Darwin’s “abominable mystery”—why flowering plants (angiosperms) rapidly rose to dominance and underwent explosive diversification in a geologically short time—has remained one of the most enduring puzzles in evolutionary biology. The research team led by Professor Zhao Jianjun of Hebei Agricultural University, collaborating with domestic and international research institutions, has provided a groundbreaking answer by studying Chinese cabbage (Brassica rapa), a model for rapid crop evolution. On February 5, 2026, the international academic journal Science published their research achievements titled “Gapless pangenome analyses reveal fast Brassica rapa subspeciation.”
The study systematically characterizes the genetic basis of rapid subspeciation in Chinese cabbage at three levels: genome, pangenome, and pan-epigenome. It transforms the classic question of angiosperm “rapid expansion” into a tangible, visible evolutionary framework. By constructing a complete centromere map, the research reveals the critical roles of satellite repeats, centromere dynamics, and structural variations in the evolution of Brassica species, significantly deepening our understanding of the origin and sequence of genome differentiation within the genus. Furthermore, this suite of high-quality genomic maps and analytical systems provides a model framework for future functional and evolutionary studies, not only in Brassica species but also across the broader Brassicaceae family of crops.
The study constructed 11 gap-free T2T genomes and a comprehensive pangenome, generating the most refined
"genomic map" of Chinese cabbage.
The research team resequenced 1,720 cabbage accessions from different subspecies, carefully selecting 11 representative materials. By integrating multiple sequencing technologies—including PacBio HiFi, Nanopore ultra-long reads, Hi-C, and MGI short reads—they successfully assembled complete telomere-to-telomere (T2T) genomes with zero gaps, covering all telomeres and 110 intact (pan)centromeres. The analysis identified 6,992 previously unknown genes. Combined with 20 previously reported cabbage genome datasets, the team constructed the most comprehensive pangenome of Brassica rapa to date, providing high-quality genomic resources for fine-scale analysis of genetic diversity and evolutionary patterns at the population level.
The study deciphered centromeres and structural variations, identifying the "genomic engine"
driving rapid subspeciation.
By developing a specific CENH3 antibody for Chinese cabbage and performing ChIP-seq, the team systematically "illuminated" functional centromeres on every chromosome across the 11 representative accessions. This effort produced the first complete structural atlas of 110 (pan)centromeres across B. rapa subspecies and revealed five previously unknown satellite repeat sequences specific to Brassica pan-centromeres. Using a graph-based pangenome framework, the researchers systematically cataloged genome-wide structural variations (SVs), constructing an SV map across 31 accessions and identifying over 270,000 SVs—the most comprehensive "structural variation map" in Brassica to date. The team proposed a "SV–subspecies-specific gene–centromere module" trinary co-evolutionary model: structural variations and subspecies-specific genes provide the primary genetic basis for morphological divergence; modular reorganization of centromeres ensures developmental robustness while creating "genomic innovation space" for evolutionary change. Together, these mechanisms enable B. rapa to rapidly diversify into multiple subspecies within a short evolutionary timeframe. In essence, the interaction between rapidly evolving centromeres and widespread structural variations constitutes the "genomic engine" driving the rapid differentiation of Chinese cabbage subspecies.
The study completed the journey from pan-genome association to functional validation, identifying BrLH1 as the
"master switch" for cabbage head formation.
Using the 1,720 cabbage accessions, the team conducted a pan-genome-wide association study (pan-GWAS) based on SNPs, InDels, and PAVs (presence/absence variations), precisely pinpointing the single-copy gene BrLH1 on chromosome A07 as the sole candidate locus strongly associated with head formation. Through repeated genetic experiments, BrLH1 was confirmed as the major-effect gene controlling leafy head development in Chinese cabbage. Functionally, BrLH1 belongs to the multi-C2 domain transmembrane protein family and regulates leaf growth direction and spatial arrangement by interacting with receptor kinases such as BrSUB, thereby shaping the compact head structure. Thus, BrLH1 is established as the core regulatory node for head formation and a key target for future molecular breeding aimed at optimizing heading traits.
The study received unanimous high praise from peer reviewers. Reviewers described the work as a "milestone leap" in Brassica genomics, with the zero-gap genomes and pangenome resources setting a "new benchmark for population genomics." It is expected to become a "landmark study in Brassica genetics." One reviewer noted that the study "represents an immense workload and will serve as a vital resource for the entire field," with broad and profound implications for understanding plant genome evolution and the genetic basis of crop phenotypic diversity.
The corresponding authors of the paper are Professor Zhao Jianjun, Professor Ma Wei, and Professor Hong Yiguo from Hebei Agricultural University; Researcher Yuan Yuxiang from Henan Academy of Agricultural Sciences; and Professor Yves Van de Peer from Ghent University, Belgium. The co-first authors are Professor Ma Wei, Associate Professor Liu Yuanming, and Associate Professor Zhang Xiaomeng from Hebei Agricultural University; Researcher Wei Xiaochun from Henan Academy of Agricultural Sciences; Professor Li Xiaonan from Shenyang Agricultural University; Associate Researcher Liu Zhaokun from Suzhou Academy of Agricultural Sciences; Professor Yuan Lingyun from Anhui Agricultural University; and Senior Agricultural Engineer Li Guangguang from the Guangzhou Academy of Agricultural and Rural Sciences. Professor Shen Shuxing from Hebei Agricultural University, Professor Zhang Tianzhen from Zhejiang University, Professor Wang Kai from Nantong University, and Professor Robin Allaby from the University of Warwick provided important guidance throughout this research. Mr. Luan Zhaoshui, Chairman of Shandong Degao Seed Co., Ltd., made significant contributions to material provision and experimental organization. This study was funded by the National Natural Science Foundation of China and the Hebei Provincial Natural Science Foundation.
