Chinese cabbage is one of the major vegetable crops in northern Asia. Its leaves are the major organ for photosynthesis and production, and leaf color directly influences its yield and quality. Here, we obtained a pale green mutant pgm3. This mutant line was derived from EMS mutagenesis of Chinese cabbage DH line FT. pgm3 exhibited chlorosis and etiolation, delayed growth, reduced photosynthetic pigment content and net photosynthetic rates, and impaired development of the chloroplast inner membrane system. Genetic analysis revealed that the pale green phenotype was controlled by a single recessive nuclear gene, Brpgm3. Mutmap analysis indicated that Brpgm3 is located on a 13.9 Mb region in A03. Within this region, a single SNP (A03: 7194530) with an SNP-index of 1, located in BraA03g015750.3C (BrClpC1), was identified from 40 differential SNPs. KASP genotyping demonstrated that the SNP co-segregated with the pale green phenotype in the F₂ population. Sanger sequencing confirmed a G-to-A SNP in exon 4 of BrClpC1, which resulted in an amino acid substitution from S to G. Furthermore, multiple sequence alignment of homologs from 28 species demonstrated that this mutated residue is highly conserved. BrClpC1 was predominantly expressed in leaves and exhibited the highest transcript abundance among the nine members of the Class I Clp gene family in Brassica rapa. This is the first report identifying ClpC1 in Brassica crops. Our results not only confirmed BrClpC1 as a strong candidate gene for the pale green mutant of Chinese cabbage, but also highlighted BrClpC1 as a target for chloroplast biology research in Brassica crops.

Leafy head formation is a critical agronomic trait that determines the yield and quality of Chinese cabbage (Brassica rapa), involving complex morphological transitions. While BEL1-like homeodomain (BLH) transcription factors regulate development, their specific roles in heading remain elusive. To systematically identify the BraBLH gene family and elucidate its expression networks and regulatory functions during leafy head formation, a total of 36 BraBLH genes were identified. The phylogenetic analysis revealed that Brassica rapa had a specific clade (Group II). A high-resolution spatiotemporal expression framework for the BraBLH family was constructed. Subsequently, comparative transcriptomics of heading, non-heading, and GA₃-treated heading plants highlighted multiple differentially expressed BraBLH genes, suggesting that this gene family may contribute to the regulation of leafy head formation in Chinese cabbage. Subsequently, a high-resolution spatiotemporal expression framework for the BraBLH family was constructed. Within this framework, BraBLH5 emerged as a pivotal node integrating GA signaling, peaking during the rosette stage to initiate heading. In contrast, a distinct negative module (BraBLH9/26) was significantly upregulated in the non-heading line. Spatial profiling further revealed functional compartmentalization within the family, where specific members maintained shoot apical meristem identity, whereas others drove inner leaf expansion and incurvature. Furthermore, subcellular localization analysis confirmed that BraBLH5 was localized to the nucleus. Ultimately, this systems-level study elucidates a transcriptome-driven framework for heading, highlighting a GA-mediated BraBLH5 mechanism and providing valuable candidates for Brassica functional genomics.