notes on Barley Genome Net Dundee 2025 (day 2)

Picture from day 1, source: https://bsky.app/profile/intbarleyhub.bsky.social/post/3lheka47ggs2z

 

(back to day 1)

Ruth Hamilton talks about her work on re-domesticating barley from crosses of wild barley (H. spontaneum) and elite cultivar RGT Planet. She looks at non-shattering, spring type, short plants and photoperiod response. This is being done in the field and polytunnels. She's asked whether she has observed fertility problems due to Planet's translocation (no).

Sariel Hubner talks about local adaptation in wild barley and how that informs future predictions about adaptation. They carry out mapping and SNP calling at AWS, code available at https://github.com/hubner-lab. They have done GEA analyses: https://www.biorxiv.org/content/10.1101/2024.09.02.610836v2 . He reports adaptative haplotype blocks with high LD that accumulate TE insertions under stress conditions.

Ernesto Igartua talks about recent work around the genomic drivers of Mediterranean barley diversity, spanning different projects. He summarizes the differences found in key flowering genes (FT1, VRN1, VRN2, CEN, Vrs1) among up to 17 Med populations. He also shows recent experiments on heat strees before flowering  that showed differential responses of genotypes. In questions Miguel Sánchez from ICARDA reminds that in wheat winter VRN1 alleles provide "protection" against both frosting and heat, likely as seen in barley.

Andreas Maurer summarizes a decade of Insights from HEB-25: Flowering Time in Wild x Cultivated Barley Crosses. They have found 8 major flowering time QTLs mapping to the usual suspect genes, plus denso and an unknown region. They are exploring the use of environmental data to model flowering time, see for instance https://pubmed.ncbi.nlm.nih.gov/33713844 . In unpublished work they are using a climatic index as a trait in GWAS analysis and found that only some flowering genes are associated to it. He also shows that an exotic ELF3 alelle similar to one in wild barley was instrumental in barley domestication: https://academic.oup.com/jxb/article/74/12/3630/7100059

The team of Morten Lillemo just started the ProteinBar project, which is using genomics and phenomics to increase protein content from 10% to 14%. 95% of barley production in Norway is for animal feed. The import soybean for that also. They have partnered with several companies. Shows field image data (multispectral, Yara N) of a barley panel with two N levels that undercoverd a 2-row vs 6-row divide. They see that modern cultivars uptake more N, with 2-row superior to 6-row. In field experiments with 2 varieties they cannot see a reponse of plants to higher N supplements, different genotypes should be tested. He insists that having a pricing policy in place that favours high protein barley will be essential for this to fly, as those varieties might be lower in yield.

Einar Haraldsson presents their work on Hordeum erectifolium, part of the pan-Hordeum consortium, particularly on the physiological and genomic study of drought-adaptive traits. It has more veins and several enlarged gene families compared to related grasses and Morex. However, has similar leaf rel water content than Morex, but maintains erect leaves during drought. 

Eyal Fridman and his group are performing analysis and mapping of barley spike traits using a cytoplasm-aware population. I missed most of this talk unfortunately. In questions he says that the cytotype diversity among barley cultivars is tiny compared to that in wild barleys.

Paolo Pesaresi presents results results on the optimization of canopy photosynthesis in barley. They are searching for allelic variants, as part of the BestCrop consortium, to reduce antenna size/reduced clorophil contentl and increased yield/photosynthetic performance. The mutants (ie hus1) are pale green and some have no effect on flower time, grain yield and tolerate higher seed density and reduce transpiration; however some are more sensitive to cold. They have published some of these mutants: https://link.springer.com/article/10.1007/s00299-024-03328-2. Explains that in nature plants compit for light and that's why they are dark green; crops are under more controlled conditions and can tolerate less efficiency.

Ronja Wonneberger talks about the identification of candidate genes conferring resistance to bird-cherry oat aphid in Hordeum spontaneum. Results after 20yr of work by previous colleagues. There are no completely resistant cultivars. Previous results published at https://doi.org/10.1007/s00122-019-03287-3 . Found an interval with 5 DEGs on 2H, all resistance-related annotations. She also mentions that other genomic regions have poor read mappings suggesting that PAV can also be involved.

Ales Pecinka talks about parental conflict and unbalanced genome dosage in barley. He finds that paternal excess is more lethal in embryo rescue experiments than maternal excess. They are carrying out functional analysis of chromatin dynamics and microscopy to find imprinted genes in barley, finding n=255. One example is gene LYS3, which encodes a prolamin box TF. Some results published at https://academic.oup.com/plcell/article-abstract/36/7/2512/7651082

We also attend a live demo of 3D-RNAseq carried out at https://sharp-ga.com , see the paper at https://www.tandfonline.com/doi/full/10.1080/15476286.2020.1858253 . The features I like most are the analysis at isoform level and the generated report. Currently it uses the lima pipeline, pathway analysis will be added in the future. Currently in beta, look like this will be a commercial service, don't know about pricing.

notes on Barley Genome Net Dundee 2025

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:

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.