Non-coding RNAs in plant development: the puzzle pieces that wire an intricate regulatory network

Noncoding RNAs (ncRNAs) play dominant roles in plant growth traits, involved in architecture shaping, reproductive timing and seed development. Increasing evidence shows that ncRNAs are versatile regulators that connect chromatin, transcriptional control, and post-transcriptional gene regulation to these developmental programs. This review synthesizes current understanding of ncRNA functions in plant growth and development across five modules: leaf and shoot development, root development, floral development, fleshy fruit development, and seed development. We integrate detailed mechanisms spanning microRNAs, small interfering RNAs, long noncoding RNAs, circular RNAs, and tRNA-derived fragments, with emphasis on how these ncRNAs influence developmental traits and their regulatory crosstalk. We also discuss opportunities for rational crop engineering by tuning endogenous ncRNA pathways and by introducing synthetic regulatory circuits. Collectively, the continued advances across multi-omic platforms and computational frameworks will refine our understanding of ncRNA regulatory landscapes, providing opportunities to enhance the design of agriculturally versatile crops.