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Bitter pit disorder development: Evidence from transcriptomic and cellular analysis in different tissues.

Yali Li1, Zuanhong Xu2, Wenjun Tan2

  • 1College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.

Plant Physiology and Biochemistry : PPB
|May 9, 2026
PubMed
Summary

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Bitter pit in apples is poorly understood. This study used transcriptomics to reveal that programmed cell death and auxin signaling are key factors in bitter pit development, involving complex gene regulation.

Area of Science:

  • Plant Physiology
  • Molecular Biology
  • Biochemistry

Background:

  • Bitter pit (BP) is a significant physiological disorder affecting apple fruit quality and marketability.
  • The underlying molecular mechanisms and genetic regulation of BP remain largely unknown, hindering effective management strategies.

Purpose of the Study:

  • To elucidate the molecular pathways and gene expression changes associated with bitter pit development in apple fruit.
  • To identify key genes, transcription factors, and signaling pathways involved in the physiological disorder.

Main Methods:

  • Transcriptomic analysis (RNA-Seq) was performed on healthy and disordered apple flesh and pericarp tissues.
  • Differential gene expression analysis identified genes involved in various biological processes.
Keywords:
Apple fruitBitter pitCellular observationProgrammed cell deathTranscriptome

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  • Fluorescence staining, transmission electron microscopy, and DNA ladder assays were used to investigate programmed cell death (PCD).

    • Main Results:

    • Differentially expressed genes (DEGs) were significantly associated with programmed cell death (PCD), calcium signaling, cell wall modification, respiration, and redox homeostasis.
    • Multiple hormone signaling pathways, particularly auxin signaling, were implicated, with DEGs showing upregulation in disordered flesh.
    • WRKY, MYB, bZIP, and NAC transcription factors were identified as potential key regulators of BP.
    • Evidence suggests PCD occurs during BP development, with specific PCD-related genes showing altered expression.
    • Genes involved in secondary metabolism (cytochrome P450, squalene cyclase, glutathione S-transferase) and reactive oxygen species (ROS) accumulation were linked to BP.

    Conclusions:

    • Bitter pit development involves a complex interplay of programmed cell death, hormonal signaling (especially auxin), and metabolic pathways.
    • Transcriptomic data reveals coordinated local and long-distance responses contributing to BP progression.
    • Identified genes and pathways provide potential targets for future research and management of apple bitter pit.