Population genomic insights into the domestication of <i>Brassica juncea</i> var. <i>tumida</i>

<i>Brassica juncea</i> var. <i>tumida</i>, commonly known as Zha Cai, is a pickled stem mustard widely cultivated in southern China. Its most distinctive trait is the swollen stem, which serves as the primary economic organ for harvest. However, the origin and domestication history of <i>tumida</i> remain unclear, hindering genetic improvement and molecular breeding efforts. Here, we assembled a chromosome-level genome of the landrace 'YAXY' from Chongqing-the center of <i>tumida</i> diversity-totaling 909.1 Mb with a contig N50 of 4.17 Mb. We also collected and resequenced 203 <i>tumida</i> accessions across southern China. By integrating the 'YAXY' reference genome with population data, we generated the first comprehensive <i>tumida</i> variation dataset, comprising 1.38 million single-nucleotide polymorphisms (SNPs) and 0.27 million insertions and deletions (InDels). Joint analysis of the newly sequenced <i>tumida</i> population and 504 public <i>B. juncea</i> datasets revealed that <i>tumida</i> and leafy types from southern China share a common origin from local oilseed mustard. <i>Tumida</i> domestication was accompanied by a strong genetic bottleneck. Additionally, we conducted genome-wide association studies (GWAS) for 21 agronomic traits and identified candidate genes linked to key domestication traits in <i>tumida</i>. For the swollen stem trait, selective sweep and GWAS analyses jointly identified candidate genes likely involved in lignification. Transcriptome data showed consistent differential expression of <i>BjuA05g15010</i>, the <i>Arabidopsis SAGL1</i> ortholog, across all swelling stages, suggesting a key role in stem morphogenesis. Collectively, our findings shed light on <i>tumida</i> evolution and provide valuable genomic resources and candidate genes to support genetic research and breeding in <i>B. juncea</i>.