Genomic Analysis of 3,330 Accessions Provides Insights into the Evolutionary History and Self-Incompatibility Locus of the Brassica A Genome

Brassica rapa has been a key oilseed and vegetable crop since the Neolithic era, yet its obscure evolutionary history has hindered understanding of its domestication and the speciation of its allotetraploid descendants, Brassica napus and Brassica juncea. Here we defined pan-blocks comprising all syntenic regions from 21 B. rapa genome assemblies and analyzed 3,330 accessions spanning the three species to reconstruct the evolutionary trajectory of the Brassica A genome. Our findings reveal its origin in Central and West Asia and subsequent spread across Eurasia by means of three routes. An ancient inversion was identified that supports the divergent origins of the A subgenomes in B. napus and B. juncea. Furthermore, the S-locus exhibited exceptional haplotype diversity, with each variant characterized by a unique transposable element barcode pattern essential for the self-incompatibility system. These findings emphasize the significant value of pan-block-integrated 3,330 A genome variants for the Brassica research community.