Genetic characteristics and agronomic traits in leafy head Chinese cabbage breeding

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is an economically important leafy vegetable cultivated widely in East Asia. Most key agronomic traits in Chinese cabbage are complex quantitative traits, and their underlying genetic regulatory mechanisms remain largely unclear. In this study, we performed a genome-wide association study (GWAS) for 15 agronomic traits using 149 homozygous inbred lines evaluated across three years of field trials. Phenotypic analysis revealed abundant variation for all 15 traits, with coefficients of variation ranging from 16.54% to 44.70% and broad-sense heritability from 0.35 to 0.81 (average = 0.62). RAD-seq yielded 260.19 Gb of clean data, from which 255,001 high-confidence variants were identified. Population structure analysis classified 149 lines into 11 genetic subpopulations, among which Pop2 represented the ancestral group. A total of 60 significant trait-associated loci were detected, several of which showed pleiotropy, while loci associated with individual traits exhibited polygenic additive effects. We predicted 66 candidate genes belonging to various gene families, including protein kinases, ubiquitin ligases, and transcription factors, which participate in key biological processes such as plant growth and development, hormone signal transduction, and cell wall biosynthesis. KASP markers for six associated loci were developed and validated in 96 accessions, and the results were highly consistent with the GWAS findings. The significant loci and candidate genes identified in this study provide novel insights into the molecular basis of agronomic traits in Chinese cabbage and offer valuable genetic resources for molecular breeding.