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State-of-the-art genome sequencing could increase locally sourced Shetland whisky potential

Bere Unst barley
Bere Barley plots. Photo by Joanne Russell The James Hutton Institute.
“A specific Bere genome will be invaluable as it will allow us to explore the underlying genetic mechanisms. This could then help to introduce these traits into elite varieties to be able to use them on what would otherwise be marginal soils”

Researchers working on an ancient form of barley grown only on Unst, Shetland’s northernmost island, have returned from a knowledge exchange trip to Germany that will help them and others better understand its specific traits.

By learning a state-of-the-art computational method for assembling plant genome sequences from their German counterparts, the researchers from The James Hutton Institute in Dundee will be able to find the unique traits of Bere Unst barley that can then be used to create higher quality and more productive varieties.

The specific traits of the Bere Unst barley could also mean a new elite variety could be bred to grow on certain marginal soils elsewhere around the world, as well as new flavours of barley.

The trip was made possible by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) International Partnering Awards BarleyEUNetwork (BBSRC BB/V018906/1). It allowed bioinformaticians Miriam Schreiber, Wenbin Guo and Runxuan Zhang to visit the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany.

There, the team learned how to apply a state-of-the-art computational method of assembling plant genome sequences, called the TRITEX pipeline (Marone et al., 2022). This was specifically for assembling the genome sequence of Bere Unst barley – known as a landrace because it’s adapted to grow only in highly localised places, in this case Unst.

Dr. Miriam Schreiber, a cereal bioinformatics specialist, based at The James Hutton Institute’s Invergowrie campus, says, “Bere barley landraces have been studied at the institute for multiple years (Schmidt et al., 2019), as they show better growth and yield under manganese deficient soils in comparison to commercial cultivars. Bere Unst is a specific ancient variety that was collected on Unst and has since been shown to grown better than commercial cultivars on marginal soils specific to the Scottish Islands.

“A specific Bere genome will be invaluable as it will allow us to explore the underlying genetic mechanisms. This could then help to introduce these traits into elite varieties to be able to use them on what would otherwise be marginal soils. These ancient barleys also have different unique flavours and, being local, there’s an obvious interest from distilleries to be able to use more locally grown barley for a high quality, heritage product.”

Joanne Russell, a geneticist at The James Hutton Institute, explains further: “Most of these ancient or heritage varieties are only stored in gene banks and so to grow on any scale you would need to request seed, usually around 5gs and multiply up over the years. This is what we have been doing since 2007, for many of the bere barleys, as well as multiplying accessions from a PhD student based at Science and Advice for Scottish Agriculture in Edinburgh who went to Shetland, Orkney and the Western isles and collected samples from farmer’s fields (Cathy Southworth, 2007), so we now have these in our seed store, as well as SASA (Science & Advice for Scottish Agriculture) holding samples. Apart from bere Orkney, which is registered as a conservation variety and only available through Orkney College, there are no other bere’s currently ‘commercially’ registered or grown on scale.”

The genome sequencing work will also help to extend the published barley pangenome – the entire set of genomes from the same group of barleys that share the same ancestors (Jayakodi et al., 2020) – under separate funding from the German Ministry of Education and Research (BMBF) through the SHAPE II (FKZ 031B0884) grant.

Dr. Isabelle Colas who is the lead principal investigator on the project said: “The aim of the BBSRC grant is to promote barley research and strengthen the link between leading barley scientists from the UK and Germany. Providing travel opportunities like this is an invaluable way to achieve these goals and this is particularly important for early/mid-career scientists who often don’t have sufficient funding for such activities.”

During the trip, The James Hutton Institute team also ran a training workshop on transcriptome data analysis – that’s the collection of RNA molecules “expressed” by plant genomes. This included developing high quality transcript reference datasets for accurate quantification (Zhang et al, 2017; Zhang et al, 2022) and using 3D RNA-sequencing to carry out comprehensive and high-quality gene expression analysis.

The latter included use of 3D RNA-seq app (Guo et al., 2021), which was developed by Dr. Wenbin Guo at The James Hutton Institute. It now has more than 8,700 users globally and, since 2019, has been cited 49 times by plant, animal and human studies.

“The workshop was attended by 18 participants, from students, post-docs and permanent staff from the IPK, including three participants travelling from Poland,” adds Dr Runxuan Zhang. “All had a chance to run through the app with a test dataset and, as soon as they could see what it could do, they were keen to use it on their own datasets. Overwhelmingly, the feedback was positive.”

Finally, the team had a chance to tour of the IPK’s impressive facilities. This included visiting their Genebank, genome centre with PacBio Sequel lle and Novoseq 6000 sequencing instruments, and their high throughput phenotyping facilities – which lets them assess plant traits in simulated growing conditions. They also had individual meetings with scientists from research groups at the IPK, exploring collaboration and funding opportunities that combine the capabilities and expertise of both IPK and The James Hutton Institute.

“As a direct result of the visit, new collaborations have been established with two postdocs are planning to visit us here at the institute to learn and utilize the RTDBox, funded by BBSRC for high quality transcriptome construction for common beans and barley anthers (the part of the barley’s stamen where pollen is produced),” added Dr Zhang. 

Dr. Colas: “This is showing what we can achieve even from a very short trip, when we get more opportunities for face-to-face meetings, and how beneficial it is for generating new ideas. I cannot wait to hear more from everyone’s else travel experience and how we can create new opportunities for barley research.”

References

Marina Püpke Marone, Harmeet Chawla Singh, Curtis J Pozniak et al. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes, 16 September 2022, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-2059469/v1] https://www.researchsquare.com/article/rs-2059469/v1

Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V.S., Gundlach, H., Monat, C., et al. (2020). The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588(7837), 284-289. doi: 10.1038/s41586-020-2947-8.

Schmidt, Sidsel Birkelund et al. “Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to manganese limitation.” Annals of botany vol. 123,5 (2019): 831-843. doi:10.1093/aob/mcy215

Guo, W., Tzioutziou, N.A., Stephen, G., Milne, I., Calixto, C.P., Waugh, R., et al. (2021). 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol 18(11), 1574-1587. doi: 10.1080/15476286.2020.1858253.

Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017 May 19;45(9):5061-5073. doi: 10.1093/nar/gkx267. PMID: 28402429; PMCID: PMC5435985.

Zhang, R., Kuo, R., Coulter, M. et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol 23, 149 (2022). https://doi.org/10.1186/s13059-022-02711-0

Press and media enquiries: 

Elaine Maslin, Media Officer, The James Hutton Institute, elaine.maslin@hutton.ac.uk, +44 01224 395089 or 0344 928 5428 (switchboard).


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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.