Intronic alternative polyadenylation in MdMYB1 regulates fruit coloration in apple

MdMYB1 gene plays a crucial role in anthocyanin synthesis in apple, with truncated MdMYB1 transcripts observed in the initial stage of coloration. However, the mechanism underlying the abnormal transcription of MdMYB1 and its role in fruit coloration remains unclear. Two transcript forms, MdMYB1-S and MdMYB1-L were identified through RNA-Seq and qRT-PCR analysis. The non-functional MdMYB1-S exhibited high expression in the initial coloration stage, while MdMYB1-L was predominantly expressed in the late coloration stage. 3′ RACE confirmed that MdMYB1-S transcripts terminated with poly(A) in intron-2nd. Additionally, three transposable elements (TEs) in intron-2nd were highly methylated, and the polyadenylation signal region in this intron demonstrated increasing methylation during fruit development. We hypothesize that intronic alternative polyadenylation (APA) in conjunction with DNA methylation, regulates the transition from MdMYB1-S to MdMYB1-L, thereby promoting fruit coloration.