Combes Marie-Christine auteur aut IRD Joët Thierry auteur aut IRD Stavrinides A. K. auteur aut IRD Lashermes Philippe auteur aut IRD text journalArticle eng text/pdf born digital access Background and Aims Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica. Methods A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways. Key Results Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species. Conclusions Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds. specialized Allopolyploidy Coffea arabica gene expression homeologue expression bias caffeine additivity expression-level dominance phenotype desiccation tolerance seed 076 054 [Early access] [14 p.] 2022 0305-7364 https://www.documentation.ird.fr/hor/fdi:010084735 10.1093/aob/mcac041 0305-7364 [F B010084735] https://www.documentation.ird.fr/hor/fdi:010084735 https://www.documentation.ird.fr/intranet/publi/2022-06/010084735.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2022-06-03 2022-06-03 fdi:010084735 fre