Transcriptomic Profiling Uncovers Molecular Basis for Sugar and Acid Metabolism in Two Pomegranate (Punica granatum) Varieties

Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. Through integrated physiological and transcriptomic analysis of pomegranate varieties 'Sharp Velvet' with high acid content and 'Azadi' with low acid content, this study demonstrated that the differences in flavor between the two varieties were mainly caused by differences in citric acid content rather than in soluble sugar content. Transcriptome profiling identified 11 candidate genes involved in sugar and acid metabolism, including three genes associated with soluble sugar metabolism (<i>FBA1</i>, <i>SS</i>, and <i>SWEET16</i>) and eight genes linked to organic acid metabolism (<i>ADH1</i>, <i>GABP1</i>, <i>GABP2</i>, <i>GABP3</i>, <i>GABP4</i>, <i>ICL</i>, <i>ME1</i>, and <i>PDC4</i>). These data indicated that differences in citric acid content between the two varieties mainly stemmed from differences in the regulation of the citric acid degradation pathway, which relies mainly on the γ-aminobutyric acid (GABA) branch rather than the isocitric acid lyase (ICL) pathway. Citric acid accumulation in pomegranate fruit was driven by metabolic fluxes rather than vesicular storage capacity. Weighted gene co-expression network analysis (WGCNA) uncovered a significant citric acid content associated module (r = -0.72) and predicted six core transcriptional regulators (<i>bHLH42</i>, <i>ERF4</i>, <i>ERF062</i>, <i>WRKY6</i>, <i>WRKY23</i>, and <i>WRKY28</i>) within this network. Notably, <i>bHLH42</i>, <i>ERF4</i>, and <i>WRKY28</i> showed significant positive correlations with citric acid content, whereas <i>ERF062</i>, <i>WRKY6</i>, and <i>WRKY23</i> demonstrated significant negative correlations. Our findings provide comprehensive insights into the genetic architecture governing soluble sugars and organic acids homeostasis in pomegranate, offering both a novel mechanistic understanding of fruit acidity regulation and valuable molecular targets for precision breeding of fruit quality traits.