting with Secobra UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Meeting with Secobra UK plant breeding to discuss potential collaborative R&D projects
Year(s) Of Engagement Activity 2018
 
Description Presentation at MAGB lunch 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Lecture on barley and IBH to a group of maltsters
Year(s) Of Engagement Activity 2018
 
Description Presentation to AB InBev 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Discussions with AB InBev about barley research relating to malting quality and possible research areas for future collaboration
Year(s) Of Engagement Activity 2016
 
Description Scottish Enterprise IBH and APGC Business Case discussions 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Review IBH business plan and identify way forward
Year(s) Of Engagement Activity 2019
 
Description Secobra Open Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation of a new breeding programme
Year(s) Of Engagement Activity 2018
 
Description Talk at Scottish Agronomy Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Invited talk on barley genetics and breeding
Year(s) Of Engagement Activity 2017