Physiological and Transcriptomic Analyses Reveal Temporal Drought Responses in Kochia prostrata

Drought adaptation in desert C4 species requires coordinated physiological and transcriptional regulation, but the temporal progression of these responses remains poorly resolved in Kochia prostrata. In this study, progressive drought stress was imposed by withholding irrigation for 7, 14, and 21 d, and physiological traits, osmotic adjustment, oxidative status, antioxidant enzyme activities, and transcriptomic responses were systematically evaluated. Transcriptome profiling was performed using drought-treated and time-matched well-watered leaves with three biological replicates per group. Leaf relative water content and visible phenotypic changes remained relatively stable after 7 d but deteriorated markedly during prolonged drought. Soluble sugar accumulation increased from day 14, whereas MDA, O2−, and H2O2 accumulation became prominent mainly on day 21. Antioxidant enzymes exhibited distinct temporal patterns, with early activation of CAT, late reduction in POD activity, and delayed induction of SOD. Transcriptome analysis identified 18,550, 20,362, and 46,178 differentially expressed genes at 7, 14, and 21 d of drought treatment, respectively. A core set of 1530 genes responded consistently throughout drought progression, including 1253 upregulated and 277 downregulated genes. Shared upregulated genes were mainly associated with photosynthesis, carbon fixation, carbon metabolism, and DNA repair-related processes, while AP2/ERF, WRKY, and NAC were the predominant transcription factor families among the consistently upregulated genes. These findings reveal distinct temporal patterns of physiological and transcriptional responses in K. prostrata, characterized by changes in antioxidant enzyme activities, soluble sugar accumulation, and extensive transcriptional responses associated with oxidative stress under prolonged water withholding.