International Barley Hub, JHI, Dundee, UK, 4-5February (jump to day 2)
Robbie Waugh walks us about the history of this event from 2003, where partners signed a collaboration agreement around the sharing of data and resources and the commitment to train scientists (http://pgrc.ipk-gatersleben.de/barleynet). Lead most of this time by Patrick Schwaizer, until his passing in 2018. He then moves on to presenting the International Barley Hub.
Micha Bayer presents EoRNA (https://ics.hutton.ac.uk/eorna) which is fed from the ENA and shows isoform-level expression in TPM, it helps find cases where gene expression changes are driven by alternative isoforms. A recent BBSRC grant is now supporting v2, to be released sometime 2025, which supports a new API that you can query with curl. It is currently based on shell script but on the way to be ported to nextflow. It includes a new reference transcriptome based on the barley pan-transcriptome (https://www.nature.com/articles/s41588-024-02069-y). Only 0.3% transcripts show no expression. It raises the challenge of fetching metadata matching the ENA data, which often requires manual curation.
Vanda Marosi talks about pantranscriptomics and barley diversification, she coauthored the barley pan-transcriptome (https://www.nature.com/articles/s41588-024-02069-y) looks at functional differences of orthologues. Most cluster in the same coexpression modules, which can be merged into 6 expression communities (root, spike, grain, leaf, etc) using Louvain clustering:
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| Module–tissue correlation and functional enrichment of the modules included in each of the communities reveal distinct associations with tissues/organs. C1–C3, plant reproductive processes; C4, photosynthesis—shoot; C5, starch metabolism—caryopsis and C6, nutrient uptake—root. Source: https://www.nature.com/articles/s41588-024-02069-y/figures/3 |
Hana Simkova talks about gene promoters and regulation in barley. They have done CAGE to describe TSSs and construct a promoterome (https://doi.org/10.1016/j.csbj.2023.12.003). She shows examples of promoter shifts and alternative promoters. They are using extensive epigenome profiling to predict cis-elements using ChromHMM (https://www.nature.com/articles/nprot.2017.124). They observed up tp 8 promoter interactions (HiChIP) across the genome. They have integrated the data in a resource named barleyEpibase, cound not find the URL. In questions she mentions that normal TSS position variability is about <20b, more than that is probably an error or differential tissue regulation.
Martin Mascher talks about the Hordeum genus superpangenome, which goes beyond cultivars and includes wild, related species. He shows some beautiful drawings by Mona Schreiber, you can see some at https://pmc.ncbi.nlm.nih.gov/articles/PMC7616794. He starts by discussing the challenges of H. bulbosum, which is a perennial outcrossing diploid/autotetraploid species, with more unique sequences than H. vulgare in the pangenome growth plot. Shows an example of conserved genomic elements, about 200k at the genome level, a good number outside CDS regions.
In my talk "Exploring barley pangenes with Barleymap", you can review the slides at https://digital.csic.es/handle/10261/379660. I showed how barley pangenes from the pangenome V1 can be browsed at https://barleymap.eead.csic.es and https://eead-csic-compbio.github.io/barley_pangenes. Please see a previous blog post for more details.
Christoph Dockter from Carlsberg talks about an induced muthagenesis approach called FIND-IT (https://onlinelibrary.wiley.com/doi/10.1111/pbi.14427) and how they used the resulting mutant collection to study a gene cluster that changes malt quality. They are using these mutants in multiple collaborations to study loss and gain of function, they have an efficient system in place to identify mutants in large populations.
Giuseppe Sangiorgi presents an update on the TILLMore mutant collection on Morex (n=3600 mutants). He then goes to show examples of root mutants that they have described and published in recent years, such as https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.19777, Egt1, Egt2, and several root hair or "waivy" mutants?
Laura Rossini presents their work on stringolactone branching inhibition and tillering in barley. They have used the HorTILLUS mutatns. Most of that work is currently under review, so I won't share details here.
Roberta Rossi talks about dissecting culm morphology in two DH populations. They focus on 6 candidate genes shared in QTL and GWAS analyses. She shows mostly unpublised data.
Ton Winkelmodel from WU talks about TFs controlling barley architecture. Reminds that vrs5 (mazie TB1 orth) affects row type and tillering, which are negatively correlated. Is it possible to decouple both phenotypes? Looked for DEGs in vrs5 mutants compared to wild type, find clusters enriched on different GO terms. Did DAP-Seq to look for Vrs5-bound genome regions and found enrichment in TCP-like, central motifs, with some peaks several Kb upstream of target genes. Data is mostly unpublished.
Ravi Koppolu talks about their work on mutants that affect barley inflorescence development. He shows the spike differences among barley, wheat and other grasses and uses mutants (ie bpi1, mfs2) to observe that some mutations change the architecture of the infloresce, for instance changing to panicle-like spike. Recent work include: https://www.sciencedirect.com/science/article/abs/pii/S1369526621001709 and https://link.springer.com/article/10.1007/s00122-021-03986-w
Raffaella Battaglia talks about the sporophytic control of male fertility in barley. She reports the SWEET4 gene, encoding a sugar transporter in the apoplast that feeds the polen grain, is required for male fertility. Not sure much is published, found https://research.uniupo.it/en/publications/sporophytic-control-of-male-fertility-the-role-of-the-sweet4-gene
Volodymyr Radchuk speaks about metabolic and hormonal regulation of grain filling (sugar and hormone transport) in barley. They use magnetic resonance imaging (RMI). Among recent papers see for instance https://academic.oup.com/plcell/article/35/6/2186/7061345
Finally, Gwen Kirschner talks about the genetic control of the root angle in barley. The gravitropic set-point angle (GSA) positions roots. Roots "remember" their angles as the plant grows, she's doing (miRNA) transcriptomics to look for candidate genes for that.
