Transcriptome profiling reveals AGAMOUS-LIKE genes associated with the reprogramming of mature endosperm cell fate in hardy kiwifruit

Abstract Background Mature endosperm is a highly differentiated storage tissue with limited capacity for developmental reprogramming. Although in vitro culture can induce endosperm dedifferentiation and regeneration in hardy kiwifruit ( Actinidia arguta ), the transcriptional changes associated with this transition remain poorly understood. This study investigated early reprogramming of mature endosperm in two cultivars with contrasting culture responses, focusing on AGAMOUS-LIKE ( AGL ) transcription factors. Methods RNA sequencing was performed on freshly isolated endosperm and explants cultured for 14 days on thidiazuron-containing medium from cultivars 'Bingo' and 'Weiki', with three biological replicates per condition. De novo transcriptome assembly was followed by functional annotation, differential expression analysis and GO and KEGG enrichment analyses. Selected AGL candidates were further characterised using sequence alignment, conserved-domain analysis, maximum-likelihood phylogenetic reconstruction and three-dimensional protein modelling. Results The assembly yielded 149,380 unigenes. Comparisons between cultured and freshly isolated endosperm identified 29,814 differentially expressed genes in 'Bingo' and 35,893 in 'Weiki', with 21,365 shared between the two comparisons. Culture-associated transcriptional changes involved ribosome biogenesis, protein synthesis, cell wall organisation, transport and carbohydrate and lipid metabolism. AP2/EREBP , WRKY and MYB transcription factors exhibited shared induction patterns alongside cultivar-dependent responses in additional regulatory families. Transcripts annotated as AGL15 , AGL61 and AGL62 were up-regulated in both cultivars, whereas additional AGL61 -, AGL62 - and AGL80 -related transcripts displayed distinct expression patterns. Sequence, domain and phylogenetic analyses supported the assignment of selected candidates to Type I and Type II MADS-box lineages. Structural modelling provided complementary support for selected annotations while identifying divergent candidates requiring cautious interpretation. Conclusions This study provides a transcriptomic resource for early reprogramming of mature endosperm in A. arguta and identifies AGL homologues as candidate regulators of this transition. The concurrent induction of transcripts related to endosperm development and embryogenic competence suggests that mature endosperm reprogramming may recruit elements of both developmental programmes. These findings establish a basis for functional testing of AGL candidates and investigation of cultivar-dependent endosperm regeneration.