ArticleNature genetics2025
A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.
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Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33citing papers in PubMed
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33 citing papers in PubMed.
- Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.The plant genome · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- Epistatic interaction of the genesbioRxiv : the preprint server for biology · 2026Article
- Pan-genome analysis reveals hidden diversity and selection signatures of auxin response factors (ARFs) associated with breeding in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Pan-Transcriptome Analyses of Multiple Tissues and Growth Stages Create Expression Atlases for the SilkwormAnimals : an open access journal from MDPI · 2026Article
- Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits.Plant molecular biology · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Evolutionary and functional characterization of BBX genes in the barley pangenome.BMC plant biology · 2026Article
- From dormant grain to beer: Unraveling barley's germination secret at the MKK3 locus.Plant communications · 2026Article
- TaPP2C-a5 fine-tunes wheat seed dormancy and germination with a Triticeae-specific, alternatively spliced transcript.Journal of advanced research · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Diversify and conquer: How effector diversity is shaped by host-microbe co-evolution.PLoS pathogens · 2026Article
- A pendant awn phenotype linked to the EMBRYONIC FLOWER 1 LIKE (EMF1L) gene in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement.Nature communications · 2025Article
- Genomic Insights Into Early-Stage Selective Filtering During the Transport Stage of Biological Invasions.Evolutionary applications · 2025Article
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
54 authors.
Wenbin Guo *International Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.ORCID http://orcid.org/0000-0002-1829-6044
Miriam Schreiber *International Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.ORCID http://orcid.org/0000-0002-3732-8822
Vanda B Marosi *Plant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0002-1444-2972
Paolo Bagnaresi *Council for Agriculture Research and Economics (CREA) Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.ORCID http://orcid.org/0000-0001-8466-4805
Morten Egevang Jørgensen *Carlsberg Research Laboratory (CRL), Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6503-0495
Katarzyna B BrauneCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.
Ken ChalmersSchool of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia.
Brett ChapmanWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.ORCID http://orcid.org/0000-0003-4484-2253
Viet DangWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.ORCID http://orcid.org/0000-0001-6408-6323
Christoph DockterCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-5923-3667
Anne FiebigLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0003-3159-3593
Geoffrey B FincherSchool of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia.
Agostino FricanoCouncil for Agriculture Research and Economics (CREA) Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.
John FullerInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.
Allison HaaningDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
Georg HabererPlant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0002-6612-6939
Axel HimmelbachLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
Murukarthick JayakodiLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0003-2951-0541
Yong JiaWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.ORCID http://orcid.org/0000-0002-0394-3966
Nadia KamalPlant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0002-3258-4130
Peter LangridgeSchool of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia.ORCID http://orcid.org/0000-0001-9494-400X
Chengdao LiWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.ORCID http://orcid.org/0000-0002-9653-2700
Qiongxian LuCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-1358-2623
Thomas LuxPlant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0002-5543-1911
Martin MascherLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0001-6373-6013
Klaus F X MayerPlant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0001-6484-1077
Nicola McCallumInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.ORCID http://orcid.org/0000-0002-9438-1697
Linda MilneInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.
Gary J MuehlbauerDepartment of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.ORCID http://orcid.org/0000-0001-9320-2629
Martin T S NielsenCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.
Sudharsan PadmarasuLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0003-3125-3695
Pai Rosager PedasCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.
Klaus PillenChair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.ORCID http://orcid.org/0000-0003-4646-6351
Curtis PozniakDepartment of Plant Sciences and Crop Development Centre, University of Saskatchewan (USASK), Saskatoon, Saskatchewan, Canada.ORCID http://orcid.org/0000-0002-7536-3856
Magnus W RasmussenCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6720-8832
Kazuhiro SatoInstitute of Plant Science and Resources, Okayama University, Kurashiki, Japan.ORCID http://orcid.org/0000-0001-8818-5203
Thomas SchmutzerChair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.ORCID http://orcid.org/0000-0003-1073-6719
Uwe ScholzLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0001-6113-3518
Danuta SchülerLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
Hana ŠimkováInstitute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic.ORCID http://orcid.org/0000-0003-4159-7619
Birgitte SkadhaugeCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-7317-4376
Nils SteinLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.ORCID http://orcid.org/0000-0003-3011-8731
Nina W ThomsenCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.
Cynthia VossCarlsberg Research Laboratory (CRL), Copenhagen, Denmark.
Penghao WangWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.
Ronja WonnebergerInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland.
Xiao-Qi ZhangWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdoch, Western Australia, Australia.
Guoping ZhangCollege of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China.
Luigi CattivelliCouncil for Agriculture Research and Economics (CREA) Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.ORCID http://orcid.org/0000-0002-6067-4600
Manuel SpannaglPlant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health (PGSB), Neuherberg, Germany.ORCID http://orcid.org/0000-0003-0701-7035
Micha BayerInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland. micha.bayer@hutton.ac.uk.ORCID http://orcid.org/0000-0003-0041-3115
Craig SimpsonInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland. craig.simpson@hutton.ac.uk.ORCID http://orcid.org/0000-0002-1723-1492
Runxuan ZhangInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland. runxuan.zhang@hutton.ac.uk.ORCID http://orcid.org/0000-0001-7558-765X
Robbie WaughInternational Barley Hub (IBH)/James Hutton Institute (JHI), Dundee, Scotland. robbie.waugh@hutton.ac.uk.ORCID http://orcid.org/0000-0003-1045-3065
Funding
Carlsbergfondet (Carlsberg Foundation) CF15-0236Carlsbergfondet (Carlsberg Foundation) CF15-0476Carlsbergfondet (Carlsberg Foundation) CF15-0672Genome Canada (Génome Canada) CTAG2Grains Research and Development Corporation (Grains Research & Development Corporation) UMU1806-002RTXNational Science Foundation (NSF) ERA-CAPS project 1844331RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/S020160/1RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/X018636/1RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) ERA-CAPS BB/S004610/1Rural and Environment Science and Analytical Services Division (Scottish Government's Rural and Environment Science and Analytical Services Division) KJHI-B1-2
Abstract
A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.
Indexed as
HordeumTranscription, GeneticTranscriptomeGene Expression ProfilingGene Expression Regulation, PlantGenome, PlantGenotypeSequence Analysis, RNA
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