Pan-genome analysis of different morphotypes reveals genomic basis ofBrassica oleraceadomestication and differential organogenesis

Abstract

AbstractThe domestication ofBrassica oleraceahas resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome ofB. oleraceaconstructed with high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant (SV) hotspot regions enriched with auxin and flowering-related genes. Population genomic analyses reveal that early domestication ofB. oleraceafocused on leaf or stem selection. Gene flows resulting from agricultural practices and variety improvement are detected among different morphotypes. Selective sweep analysis identifies an auxin-responsive SAUR gene and a CLE family gene as the crucial players in the leaf-stem differentiation during the early stage ofB. oleraceadomestication, and theBoKAN1gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further discover that variations in theBoFLC2gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron ofBoFLC3are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome ofB. oleraceaand sheds light on the domestication and differential organ development of this globally important crop species.