Comparative enzymatic browning transcriptome analysis of three apple cultivars unravels a conserved regulatory network related to stress responses

Bielsa González, Francisco Javier; Grimplet, Jérôme; Irisarri, Patricia; Miranda Jiménez, Carlos; Errea, Pilar; Pina, Ana

Comparative enzymatic browning transcriptome analysis of three apple cultivars unravels a conserved regulatory network related to stress responses

dc.contributor.author	Bielsa González, Francisco Javier
dc.contributor.author	Grimplet, Jérôme
dc.contributor.author	Irisarri, Patricia
dc.contributor.author	Miranda Jiménez, Carlos
dc.contributor.author	Errea, Pilar
dc.contributor.author	Pina, Ana
dc.contributor.department	Agronomía, Biotecnología y Alimentación	es_ES
dc.contributor.department	Agronomia, Bioteknologia eta Elikadura	eu
dc.contributor.department	Institute for Multidisciplinary Research in Applied Biology - IMAB	en
dc.date.accessioned	2025-06-17T11:01:31Z
dc.date.available	2025-06-17T11:01:31Z
dc.date.issued	2025-04-12
dc.date.updated	2025-06-17T10:50:21Z
dc.description.abstract	Enzymatic browning (EB) endangers the adaptation of apple fruit cultivars to new markets, affecting organoleptic properties and producing economic losses. Polyphenol oxidases and polyphenol compounds play a key role in EB development in apple. However, the regulation of apple response to EB remains to be uncovered. In this study, three apple cultivars with different EB phenotypes ranging from low to high browning in apple pulp were used to study transcriptomic changes over time after fresh cutting (0, 30 and 60 min). This study allowed the identification of 1448 differentially expressed genes (DEGs), revealing both shared and genotype-specific responses, particularly in the affected metabolic pathways associated with EB. At 60 min (T60 vsT0), 77 DEGs were shared by all genotypes, suggesting a conserved regulatory network. This network included genes encoding for protein families such as calcium-binding proteins, heat-shock proteins, redox-responsive transcription factors, WRKY family transcription factors, zinc finger family proteins and disease resistance proteins among others. A co-expressed gene cluster, identified through Weighed Gene Co-Expression Network Analysis (WGCNA), was found to correlate with EB and included 323 genes enriched in several biological terms according to Gene Ontology analysis. Moreover, a more detailed analysis of identified WGCNA gene cluster regulatory sequences allowed the detection of cis-regulatory elements belonging to CAMTA, WRKY and WUSCHEL transcription factor families. The identification of these sequences alongside with an abundant and diverse amount of overexpressed transcription factors from various families (WRKY, ERF, GRAS, GATA, etc.) point out to a highly regulated stress-response that is strictly connected to innate plant immunity. These findings provide valuable insights into the molecular mechanism involved in apple fresh-cut browning and offer new potential targets for EB regulation.	en
dc.description.sponsorship	This work has been funded by PID 2019 108081 RR Project (funded by MCIN/AEI 10 13039 501100011033 and the consolidated group A12 of Gobierno de Aragón - European social fund of the European Union.
dc.format.mimetype	application/pdf
dc.format.mimetype	application/zip
dc.identifier.citation	Bielsa, F. J., Grimplet, J., Irisarri, P., Miranda, C., Errea, P., Pina, A. (2025). Comparative enzymatic browning transcriptome analysis of three apple cultivars unravels a conserved regulatory network related to stress responses. BMC Plant Biology, 25, 1-25. https://doi.org/10.1186/s12870-025-06445-6.
dc.identifier.doi	10.1186/s12870-025-06445-6
dc.identifier.issn	1471-2229
dc.identifier.uri	https://academica-e.unavarra.es/handle/2454/54234
dc.language.iso	eng
dc.publisher	BMC
dc.relation.ispartof	BMC Plant Biology (2025), núm. 467
dc.relation.projectID	info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-108081RR-C21/ES/
dc.relation.projectID	info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-108081RR-C22/ES/
dc.relation.publisherversion	https://doi.org/10.1186/s12870-025-06445-6
dc.rights	© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it.
dc.rights.accessRights	info:eu-repo/semantics/openAccess
dc.rights.uri	http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject	Cis-regulatory elements	en
dc.subject	Differentially expressed genes	en
dc.subject	Fresh-cut	en
dc.subject	Malus domestica × Borkh	en
dc.subject	Oxidation	en
dc.subject	RNA-seq	en
dc.subject	Transcription factor binding sites	en
dc.subject	WGCNA	en
dc.title	Comparative enzymatic browning transcriptome analysis of three apple cultivars unravels a conserved regulatory network related to stress responses	en
dc.type	info:eu-repo/semantics/article
dc.type.version	info:eu-repo/semantics/publishedVersion
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