The effects of foliar spraying of organic selenium and nano-selenium fertilizer on pak choi (Brassica chinensis var. pekinensis. cv. ‘Suzhouqing’) under low temperature were investigated. The impacts on plant growth, antioxidant capacities, and nutritional profiles were studied. Exogenous selenium was applied at three rates: 5, 10, 20 mg L−1, and RNA-Seq technology was used to sequence the transcriptome of leaves. The study revealed that selenium influenced leaf weight and total selenium content through three main mechanisms. First, it protected photosynthetic pigments and boosted photosynthetic capacity by up-regulating LHca2, LHcb1, LHca1, and LHcb4. Second, it enhanced antioxidant capacity by elevating the expression of genes such as superoxide dismutase and monodehydroascorbic acid. Third, it facilitated selenium absorption through endocytosis, transported selenium using the ABC transport gene family, and regulated selenium metabolism-related genes like cysteine synthetase and glutaredoxin. Nine hub genes identified with a weighted gene co-expression network analysis were closely associated with these mechanisms. The results of a functional enrichment analysis were consistent with those of a Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis conducted on DEGs, thus confirming the reliability of these findings. Therefore, this study can provide scientific basis for pak choi production with selenium fortification by selenium application.
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