A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation.

SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone acetyltransferases and deacetylases, which play crucial roles in the regulation of transcription activation. There is an increasing research focus on histone deacetylation in crops, but the role of histone deacetylase genes (HDACs) in tomato has not been elucidated. With the aim of characterizing the tomato RPD3/HDA1 family histone deacetylase genes, SlHDA3 was isolated and its RNA interference (RNAi) lines was obtained. The fruit of SlHDA3 RNAi lines exhibited accelerated ripening process along with short shelf life characteristics. The accumulation of carotenoid was increased due to the alteration of the carotenoid pathway flux. Climacteric ethylene production also stimulated along with significantly up-regulated expression of ethylene biosynthetic genes (ACS2, ACS4, ACO1 and ACO3) and fruit ripening-associated genes (RIN, E4, E8, PG, Pti4, LOXB, Cnr and TAGL1) in SlHDA3 RNAi lines. Besides, fruit cell wall metabolism-associated genes (HEX, MAN, TBG4, XTH5 and XYL) were enhanced in transgenic lines. Relative to wild type (WT) plants, SlHDA3 RNAi seedlings displayed shorter hypocotyls and more sensitivity to ACC (1-aminocyclopropane-1-carboxylate). These results indicated that SlHDA3 is involved in the regulation of fruit ripening by affecting ethylene biosynthesis and carotenoid accumulation.