An InDel variant in the promoter of the NAC transcription factor MdNAC18.1 plays a major role in apple fruit ripening

作者：Qianyu Yue, Yinpeng Xie, Xinyue Yang, Yuxin Zhang, Zhongxing Li, Yunxiao Liu, P.Y. Cheng, Ruiping Zhang, Yue Yu, Xiao‐Fei Wang, Liao Liao, Yuepeng Han, Tao Zhao, Xuewei Li, Hengtao Zhang, Fengwang Ma, Qingmei Guan · 发表于：The Plant Cell · 年份：2024 · DOI：10.1093/plcell/koaf007 · 被引用次数：22 · 研究领域：Postharvest Quality and Shelf Life Management、Plant Physiology and Cultivation Studies、Plant Gene Expression Analysis

A complex regulatory network governs fruit ripening, but natural variations and functional differentiation of fruit ripening genes remain largely unknown. Utilizing a genome-wide association study (GWAS), we identified the NAC family transcription factor MdNAC18.1, whose expression is closely associated with fruit ripening in apple (Malus × domestica Borkh.). MdNAC18.1 activated the transcription of genes related to fruit softening (Polygalacturonase, PG) and ethylene biosynthesis (1-aminocyclopropane-1-carboxylic acid synthase, ACS), thereby promoting fruit ripening of apple and tomato (Solanum lycopersicum). There were two single-nucleotide polymorphisms (SNP-1,545 and SNP-2,002) and a 58-bp insertion-deletion (InDel-58) in the promoter region of MdNAC18.1. Among these, InDel-58 serves as the main effector in activating the expression of MdNAC18.1 and driving fruit ripening. InDel-58 determines the binding affinity of the class D MADS-box protein AGAMOUS-LIKE 11 (MdAGL11), a negative regulator of fruit ripening. The InDel-58 deletion in the early-ripening genotype reduces the inhibitory effect of MdAGL11 on MdNAC18.1. Moreover, MdNAC18.1 and its homologous genes originated from a common ancestor across 61 angiosperms, with functional diversification attributed to tandem replications that occurred in basal angiosperms. In summary, our study revealed how a set of natural variations influence fruit ripening and explored the functional diversification of MdNAC18.1 during evolut...