Molecular and genetic networks determining row number in cultivated barley
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The number of fertile rows of grain (i.e. two vs. six) on a barley inflorescence is determined by complex interactions between different SIX-ROWED SPIKE (VRS) genes. One of these genes, VRS1, is generally considered both necessary and sufficient for this developmental switch, with recessive alleles (denoted as vrs1) found in all six-row varieties. However up to 10 additional independent genetic loci affecting row-type have been characterised genetically. They all represent induced recessive mutations, generated in two-rowed accessions with an ancestral (or 'wild type (wt)') VRS1 gene. Spikes of these mutant lines have either complete or partial fertility restoration compared to sterile lateral florets of the wt spikes. We genetically mapped these VRS mutant alleles by SNP genotyping BC6 NILs in a two-row recurrent parent background. We also conducted a GWAS experiment for 'row-type' using a large collection of elite barley two- and six-row cultivars. The latter analysis identified four highly significant associations with row-type segregating in this germplasm set. As expected, one of these corresponded to VRS1. Two others corresponded to the proposed genetic locations of VRS3 and VRS5 genes, and one remains unassigned. We subsequently identified and validated VRS3 and VRS5 genes, while colleagues in Germany have identified VRS4. Of these four characterised genes, three are transcription factors and one is a chromatin remodelling factor. Here we propose to investigate how these components interact genetically, physically and phenotypically, and attempt to identify other genes in the network (i.e. interactors) that ultimately control lateral floret fertility. Finally, with breeders' support, we will explore the potential of novel six-row varieties in European agriculture.
Planned Impact
The underlying thrust of the proposed research is to understand the development and architecture of the grain bearing inflorescence of the world's 4th largest cereal crop. Morphological and developmental changes have been central to yield increases in many crop species thus this research directly relates to the BBSRC priority of Crop Science (Food Security). As well as gaining a detailed mechanistic understanding of the genes involved in converting lateral florets from sterile into fertile, this project has the realistic potential of developing genetically novel six-rowed barleys with evenly-filled grains without a concomitant reduction in tillering. There may also be benefits of this research for two-row barleys of the 'deficiens' class that are emerging strongly in current markets where the lateral florets are virtually absent. There, an increase in tillering could potentially be effected without impacting inflorescence structure. The complexities of yield determination in the field mean that yield potential offered by such lines may not be realised in some environments. However, the range of lines produced (both by ourselves and by our commercial partner) will allow us to explore how it may be possible to optimize yield potential by manipulating these specific crop architectural traits. Existing NILs and newly developed lines will facilitate the proposed detailed genetic interaction and developmental studies required to promote the rapid exploitation of alternative six-row genes.
The Triticeae cereals are a dominant component of European agriculture. As a collaborator on this project, the immediate commercial beneficiary of this project will likely be Limagrain, a leading commercial sector organisation that breeds new barley and wheat varieties along with the farmers that grow new varieties in their fields (UK farm gate value >£500M). Current six-row lines do not have suitable grain quality for the malting industry - so, if it is possible to maintain malting quality in a novel six-row spring or winter phenotype, there may also be benefits to the malting and distilling sector. The European brewing (and Scotch whisky) industry is the largest in the world. Four of the seven largest brewers in the world are European, with their product directly / indirectly generating total government revenues estimated at ~$57.5 billion annually. Novel six-row barleys generated in an existing high quality two-row background may overcome some of the hurdles associated with breeding efforts that have repeatedly failed to generate a good quality (for malting) six-row type (with rare exception).
Barley is a key feedstock for the livestock industry and remains a traditional food in marginal environments 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 FDA recently allowing barley products to claim a role in the 'reduction in risk' of coronary heart disease. Furthermore, barley straw (which may be enhanced through increased tillering) has a potentially expanding role in animal nutrition and in the second-generation bioenergy sector. A simple increase in yield in either two- or six-rowed types would be an important outcome.
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, and as such translational activities from basic science to application are crucial. A novel six-row barley would generate an unique selling proposition in the marketplace and a pathway to deployment through the involvement of Limagrain is an intrinsic component of this project proposal.
The Triticeae cereals are a dominant component of European agriculture. As a collaborator on this project, the immediate commercial beneficiary of this project will likely be Limagrain, a leading commercial sector organisation that breeds new barley and wheat varieties along with the farmers that grow new varieties in their fields (UK farm gate value >£500M). Current six-row lines do not have suitable grain quality for the malting industry - so, if it is possible to maintain malting quality in a novel six-row spring or winter phenotype, there may also be benefits to the malting and distilling sector. The European brewing (and Scotch whisky) industry is the largest in the world. Four of the seven largest brewers in the world are European, with their product directly / indirectly generating total government revenues estimated at ~$57.5 billion annually. Novel six-row barleys generated in an existing high quality two-row background may overcome some of the hurdles associated with breeding efforts that have repeatedly failed to generate a good quality (for malting) six-row type (with rare exception).
Barley is a key feedstock for the livestock industry and remains a traditional food in marginal environments 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 FDA recently allowing barley products to claim a role in the 'reduction in risk' of coronary heart disease. Furthermore, barley straw (which may be enhanced through increased tillering) has a potentially expanding role in animal nutrition and in the second-generation bioenergy sector. A simple increase in yield in either two- or six-rowed types would be an important outcome.
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, and as such translational activities from basic science to application are crucial. A novel six-row barley would generate an unique selling proposition in the marketplace and a pathway to deployment through the involvement of Limagrain is an intrinsic component of this project proposal.
Publications
Bull H
(2017)
Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility.
in Nature communications
Dixon L
(2018)
Annual Plant Reviews online
Jöst M
(2024)
The gain-of-function mutation blf13 in the barley orthologue of the rice growth regulator NARROW LEAF1 is associated with increased leaf width
in Journal of Experimental Botany
McKim S
(2018)
The Barley Genome
Rapazote-Flores P
(2019)
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.
in BMC genomics
Zwirek M
(2019)
Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain.
in The New phytologist
Description | The selection of beneficial architectural variation in cereals, especially that of the grain-bearing inflorescence, remains key to increasing grain yield. In barley, the inflorescence is a stalk lined with flowering units or spikelets which set grain. The spikelets are arranged into triplet clusters with a central spikelet flanked by two lateral spikelets. Depending on whether the central spikelets alone or the central and both lateral spikelets are fertile, the spike forms two or six rows of grain, respectively. In this project, we investigated the genetic and molecular interactions between the Six-rowed spike or VRS loci which repress fertility of lateral spikelets. By following lateral fertility in the vrs mutants, we reveal the earliest events associated with lateral fertility due to loss of vrs function and a critical window during spikelet growth where lateral spikelets can become fertile. Double mutant analyses suggest novel routes to complete lateral fertility and benefical effects on grain size relevant to downstream uses of barley grain. We also discovered new roles for the VRS genes in controlling other yield-related traits, such as branching in the stem and inflorescence, and growth rate. Unfortunately, we were not able to test interactions on the protein level due to the self-activating nature of these proteins; however, we investigated the control of the VRS proteins on gene expression, both for specific targets and over the entire genome. Integrating these data, we propose a model whereby VRS genes regulate each other and feed into growth control pathways already implicated in lateral growth fertility as well as some pathways not previously associated with lateral spikelet fertility. Taken together, this work reveals mechanisms by which VRS genes work together to control lateral fertiltiy and new traits under VRS control, opening up new research questions for future work. Results from this work form the basis of new collaborations with other groups studying lateral fertility in barley. The research staff employed on the project developed new and high-proficiency skills in bioinformatics and programming as well as experience presenting their research at international conferences. The reserach staff have secured new scientific positions. Datasets generated in this project have supported further analyses and subsequent publication about the barley reference transcriptome. |
Exploitation Route | Our current work may be applied by breeders in the future to increase seed number per barley spike as well as to control other agronomic features. Our findings suggest a significant role of the VRS genes in controlling additional aspects of barley architecture which will form the basis of future grant funding. |
Sectors | Agriculture Food and Drink |
Description | BRACT transformation |
Amount | £21,200 (GBP) |
Funding ID | BB/N019466/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 02/2018 |
Description | Testing a cytokinin dilution model of floral duration in barley |
Amount | £654,859 (GBP) |
Funding ID | BB/X001423/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2023 |
End | 12/2025 |
Title | Barley reference transcriptome |
Description | A high confidence barley reference transcript dataset (BaRTv1.0) was generated from multiple RNA-seq datasets. The BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads compared to other barley transcripts available. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | The reference transcriptome available in BaRT v1.0 enables precise transcript quantification from gene expression and alternative splicing. |
URL | https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6243-7 |
Title | Genetic Resources to study yeild-related traits in barely |
Description | Barely double mutants generated through genetic crosses provide a unique resource to study genetic interactions between loci governing yield-related traits such as grain number. |
Type Of Material | Biological samples |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | These resources have supported a new collaboration with researchers who are also studying grain number in barley. |
Title | Barley vrs3 gene - RNA-Seq |
Description | Highly replicated RNAseq of different barley genotypes varying for row-type. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Available for construction of the barley transcriptome. Available for other researchers interested in row-type regulation. |
URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB19243 |
Title | MOESM1 of BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq |
Description | Additional file 1: Table S1. RNA-seq datasets from both public databases and in house unpublished data. Table S2. StringTie Parameters used in the different assemblies (sorted by transcript number). Table S3. Mean proportions of alternatively spliced products by HR-RT-PCR analyisis. Table S4. Correlation of HR RT-PCR data with BaRTv1.0, BaRTv1.0- QUASI and HORVU transcripts. Table S5. Splice Junctions and intron lengths. Table S6. Differentially expressed gene clusters and differential transcript usage gene clusters. Table S7. Pairwise significant changes in alternatively spliced transcripts detected by HR RT-PCR between different organs. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Contribution to a key publication and resource for the wider community |
URL | https://springernature.figshare.com/articles/MOESM1_of_BaRTv1_0_an_improved_barley_reference_transcr... |
Description | Collaboration with Matthew Tucker at Adelaide University on row-type and grain development |
Organisation | University of Adelaide |
Country | Australia |
Sector | Academic/University |
PI Contribution | Joint funding bid to understand the role of epigenetics in controlling row-type in barley made in 2019 was unsuccessful. We have now applied for future funding to the ARC to understand the roles of the row-type genes in basal branching and are awaiting the outcome. We have also started a direct collaboration to understand regulatory factors controlling grain development. This was very successful and is ongoing. |
Collaborator Contribution | Prof Tucker and his team contributed new research findings and in collaborative experiments for a manuscript published in 2021. Prof Tucker supported a my grant proposals for an Australian Partnering Award and a BBSRC Standard Response Mode Grant (the Generation Gap), both of which were successful. Prof Tucker is currently sharing unpublished data and generating resources to continue our study on grant development. Members of my research team will also be hosted by Prof Tucker during a research visit planned for 2024. |
Impact | Prof Tucker and his team contributed new research findings and in collaborative experiments for a manuscript published in 2021. |
Start Year | 2019 |
Description | Collaboration with Prof Tom Bennett at the University of Leeds |
Organisation | University of Leeds |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We worked together to write a grant for further funding from BBSRC which was successful |
Collaborator Contribution | We worked together to write a grant for further funding from BBSRC which was successful |
Impact | Further funding - Testing a cytokinin dilution model of floral duration in barley" £621,745 BB/X001423/1 |
Start Year | 2022 |
Description | Collaboration with researchers at Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) |
Organisation | Leibniz Association |
Department | Leibniz Institute of Plant Genetics and Crop Plant Research |
Country | Germany |
Sector | Charity/Non Profit |
PI Contribution | We are actively collaborating to understand more about the involvement of the SPL transcription factors in controlling agronomic traits in barley, including row-type. |
Collaborator Contribution | Researchers at IPK sharing research findings about their experiments on row-type |
Impact | preliminary results will form the basis of a publication currently in development. |
Start Year | 2019 |
Description | Cereals in Practice 2016 |
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 | The post-doc employed on the grant participated in Cereals in Practice: a day long event where scientists engage with the national farming industry and community about current cereal research and trials conducted at the University of Dundee, the James Hutton Institute and Scottish Rural Agricultural College. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.hutton.ac.uk/events/cereals-practice-2016 |
Description | Demonstration Plot for Arable Scotland |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | I set up a demonstration plot to show barley growers our work on the genetic control of row-type in barley. |
Year(s) Of Engagement Activity | 2019 |
Description | Fascination of Plants Day at the Botanic Gardens |
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 | This event involved a collaboration between the Division of Plant Sciences, University of Dundee, the James Hutton Institute and the University of Dundee Botanic Gardens. This free event celebrated plants and plant research with numerous activities including garden tours, plant pressing, and scientific activities including raspberry DNA isolation and thermal imaging. The event was a resounding success with over 700 attendees. |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.dundee.ac.uk/news/2015/what-did-plants-ever-do-for-you.php |
Description | General Board Meeting of EPSO |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | PI attended the European Plant Biology Association Annual meeting in Prague in June 2016. Two day meeting where strategies for European Plant Science funding were discussed. Great networking opportunities across Europe. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.epsoweb.org/ |
Description | International Conference (Australia) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The Australian Barley Technical Symposium (ABTS) is a meeting every two years of the top barley researchers and industry representatives vin Australia. Several international speakers are invited. Speaking at this event allowed my BBSRC-funded research to reach a wide international audience which included heads of breeding from several major brewing companies including Carlsberg and Miller. |
Year(s) Of Engagement Activity | 2015 |
Description | Invited Presentation at Plant Animal and Genome Conference 2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Delivered a talk about our research on the vrs3 row-type gene, it's role in lateral spikelet fertility and it's interactions with other row-type genes. |
Year(s) Of Engagement Activity | 2017 |
URL | https://pag.confex.com/pag/xxv/meetingapp.cgi |
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 International Barley Mutant Workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I delivered a lecture on the latest findings from my research group investigating genetic interactions which determine row-type in barley. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited talk at the First International Workshop on Barley Mutant Research |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | I introduced my research program to the greater barley community. After my talk I was invited to co-author a book chapter. |
Year(s) Of Engagement Activity | 2014 |
URL | http://meetings.ipk-gatersleben.de/bmws2014/index.php |
Description | Media Interviews and Press Articles about new publication |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Interviewed for local TV regarding a recent publication. Press Release about the publication carried in several local papers and in international trade magazine. |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.thecourier.co.uk/fp/news/local/dundee/779425/new-elite-barley-developed-using-dundee-rese... |
Description | Open Doors Day school visit |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | PI lead an ethics workshop on GM technology with classes from Braeview Academy, a local secondary school. |
Year(s) Of Engagement Activity | 2016 |
Description | Plant Power Day at the Botanic Gardens |
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 | Scientific displays and interactive activities which showcase the plant science ongoing at the University of Dundee. The PI organised this event in collaboration with the Botanic Gardens. Display to showcase research on cereal architecture. Living genetics and cereal gardens. Botany trails. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.dundee.ac.uk/news/2016/fun-in-dundee-botanic-garden-for-plant-power-day.php |
Description | Poster Presentation at the International Barley Genetics Symposim |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The PDRA employed on the grant presented a poster at the International Barley Symposium in Minnesota in June 2016. This five day long conference happens only every four years and is a critical event for the barley research community. |
Year(s) Of Engagement Activity | 2016 |
URL | http://ibgs2016.org/ |
Description | Presentation for Cafe Science (Dundee) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | I gave a public lecture as part of the Cafe Science series in Dundee. I spoke about our work on stem elongation and row-type in cereals which stimulated much discussion and questions (>1hour) and led to several emails from interested audience members. |
Year(s) Of Engagement Activity | 2019 |
URL | http://www.lifesci.dundee.ac.uk/news/2019/may/16/expert-share-ground-breaking-grains-crop-science |
Description | Presentation for Cafe Science group (Pitlochry/ Aberfeldy/ Dunkeld) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | I gave a public lecture on our work on stem elongation in cereals which stimulated much discussion and questions (>1hour) and led to several emails from interested audience members. |
Year(s) Of Engagement Activity | 2019 |
URL | http://cafescientifique.org/uk/pitlochry-aberfeldy-dunkeld |
Description | You Tube Channel 'Arabidopsis Events UK' associated with GARNET interviews Sarah McKim about Barley Spikelet Formation |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | You Tube Video - "Sarah McKim talks to GARNet about a recent paper published in New Phytologist entitled 'Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain'." |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.youtube.com/watch?v=FBPaKZ_E6ic |
Description | invited talk at the Monogram Network Meeting 2014, Reading |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Talk described work planned for this project to the greater cereal community in the UK The talk was well received by the community and I made contacts in the breeding industry. |
Year(s) Of Engagement Activity | 2014 |