Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis

MdPG1 encoding polygalacturonase in apple (Malus x domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNPA/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNPA, rather than the SNPC, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNA(PG1), in the promoter of MdPG1 was a causative variant. lncRNA(PG1) was specifically expressed in fruit tissues postharvest. lncRNA(PG1) could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.

Automated summary

MdPG1 encoding polygalacturonase is a key gene related to fruit firmness and texture variations in apple. We identified a SNPA/C variant in the promoter region of MdPG1 and found that the promoter with SNPA could be strongly bound and activated by MdCBF2, while the promoter with SNPC could not. We also discovered a novel long non-coding RNA, lncRNA(PG1), in the promoter of MdPG1, which was a causative variant. Our study provides new insights into the genetic regulation of MdPG1 allele expression and has implications for apple breeding.