Gapless pangenome analyses reveal fast <i>Brassica rapa</i> subspeciation
<i>Brassica rapa</i> (<i>Br</i>) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 <i>Br</i> accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with <i>Br</i> morphotypes and subspecies and <i>Brassica</i> species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among <i>Br</i> subspecies. Pangenome-wide association studies uncovered that the gene <i>BrLH1</i> controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of <i>Br</i> cultivation, providing invaluable resources for <i>Brassica</i> breeding.
Authors
- Xinlong Wang (ORCID: https://orcid.org/0009-0007-8122-6974)
- Yujie Gu
- Liu Zhaokun (ORCID: https://orcid.org/0000-0001-8856-4940)
- Tianzhen Zhang (ORCID: https://orcid.org/0000-0001-7873-4547)
- Shuangxia Luo
- Robin G. Allaby (ORCID: https://orcid.org/0000-0001-5046-002X)
- Lei Yang (ORCID: https://orcid.org/0009-0009-6678-9255)
- Shu Zhang (ORCID: https://orcid.org/0000-0002-4478-0374)
- Qihang Yang (ORCID: https://orcid.org/0009-0006-6442-5544)
- Xiaonan Li (ORCID: https://orcid.org/0009-0006-4107-9167)
- Yiguo Hong
- Xuan Chang
- Qianyun Wang
- Daling Feng
- Shuxing Shen
- Yves Van de Peer
- Qing Liu
- Mengyang Liu
- Hao Liang
- Zhaoshui Luan
- Mengyuan Li
- Zizhuo Han
- Lingyun Yuan
- Xiaomeng Zhang
- Yuxiang Yuan
- Yin Lu
- Kai Wang
- Yuanming Liu
- Xiaoxue Sun
- Xianlei Zhao
- Jianjun Zhao
- Guangguang Li
- Wei Ma
- Xiaochun Wei
Institutions
- Hebei Agricultural University (CN)
- Nanjing Agricultural University (CN)
- Shenyang Agricultural University (CN)
- Anhui Agricultural University (CN)
- Nantong University (CN)
- Ghent University (BE)
- University of Warwick (GB)
- Jiangsu Academy of Agricultural Sciences (CN)
- Henan Academy of Agricultural Sciences (CN)
- VIB-UGent Center for Plant Systems Biology (BE)
- Guangdong Academy of Agricultural Sciences (CN)
- ZheJiang Academy of Agricultural Sciences (CN)
- Suzhou Academy of Agricultural Sciences (CN)
- Nextomics Biosciences (China) (CN)
- Dezhou University (CN)
- University of Pretoria (ZA)
Publication Details
- Journal
- Science
- Published
- 2026-02-05
- DOI
- https://doi.org/10.1126/science.ady7590
- Citations
- 1
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 31.34