Simple item page
 

Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos

dc.abstract.enBackground Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic and metabolomic changes in ABA-treated germinating barley (Hordeum vulgare) embryos. To map ABA-responsive gene expression across embryonic tissues, we employed the Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied in plant tissues, enabled the precise localization of gene expression across six embryo regions, offering insights into tissue-specific expression patterns that cannot be resolved by traditional RNA-seq. Results Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses linked ABA-inhibited genes to energy metabolism, lignin biosynthesis, cell wall organization, and photosynthesis, while induced genes were associated with environmental adaptation and phytohormone signaling. Differentially expressed genes (DEGs) correlated with metabolites involved in phytohormone pathways, including gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, and ABA metabolism. Comparisons with developing seed transcriptomes suggested an ABA-associated gene expression signature in embryos. Spatial transcriptomics technique made possible the precise identification of ABA-induced transcriptional changes within distinct embryonic tissues. Conclusions Integrating transcriptomics, metabolomics and spatial transcriptomics defined the molecular signature of ABA-induced modulation of phytohormonal crosstalk, energy metabolism, and tissue-specific gene activity in germinating seeds. The successful use of spatial transcriptomics adds a novel layer of resolution for understanding tissue-specific ABA responses during barley seed germination. These findings offer new insights into the ABA role in seed germination and potential strategies for enhancing crop resilience.
dc.affiliationWydział Rolnictwa, Ogrodnictwa i Biotechnologii
dc.affiliation.instituteKatedra Biochemii i Biotechnologii
dc.contributor.authorSybilska, Ewa
dc.contributor.authorHaddadi, Bahareh Sadat
dc.contributor.authorMur, Luis A. J.
dc.contributor.authorBeckmann, Manfred
dc.contributor.authorHryhorowicz, Szymon
dc.contributor.authorSuszyńska-Zajczyk, Joanna
dc.contributor.authorKnaur, Monika
dc.contributor.authorPławski, Andrzej
dc.contributor.authorDaszkowska-Golec, Agata
dc.date.access2025-06-17
dc.date.accessioned2025-06-17T12:01:47Z
dc.date.available2025-06-17T12:01:47Z
dc.date.copyright2025-05-10
dc.date.issued2025
dc.description.abstract<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic and metabolomic changes in ABA-treated germinating barley (<jats:italic>Hordeum vulgare</jats:italic>) embryos. To map ABA-responsive gene expression across embryonic tissues, we employed the Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied in plant tissues, enabled the precise localization of gene expression across six embryo regions, offering insights into tissue-specific expression patterns that cannot be resolved by traditional RNA-seq.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses linked ABA-inhibited genes to energy metabolism, lignin biosynthesis, cell wall organization, and photosynthesis, while induced genes were associated with environmental adaptation and phytohormone signaling. Differentially expressed genes (DEGs) correlated with metabolites involved in phytohormone pathways, including gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, and ABA metabolism. Comparisons with developing seed transcriptomes suggested an ABA-associated gene expression signature in embryos. Spatial transcriptomics technique made possible the precise identification of ABA-induced transcriptional changes within distinct embryonic tissues.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Integrating transcriptomics, metabolomics and spatial transcriptomics defined the molecular signature of ABA-induced modulation of phytohormonal crosstalk, energy metabolism, and tissue-specific gene activity in germinating seeds. The successful use of spatial transcriptomics adds a novel layer of resolution for understanding tissue-specific ABA responses during barley seed germination. These findings offer new insights into the ABA role in seed germination and potential strategies for enhancing crop resilience.</jats:p> </jats:sec>
dc.description.accesstimeat_publication
dc.description.bibliographyil., bibliogr.
dc.description.financepublication_nocost
dc.description.financecost0,00
dc.description.if4,3
dc.description.points140
dc.description.versionfinal_published
dc.description.volume26
dc.identifier.doi10.1186/s12870-025-06654-z
dc.identifier.issn1471-2229
dc.identifier.urihttps://sciencerep.up.poznan.pl/handle/item/2861
dc.identifier.weblinkhttps://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-025-06654-z
dc.languageen
dc.relation.ispartofBMC Plant Biology
dc.relation.pagesart. 619
dc.rightsCC-BY
dc.sciencecloudnosend
dc.share.typeOTHER
dc.subject.enABA
dc.subject.enbarley
dc.subject.enembryo
dc.subject.enmetabolomics
dc.subject.enseed germination
dc.subject.enspatial transcriptomics
dc.subject.entranscriptomics
dc.titleMapping the molecular signature of ABA-regulated gene expression in germinating barley embryos
dc.typeJournalArticle
dspace.entity.typePublication
oaire.citation.issue1
oaire.citation.volume25