BMC Genomics (Aug 2025)

Organic acid accumulation pattern and its key genes in Chinese cherry fruits

  • Yan Wang,
  • Jingting Zhou,
  • Xiaocheng Liu,
  • Lisu Hao,
  • Yunfan Yang,
  • Shuaiwei Yang,
  • Hao Wang,
  • Zhenshan Liu,
  • Jing Zhang,
  • Wen He,
  • Yuanxiu Lin,
  • Yunting Zhang,
  • Mengyao Li,
  • Yong Zhang,
  • Ya Luo,
  • Haoru Tang,
  • Qing Chen,
  • Xiaorong Wang

DOI
https://doi.org/10.1186/s12864-025-11969-0
Journal volume & issue
Vol. 26, no. 1
pp. 1 – 15

Abstract

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Abstract Background Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit species native to southwestern China, plays a key role in regional agriculture. Organic acid composition is crucial for determining organoleptic quality of Chinese cherry, yet the underlying regulatory mechanisms remain unclear. Results In this study, we analyzed organic acid composition in mature fruits from 34 Chinese cherry accessions and tracked dynamic changes throughout fruit development in two landraces with distinct acidity levels (high and low), via HPLC and transcriptomics. Malic acid is the predominant organic acid component, which accounted for 73.66% of total acids. The high-acid landrace exhibited very rapid malate accumulation and relatively fast degradation, while the low-acid landrace showed minor changes in malate levels throughout fruit development. A total of 7,698 DEGs were clustered into six clusters, with DEGs from three clusters being significantly enriched in the “pyruvate metabolism” and “TCA cycle” pathways. Key genes involved in malate biosynthesis (cMDH, PEPC2) and transport (ALMT4, VHP) were up-regulated in the high-acid landrace, while NADP-ME, a gene associated with malate degradation, was down-regulated. Co-expressed network analysis highlighted strong correlations between key structural genes and transcription factors (MYB, ARF, AP2, and bHLH). Notably, CpODORANT1like and CpARF2Blike were identified as potential regulators of acidity, modulating NADP-ME and PEPC2 expression, respectively. These candidate genes were validated through an integrated analysis of phenotypic data and expression pattern of 34 genotypes. Conclusions Our results suggest that malate accumulation in Chinese cherry is regulated at both the metabolic and vacuolar storage levels. This study deepens our understanding of the mechanisms regulating fruit acidity in Chinese cherry, which could inform future breeding efforts aimed at improving fruit flavor.

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