Mechanisms underlying variation in barley hull adhesion
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
This research explores a central but little studied problem in plant biology - how do plant surfaces influence plant architecture? We know that the protective cuticle covering the plant body, beyond preventing water loss and pathogen invasion, also ensures that closely growing plant organs remain separate and plays important roles in organ absicssion. However, less is known about the biology underlying plant interfaces that fuse, such as in tubular flowers, or organs that stick together as in the barley grain. In the latter, a species-specific pathway leads to secretion of a special cementing layer onto the outer pericarp cuticle. Loss of this layer, caused by mutations in a single master regulatory factor, NUDUM (NUD), occurred once during barley cultivation, leading to a complete loss of hull adherence or 'naked' grain, ideal for human consumption. However, most barley grown in the UK is used for animal feed and malt where 'covered' grain, retaining the adherent hull, is preferred as hulls protect the germ and aid in filtration after malting. Thus, the changing relationship of the hull to the grain is a critical quality that largely determines barleys downstream uses. Despite this, we understand practically nothing about the steps between NUD expression and the extrusion of the cementing material on the pericarp or the chemistry explaining the adherent properties of the layer.
Genetic variation in newer elite barley malting cultivars is linked to an increasing incidence of a highly undesirable, intermediate phenotype whereby grain partially sheds its hull during harvest or processing, a phenomenon called 'skinning'. However, identifying the causal variation underlying skinning has proved very difficult, due to its environmental sensitivity and lack of robust screening methods, so to date breeders do not have genetic markers to help control this trait. In addition to addressing these important agronomic concerns, we are interested in identifying the genes and genetic mechanisms underlying skinning since these alleles may represent defective steps along unresolved NUD-driven pathway(s). Moreover, by characterising the molecular and chemical changes occuring in skinning, we may reveal the critical features of the cementing layer and/or other grain characters which influence hull adhesion that are lost in skinning mutants.
To circumvent issues of studying the cultivated germplasm for quantitative skinning variation, we have assembled a panel of mutants with stable skinning phenotypes. We screened a wax-deficient collection of mutants in a single near-isogenic background and identified a small subset that show defective hull adhesion. This foundation work provides a robust and genetically powerful platform to dissect the molecular, chemical and genetic mechanisms that explain variation in hull adhesion.
Our panel suggests that specific components of the surface lipid regulatory pathway may be defective in grain that skins. In this proposal, we seek to define the chemical and ultrastructural surfaces changes associated with hull adhesion and how they are altered by skinning loci. We will also reveal related changes in gene expression, both globally and on a tissue-specific level, that promote hull adherence and assess their importance to the skinning phenotype. Furthermore, we will identify individual genes that control skinning and evaluate diversity at these loci in cultivated germplasm, a critical milestone which will resolve which allelic variants track with incidence of skinning and allow us to develop markers for use in breeding. Taken together, our work will reveal the chemical and genetic components that cause partial loss of adherent hulls in barley, closing a vast knowledge gap about a critical grain quality trait, and delivering routes to improved germplasm selection
Genetic variation in newer elite barley malting cultivars is linked to an increasing incidence of a highly undesirable, intermediate phenotype whereby grain partially sheds its hull during harvest or processing, a phenomenon called 'skinning'. However, identifying the causal variation underlying skinning has proved very difficult, due to its environmental sensitivity and lack of robust screening methods, so to date breeders do not have genetic markers to help control this trait. In addition to addressing these important agronomic concerns, we are interested in identifying the genes and genetic mechanisms underlying skinning since these alleles may represent defective steps along unresolved NUD-driven pathway(s). Moreover, by characterising the molecular and chemical changes occuring in skinning, we may reveal the critical features of the cementing layer and/or other grain characters which influence hull adhesion that are lost in skinning mutants.
To circumvent issues of studying the cultivated germplasm for quantitative skinning variation, we have assembled a panel of mutants with stable skinning phenotypes. We screened a wax-deficient collection of mutants in a single near-isogenic background and identified a small subset that show defective hull adhesion. This foundation work provides a robust and genetically powerful platform to dissect the molecular, chemical and genetic mechanisms that explain variation in hull adhesion.
Our panel suggests that specific components of the surface lipid regulatory pathway may be defective in grain that skins. In this proposal, we seek to define the chemical and ultrastructural surfaces changes associated with hull adhesion and how they are altered by skinning loci. We will also reveal related changes in gene expression, both globally and on a tissue-specific level, that promote hull adherence and assess their importance to the skinning phenotype. Furthermore, we will identify individual genes that control skinning and evaluate diversity at these loci in cultivated germplasm, a critical milestone which will resolve which allelic variants track with incidence of skinning and allow us to develop markers for use in breeding. Taken together, our work will reveal the chemical and genetic components that cause partial loss of adherent hulls in barley, closing a vast knowledge gap about a critical grain quality trait, and delivering routes to improved germplasm selection
Technical Summary
This project aims to discover the genetic and molecular processes that contribute to the distinctive adherent hull of barley grain. This research not only addresses fundamental questions about adhesion between plant surfaces, but is also relevant to a critical, unfavourable feature of many elite barley malting cultivars which have a genetic defect known as 'skinning' (partial hull shed) which can result in otherwise premium grain being downgraded to feed. Mutations in a single master factor called NUD result in failure to secrete the so-called cementing layer that normally sticks the hull tightly to the developing seed. One possibility is that NUD coordinates expression of genes responsible for the cementing layer and that skinning is the manifestation of defective alleles of these genes. Due to its intermediate, quantitative nature and acute environmental sensitivity, resolving the genetic basis of natural variation in skinning is difficult. We have identified a series of barley mutants in a near-isogenic background that exhibit partial skinning phenotypes. Although the mutated genes are unknown, our skinning mutants are classified as wax-deficient, consistent with our hypothesis that these mutated genes are defective variants of the genes involved in making the cementing layer. They are thus powerful tools for unravelling the complex and commercially important processes that underpin the skinning phenotype. We propose to use these mutants to investigate the structural, chemical and developmental properties that contribute to hull adhesion. We will: define the critical developmental stages, morphologies and cuticular wax chemistries associated with hull adherence; explore the temporal and spatial transcriptional programme associated with adhesion and adhesion defects; identify the mutated genes in the partial skinning near-isogenic lines, explore their contribution to skinning in modern barley cultivars, and develop diagnostics for use in breeding.
Planned Impact
This proposal will reveal the mechanisms that control hull adhesion in barley, a feature strongly relevant to the barley breeding, farming and processing industries, especially those on the premium end of the market (malting). A critical issue with many recently released cultivars is that the grain "skins" during harvest. Skinning occurs when the hull fails to adhere tightly to the grain, partially sheds and causes variability in malting and poor downstream processing performance. It can lead to grain lots being rejected at intake to the malthouse. Despite its importance, the mechansisms underlying variation in hull adherence are understudied with the causal genes remaining unknown. This partly reflects subjective phenotyping methods combined with a large environmental effects generating sizable phenotypic plasticity. Our proposed research programme will quantitatively, chemically and structurally characterise both normal and defective hull adhesion and identify its genetic causes, addressing a major problem for industry while providing fundamental insight into the mechanisms of organ adhesion in plants.
As illustrated clearly in the letters of support, our research is relevant to:
i) Breeders. Breeders currently have no way to select for skinning resistant varieties in their breeding program. Defining the contributions made by different alleles of genes that control skinning would enable development of diagnostic molecular markers that can be routinely deployed to control this trait during breeding.
ii) Growers. Losing the premium payment for malting barley (grain for animal feed is worth less) is a serious financial disincentive to growers which can make growing barley uneconomical. However, the level of skinning is hard to predict because of the environmental influence. We will produce practical outputs that allow the development of varieties that do not skin.
iii) Maltsters. Maltsters reject grain lots that suffer excessive skinning and need to find alternative grain sources, causing a financial knock-on all along the supply chain. In addition to breeding tools, our plans to develop a quantitative screening tool - using a barley pearler - could remove subjectivity for maltsters.
iv) Brewers and Distillers. Years when skinning is widespread and prevalent can lead to lack of local supply of high quality malting barley and subsequent increased costs.
v) Public. Pathways to Impact Projects will contribute to better understanding of plant biology and engage with the wider research community. This research has the potential to inform the public about the genetic control of agronomic traits and, in PtI Project 2, its importance for enlightened breeding strategies.
vi) RCo-I Campoli will benefit by continuing her career in cereal genetics and gaining skills in cutting edge biochemical, genetic and bioinformatics analyses. A newly started PhD student and honours students will also benefit from training over the course of the project. Dr. McKim (PI) will ensure that all staff and students develop transferrable skills, such as scientific writing and presenting.
vii) UK economy. Processed barley products contribute more than any other crop to the UK food and drink sector, with the premium 30% of the national barley crop ultimately contributing close to 20 billion pounds annually to the UK economy through beer and whisky. Non-skinning barley varieties will safeguard this important national industry.
We will ensure that developers, growers and users of premium quality barley benefit from the proposed research through the extended reach of the IBH. IBH has cultivated strong links with the international breeding community and has enhanced links to the farming, food and drink sectors. The PI's are well known within the academic sector and have a strong reputation and identity within the global community. Together, we have the relevant expertise, track-record and motivation to ensure the project deliverables are achieved.
As illustrated clearly in the letters of support, our research is relevant to:
i) Breeders. Breeders currently have no way to select for skinning resistant varieties in their breeding program. Defining the contributions made by different alleles of genes that control skinning would enable development of diagnostic molecular markers that can be routinely deployed to control this trait during breeding.
ii) Growers. Losing the premium payment for malting barley (grain for animal feed is worth less) is a serious financial disincentive to growers which can make growing barley uneconomical. However, the level of skinning is hard to predict because of the environmental influence. We will produce practical outputs that allow the development of varieties that do not skin.
iii) Maltsters. Maltsters reject grain lots that suffer excessive skinning and need to find alternative grain sources, causing a financial knock-on all along the supply chain. In addition to breeding tools, our plans to develop a quantitative screening tool - using a barley pearler - could remove subjectivity for maltsters.
iv) Brewers and Distillers. Years when skinning is widespread and prevalent can lead to lack of local supply of high quality malting barley and subsequent increased costs.
v) Public. Pathways to Impact Projects will contribute to better understanding of plant biology and engage with the wider research community. This research has the potential to inform the public about the genetic control of agronomic traits and, in PtI Project 2, its importance for enlightened breeding strategies.
vi) RCo-I Campoli will benefit by continuing her career in cereal genetics and gaining skills in cutting edge biochemical, genetic and bioinformatics analyses. A newly started PhD student and honours students will also benefit from training over the course of the project. Dr. McKim (PI) will ensure that all staff and students develop transferrable skills, such as scientific writing and presenting.
vii) UK economy. Processed barley products contribute more than any other crop to the UK food and drink sector, with the premium 30% of the national barley crop ultimately contributing close to 20 billion pounds annually to the UK economy through beer and whisky. Non-skinning barley varieties will safeguard this important national industry.
We will ensure that developers, growers and users of premium quality barley benefit from the proposed research through the extended reach of the IBH. IBH has cultivated strong links with the international breeding community and has enhanced links to the farming, food and drink sectors. The PI's are well known within the academic sector and have a strong reputation and identity within the global community. Together, we have the relevant expertise, track-record and motivation to ensure the project deliverables are achieved.
Publications
Campoli C
(2024)
A GDSL-motif Esterase/Lipase Affects Wax and Cutin Deposition and Controls Hull-Caryopsis Attachment in Barley
in Plant And Cell Physiology
Dixon L
(2018)
Annual Plant Reviews online
Liu L
(2022)
Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley.
in Nature communications
McAllister T
(2022)
A WAX INDUCER1/SHINE transcription factor controls cuticular wax in barley
McKim S
(2018)
The Barley Genome
McKim SM
(2020)
Moving on up - controlling internode growth.
in The New phytologist
Description | We have discovered more about why some barley grain is prone to shed or skin their husk or hull. In particular we have identified variation within five genes which is associated with this trait. Our findings suggest that transcriptional networks and phosphorylation cascades are critical for grain to hull adhesion in barley. We have also discovered links between the differentiation of the grain surface and the strength of hull attachment. More broadly, we discovered that several interacting genes controlling hull attachment also control the arrangement and identity of special epidermal cells on the surfaces of leaves and stems which are important for gas exchange and defense. |
Exploitation Route | We hope to learn how to prevent hull shedding in cultivated barley by learning more about the underlying molecular and genetic causes. |
Sectors | Agriculture Food and Drink |
Description | Our findings are being used to engage with industry for possible assays for grain quality with first experiments underway. |
First Year Of Impact | 2023 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | Australia Partnering Award: International pooling for advanced cereal science - IPAC |
Amount | £47,766 (GBP) |
Funding ID | BB/V018299/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2022 |
End | 03/2025 |
Description | Carnegie Trust PhD studentship |
Amount | £75,000 (GBP) |
Organisation | Carnegie Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2018 |
End | 09/2022 |
Description | China Scholarship Council PhD studentship |
Amount | £72,000 (GBP) |
Organisation | Government of China |
Sector | Public |
Country | China |
Start | 09/2018 |
End | 09/2022 |
Description | Facing Forwards - Understanding epidermal development in cereals |
Amount | £1,164,671 (GBP) |
Funding ID | BB/Y001850/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2024 |
End | 12/2026 |
Description | The Generation Gap - Mechanisms of maternal control on grain |
Amount | £588,538 (GBP) |
Funding ID | BB/W003074/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2022 |
End | 09/2025 |
Description | UKRI-BBSRC East of Scotland Doctoral Training Partnership 3 |
Amount | £17,009,440 (GBP) |
Funding ID | BB/T00875X/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2020 |
End | 09/2028 |
Title | Cutin assay for barley grain samples |
Description | We modified other techniques to measure cutin levels in barley grain |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | No |
Impact | We plan to publish this method in papers planned for submission in 2023/2024 |
Title | Quantitative Grain Skinning Assay |
Description | We developed and calibrated a hull detachment (grain skinning) assay using a mechanical grain debranner. |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | We are in discussions with industry to test this assay on commercial grain samples |
Title | RNA-Seq and exome capture data sets deposited into the European Nucleotide Archive (ENA), http://www.ebi.ac.uk/ena, under this project accession number PRJEB53837 |
Description | Project: PRJEB53837 Faced with terrestrial threats, land plants seal their aerial surfaces with a lipid-rich cuticle. To breathe, plants interrupt their cuticles with adjustable pores, called stomata, that regulate gas exchange, and develop other specialised epidermal cells such as defensive hairs. Mechanisms coordinating epidermal features remain poorly understood. Addressing this, we studied two loci whose allelic variation causes both cuticular wax-deficiency and misarranged stomata in barley, identifying the underlying genes, Cer-g/ HvYDA1, encoding a YODA-like (YDA) MAPKKK, and Cer-s/ HvBRX-Solo, encoding a single BREVIS-RADIX-Like (BRX) domain protein. Both genes control cuticular integrity, the spacing and identity of epidermal cells, and barley's distinctive epicuticular wax blooms, as well as stomatal patterning in elevated CO2 conditions. Genetic analyses reveal epistatic and modifying relationships between HvYDA1 and HvBRX-Solo inferring that their products participate in interacting pathway(s) linking epidermal patterning with cuticular properties in barley. This may represent a mechanism for coordinating multiple adaptive features of land plant epidermises in a cultivated cereal. The data involved in this study includes Illumina sequence from exome capture, RNA-Seq and whole genome shotgun sequencing (WGS). |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | Enabled us to conduct analyses published in Liu et al (2022) |
URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB53837 |
Description | Collaboration with Alastair Hetherington, University of Bristol |
Organisation | University of Bristol |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We pooled data together to write a manuscript recently submitted to Nature Communictions |
Collaborator Contribution | We pooled data together to write a manuscript recently submitted to Nature Communictions |
Impact | Manuscripts in review and in preparation. |
Start Year | 2020 |
Description | Collaboration with James Cockram at National Institutes of Agricultural Botany |
Organisation | National Institute of Agronomy and Botany (NIAB) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Our collaboration involved information sharing and invitations to participate in a grant application to the BBSRC which was successful (BB/Y001850/1) |
Collaborator Contribution | Our partners shared information and contributed to the BB/Y001850/1 grant application to the BBSRC (successful) |
Impact | BB/Y001850/1 - BBSRC Standard Response Mode, lead PI: Facing Forwards - "Understanding epidermal development in cereals" £1,164,671 |
Start Year | 2023 |
Description | Collaboration with Prof Madelaine Bartlett at the University of Massachusetts |
Organisation | University of Massachusetts Amherst |
Country | United States |
Sector | Academic/University |
PI Contribution | Sharing new, unpublished data to help inform a new collaborative research project |
Collaborator Contribution | Prof Bartlett has shared new data and experimental insight from her own research |
Impact | We have developed a project together which will run over several years. |
Start Year | 2023 |
Description | Collaboration with Prof Michael Raissig at University of Bern |
Organisation | University of Bern |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | Prof Raissig and his team are sharing unpublished datasets to help us achieve our BBSRC funded research grants. |
Collaborator Contribution | We are also sharing research advances with Prof Raissig to help inform his research |
Impact | We are working with provided datasets to inform current work in a new grant |
Start Year | 2023 |
Description | Collaboration with Tracy Lawson at University of Essex |
Organisation | University of Essex |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Collaboration with Tracy Lawson at University of Essex to explore the interaction between epidermal patterning and functional leaf traits in barley |
Collaborator Contribution | Assays for leaf functional traits |
Impact | We submitted a joint grant in January 2023 round. |
Start Year | 2022 |
Description | Barley - More than just a crop? |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Online discussion panel as part of the Royal Society of Edinburgh Curious Science Festival 2023. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.rse-curious.com/barley-more-than-just-a-crop/ |
Description | Gordon Conference on Plant Lipids |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I was invited to a high-profile Gordon Conference on Plant Lipids to speak our work funded by this grant. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited Speaker Monogram 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | I gave a Keynote Talk in the Plant Development Session at the Monogram Meeting in 2022. My talk gave rise to new collaborative grant applications. |
Year(s) Of Engagement Activity | 2022 |
Description | Invited Speaker University of Leeds seminar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | I delivered a summary of our research findings to a mixed audience of researchers, postgraduate and undergraduate students as part of the University of Leeds Biological Sciences seminar series. |
Year(s) Of Engagement Activity | 2023 |
Description | Invited Speaker at the Society for Experimental Biology Annual Meeting 2023 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Keynote Speaker in a session at the SEB's annual meeting in 2023. The session was well attended and resulted in a new collaboration with colleagues at the University of Massachusetts |
Year(s) Of Engagement Activity | 2023 |
Description | Medicine and Life Sciences Walking Tour launched at Dundee Science Festival 21 - 22 November 2020 |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | This was a project between the University of Dundee School of Life Sciences, Museum Services and Medicine. My submission complemented historical information about plant research that took place in Dundee, helping those undertaking the walks to learn about past work/events and current research taking place today. The information captured was used on the map and on an accompanying webpage. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.lifesci.dundee.ac.uk/impact/public-engagement/public-engagement-projects-and-events/dund... |
Description | Online Seminar for International Barley Hub Community |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Online seminar across the cereal community |
Year(s) Of Engagement Activity | 2023 |
Description | Presentation at international conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Invited Speaker at the Plant Genomes in a Changing Environment conference, Wellcome Genome Campus. Held virtually due to COVID-19 |
Year(s) Of Engagement Activity | 2020 |
URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/plantgenomes20/ |