A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification
文献类型： 外文期刊
作者： Guo, Ning 1 ; Wang, Shenyun 1 ; Wang, Tianyi 2 ; Duan, Mengmeng 1 ; Zong, Mei 1 ; Miao, Liming 1 ; Han, Shuo 1 ; Wang, Guixiang 1 ; Liu, Xin 1 ; Zhang, Deshuang 1 ; Jiao, Chengzhi 2 ; Xu, Hongwei 1 ; Chen, Liyang 2 ; Fei, Zhangjun 3 ; Li, Jianbin 1 ; Liu, Fan 1 ;
作者机构： 1.Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Beijing Vegetable Res Ctr, State Key Lab Vegetable Biobreeding,Key Lab Biol &, Beijing 100097, Peoples R China
2.Jiangsu Acad Agr Sci, Jiangsu Key Lab Hort Crop Genet Improvement, Vegetable Res Inst, Nanjing 210014, Jiangsu, Peoples R China
3.Smartgen Technol Inst, Tianjin 301700, Peoples R China
4.Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA
关键词： Brassica oleracea; graph-based pan-genome; structural variants; SV; domestication; morphotype diversification
期刊名称：PLANT COMMUNICATIONS （ 2022影响因子：10.5； 五年影响因子：10.5 ）
ISSN： 2590-3462
年卷期： 2024 年 5 卷 2 期
收录情况： SCI
摘要： 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.
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