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Chinese cabbage (Brassica rapa L. ssp. Pekinensis) in the genus Brassica of the family Brassicaceae (Cruciferae) originates from China and is one of the most consumed leafy vegetables in East Asian countries. The leaf color is tightly linked with its growth, development, and yield. By screening an EMS mutagenized population of Chinese cabbage inbred line A03, we identified a yellowgreen leaf mutant ygl. This mutant developed abnormal ultrastructure in chloroplasts. Transcriptome and Gene Ontology (GO) analyses unveiled that abiotic stress response and glucan metabolism pathways were enriched in ygl compared to A03. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis reveals that differentially expressed genes were mainly associated with plant hormone signal transduction, photosynthesis, and starch and sucrose metabolism. In ygl, the expression of some photosynthetic pathway genes was significantly up-regulated, while the transcription of key genes related to carbon fixation, starch syntheses, and sugar metabolism pathways, such as RBCS1A, APS1, APL3, and SUS1, was markedly down-regulated. We also found a similar reduction trend in mRNA levels of IAA19, IAA29, and ARR4 associated with auxin and cytokinin pathways. Taken together, we uncovered transcriptional profiles for some important genes that may be responsible for leaf color development, and such gene expression repertoire may be useful for further investigation into the phenotype-to-genotype link in the ygl mutant Chinese cabbage. [ABSTRACT FROM AUTHOR]