Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage.

Introduction: Anthocyanins are important natural pigments and bioactive compounds in colored maize kernels. Although colored fresh-eating maize has attracted increasing attention because of its nutritional and functional value, the molecular basis underlying anthocyanin accumulation in maize kernels with different colors remains incompletely understood. Methods: In this study, four fresh-eating maize cultivars with contrasting kernel colors, including white (WN 2000), yellow (HN), multicolored (CN1), and black (HTN188), were used to investigate the mechanism of anthocyanin accumulation. Total anthocyanin content was measured across developmental stages, and integrated metabolomic and transcriptomic analyses were performed to identify anthocyanin-related metabolites, differentially expressed genes, and candidate regulatory factors associated with kernel pigmentation. Results: Metabolomic profiling identified 49 anthocyanin-related metabolites/features, with marked enrichment of cyanidin-, peonidin-, and pelargonidin-related compounds in the black maize cultivar HTN188. Transcriptomic analysis identified 12,557 differentially expressed genes among the four cultivars, which were mainly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, glutathione metabolism, fructose and mannose metabolism, and glyoxylate and dicarboxylate metabolism pathways. Several anthocyanin biosynthetic genes and regulatory transcription factor candidates were upregulated in anthocyanin-rich kernels, including DFR (Zm00001d011438), MYB (Zm00001d003052), bHLH (Zm00001d015990), and NAC (Zm00001d012508). In particular, the expression of DFR (Zm00001d011438) was strongly positively correlated with total anthocyanin content. Weighted gene co-expression network analysis further identified gene modules and candidate hub regulators associated with anthocyanin accumulation. Discussion: These findings provide a comparative multi-omics perspective on anthocyanin accumulation in fresh-eating maize kernels of different colors. The results suggest that the high anthocyanin accumulation in black maize is associated with the coordinated enrichment of anthocyanin-related metabolites and the upregulation of key structural genes and transcription factors. This study provides candidate genes and regulatory information for future functional studies and anthocyanin-oriented breeding in fresh-eating maize.

Drought restricts maize establishment by suppressing growth and promoting oxidative damage, while exogenous melatonin has been widely investigated for its