Physiological Response and Transcriptome Analysis of Waxy Near-Isogenic Lines in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) Under Drought Stress

To identify key genes involved in drought stress response among Chinese cabbage materials with different drought resistance, a pair of waxy near-isogenic lines (NILs) of Chinese cabbage were used as materials, and a 10% polyethylene glycol (PEG) 6000 solution was employed to simulate drought stress. A comparative analysis of phenotypes, physiology, and transcriptomes under drought stress was conducted in this study. Compared with the non-waxy material T065-2, the waxy material T065-1 exhibited 5068, 5512, 5210, and 5875 significantly differentially expressed genes (DEGs) at 0, 6, 12, and 24 h under drought stress, respectively. These DEGs were primarily enriched in “response to oxygen levels” and “secondary metabolite biosynthesis” biological processes and “biosynthesis of secondary metabolites” and “glucosinolate biosynthesis” pathways. Combined with gene function annotation, 26 genes related to the abscisic acid (ABA) signaling pathway (e.g., PYL2, PYL6, SnRK2.5, and SnRK2.10), 63 genes associated with wax synthesis and transport (e.g., MAH1, CER3a, ABCG25, and LTPG1), and 84 transcription factor genes (e.g., ERF, WRKY, and MYB) were identified, all of which showed significant differential expression in the waxy NILs of Chinese cabbage, potentially participating in drought stress response. The reliability of the transcriptomic analysis was validated using qRT-PCR. These findings provide a crucial theoretical foundation for exploring drought-resistant molecular markers and editing targets in Chinese cabbage, significantly accelerating the breeding of superior drought-resistant varieties.