# Metabolic profiling of red-fleshed apple and functional characterization of MdERF072 in anthocyanin biosynthesis

## TL;DR

Red-fleshed apples have higher levels of health-boosting flavonoids in their edible flesh, and a gene called MdERF072 helps control the production of red pigments and other beneficial compounds.

## Contribution

Identified MdERF072 as a key transcriptional activator in anthocyanin biosynthesis in red-fleshed apples.

## Key findings

- Red-fleshed apples show increased polymethoxyflavones and cyanidin-3-O-glucoside, but reduced flavan-3-ols and proanthocyanidins.
- Transcriptomic analysis shows upregulation of flavonoid pathway genes and downregulation of LAR and ANR in red-fleshed apples.
- MdERF072 was found to activate anthocyanin biosynthesis and upregulate structural genes in the pathway.

## Abstract

Red-fleshed apples, with their flavonoid-rich edible flesh, offer superior nutritional advantages over traditional varieties, where these antioxidants are concentrated primarily in the less-consumed peel. The distinct metabolic profile of red-fleshed apples, particularly their compositional uniqueness and deposition characteristics, therefore requires systematic deconstruction through comparative metabolomics.

In this work, comparative metabolomics of three apple cultivars with distinct flesh coloration revealed a substantial upregulation of specialized flavonoids in the red-fleshed variety. Notably, we identified an accumulation of polymethoxyflavones (PMFs) with antitumor activity and found cyanidin-3-O-glucoside to be the predominant anthocyanin responsible for red pigmentation in red-fleshed apple. Conversely, the accumulation of flavan-3-ols and proanthocyanidins (PAs) was decreased in red-fleshed apple. Volatile metabolome analysis interestingly demonstrated that the majority of volatile organic compounds (VOCs), such as esters, terpenoids, and alcohols, were significantly more abundant in the red-fleshed apple. Transcriptomic profiling revealed the upregulation of key flavonoid pathway genes, including early synthase genes (PAL, C4H, 4CL, CHS) and anthocyanin-specific genes (UFGT, GST), in red-fleshed apple, consistent with the observed accumulation of PMFs and anthocyanins in the flesh. Conversely, the downregulation of LAR and ANR accounts for the reduced biosynthesis of flavan-3-ols and PAs in the red-fleshed apple. Systematic TF screening, expression analyses and transient verification assays revealed that MdERF072 acts as an important transcriptional activator of anthocyanin biosynthesis and potentially upregulates the expression of structural genes in the anthocyanin pathway.

Overall, this work reveals the metabolic and transcriptional basis of flavonoid enrichment in red-fleshed apple and provides a foundation for breeding nutritionally improved cultivars.

The online version contains supplementary material available at 10.1186/s12870-025-07987-5.