A comprehensive analysis to speculate the role of trithorax genes in photoperiod-mediated tuberization in potato and comparison with storage root crops

Abstract

Background: Trithorax genes are crucial epigenetic regulators, driving gene activation through histone tail modifications and chromatin remodeling. These genes are fundamental in multifaceted aspects of plant development. However, our knowledge of trithorax genes is predominantly focused on model plant Arabidopsis, particularly in flowering. Considering the similarities between flowering and potato tuberization, we hypothesise the role of trithorax genes in stolon-to-tuber transition. To explore their origin, diversification, and molecular conservation, we conducted a comprehensive bioinformatic analysis of trithorax proteins in selective plant lineages with an emphasis on potato. Further, selected trithorax members were analyzed in five storage root crops to assess their potential role in storage organ development. Results: We identified 268 trithorax family members across 9 species, including 2 algae, 2 bryophytes, and 5 angiosperms, categorised into three groups: SET domain proteins, chromatin remodelers, and associated proteins based on functional domains and motifs. These proteins were analyzed in potato and subsequently compared with other storage root crops. It was observed that the distribution of trithorax genes is universal among photosynthetic organisms from unicellular algae to highly evolved storage crops like potato, with the whole genome, segmental, and tandem duplications driving their expansion. The trithorax proteins cluster in unique monophyletic groups with conserved functional domains across species. The predicted physico-chemical properties, cis-regulatory elements (CREs), and transcription factors (TFs) reflected the involvement of trithorax genes in different developmental events, including tuberization in potato, stress-responsiveness, and flowering. Moreover, expression analysis confirmed the role of the identified genes in potato tuberization under photoperiod-inductive conditions. The study revealed the clustering of trithorax genes in potato into four groups of 7 slightly upregulated, 9 downregulated, and 8 highly upregulated genes during the stolon-to-swollen stolon transition stage. The functional domains and the abundance of CRE and TFs were found consistent in storage root crops as that of potato. Conclusions:We show the existence of trithorax genes in photosynthetic organisms and demonstrate their potential role in photoperiod-mediated potato development. The gene regulatory mechanism appears to be conserved amongst potato and other storage root crops. This study may act as a prelude for further biotechnological interventions in potato and other storage crops.