Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation

Synonymous mutations, once known as "silent" mutations, are increasingly attracting the interest of biologists. Although they may affect transcriptional or post-transcriptional processes, their impact on biological traits remains under-investigated, particularly at the organismal level. Here, we identified two closely linked, epistatically interacting genes: YTH1, an RNA N⁶-methyladenosine (m⁶A) reader, and ACS2, an aminocyclopropane-1-carboxylic acid (ACC) synthase, which contribute to cucumber fruit length domestication. The causative mutation in ACS2 is a synonymous substitution at 1287C>T. In wild cucumber, ACS2^1287C results in m⁶A modification on nearby adenosine residues and the formation of loose RNA structural conformations. YTH1 recognizes the m⁶A modification, alters the folding equilibrium toward the weakest RNA structural conformation, and increases the ACS2 protein level, resulting in shorter fruit. In cultivated cucumber, ACS2^1287T disrupts m⁶A methylation and forms compact RNA structural conformations, leading to attenuated protein production and fruit elongation. This study provides genetic evidence of synonymous variation shaping a biological trait through epitranscriptomic regulations.