PDF(Pubmed)
Abstract：
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
摘要：
甘蓝的驯化导致了具有不同器官发育模式的不同形态类型。在这里，我们报告了一种基于图形的广谱双歧杆菌的全基因组，该基因组由不同形态类型的高质量基因组组装而成。泛基因组包含超过200个富含生长素和开花相关基因的结构变体（SV）热点区域。群体基因组分析显示，甘草的早期驯化集中在叶或茎的发育上。在不同的形态类型中检测到由农业实践和品种改良产生的基因流。选择性扫描和全基因组分析确定了生长素反应性SAUR基因和CLE家族基因在甘草驯化的早期阶段是叶茎分化的关键参与者，和BoKAN1基因有助于塑造卷心菜和布鲁塞尔豆芽的绿叶头。我们的泛基因组和功能分析进一步发现，BoFLC2基因的变异在不同形态之间春化和开花特征的差异中起关键作用。BoFLC3的第一个内含子的变异参与了花椰菜开花过程的微调。这项研究提供了对甘蓝的泛基因组的全面了解，并揭示了这种全球重要作物物种的驯化和差异器官发育。
