Salt Stress Disrupts Color Stability in Black Rice Pericarp: Integrated Transcriptomic and Physiological Metabolism Analyses Reveal Dual Regulation of Anthocyanin Metabolism

Anthocyanins are the primary colorants and antioxidants in black rice pericarp. However, the mechanisms by which salt stress affects anthocyanin metabolism and color remain unclear. Here, a two-year field experiment was performed on two black rice varieties under irrigation with freshwater, 2.0‰ brine, and 4.0‰ brine. Results showed that salt stress decreased the anthocyanin content and antioxidant capacity while increasing the <i>L</i>*, <i>a</i>*, <i>b</i>*, and Δ<i>E</i> values in pericarp. This color loss resulted from dual regulatory mechanisms: salt stress suppressed the anthocyanin biosynthetic pathway (by downregulating key genes including <i>PAL</i>, <i>4CL</i>, <i>CHS</i>, <i>CHI</i>, <i>F3H</i>, <i>ANS</i>, and their corresponding enzyme activities) and activated its degradation (by upregulating <i>BGLU</i> and <i>Prx</i> genes), thereby reducing the accumulation of the main anthocyanins (cyanidin-3-<i>O</i>-glucoside and peonidin-3-<i>O</i>-glucoside). Fifteen transcription factors were identified as candidates for regulating anthocyanin metabolism. This study provides new insights into salt-induced color loss and offers potential targets for breeding salt-tolerant black rice varieties with stable pigments.