Shandong, China — Wheat, the “pillar of the granary,” is central to China’s food security and rural revitalization. Wheat has long been a focus for scientists seeking to improve its yield and quality. However, its exceptionally complex genome has posed persistent challenges to in-depth research and breeding applications.

 

On April 7, 2025, a team led by Academician Xing Wang Deng, Dr. Hang He, and Dr. Bosheng Li (Shandong Laboratory of Advanced Agriculture Sciences in Weifang / Peking University Institute of Advanced Agricultural Sciences / National Key Laboratory for Wheat Improvement) reported in Nature Genetics a landmark study entitled “A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.” This work presents the world’s first T2T assembly of hexaploid bread wheat, completed in Shandong, providing a strategic resource for national food security.

 

 

A multi-platform sequencing strategy sets the foundation

 

By integrating cutting-edge sequencing technologies and multiple algorithmic approaches, the researchers generated the T2T wheat reference CS-IAAS v1.0 spanning 14.51 Gb. All 21 chromosomes are assembled telomere-to-telomere (Fig. 1), representing a step-change in completeness, contiguity, and accuracy, and setting a new global benchmark.

 

Fig. 1. The gap-free T2T wheat genome, CS-IAAS v1.0

 

Resolving the most complex regions

 

The assembly provides the first clear, contiguous views of centromeres, telomeres, and rDNA arrays. Centromeres are 47% longer than previously reported and dominated by distinct transposon satellites. Each subgenome (A, B, D) shows independently evolved centromeres, with Retand elements from the D subgenome infiltrating A and B — evidence of inter-subgenome crosstalk. Wheat telomeres display both plant- and vertebrate-type repeats, a rarity among plants. rDNA arrays are resolved as tandem ribosomal-gene clusters embedded in dense transposon neighborhoods, with chromosome-specific patterns — together opening new windows on the evolution of repetitive landscapes.

 

From tetraploid to hexaploid: chromosome-scale remodeling

 

Leveraging the T2T map, the team identified 23 major inversions (~518 Mb) that arose during the transition from tetraploid to hexaploid wheat; all are retained in modern bread wheat and are flanked by short unique repeats likely involved in breakage-fusion (Fig. 2).

 

Fig. 2. Chromosomal rearrangements and breakpoint structures from diploid to hexaploid wheat

 

Repeats as engines of evolution

 

Far from “junk,” repetitive elements have shaped wheat’s genome. Two recently expanded transposon families and two bursts of LTR retrotransposons coincide with key evolutionary nodes, supplying raw material for large-scale restructuring. Segmental duplications further provide templates for gene innovation, bolstering diversity and environmental adaptability.

 

Refined gene annotation fuels breeding

 

Integrating RNA-seq and full-length transcript data, the authors annotated 141,035 high-confidence protein-coding genes, including 34,120 newly identified genes and numerous NLR disease-resistance loci. Proteomics-based validation strengthens confidence, yielding a rigorously calibrated resource for functional genomics.

 

A new era for wheat genomics and precision breeding

Leveraging this high-quality reference genome, scientists will be able to more precisely identify key genes related to yield, quality, and disease resistance, paving the way for revolutionary breakthroughs in wheat variety improvement.

 

Co-corresponding authors: Academician Xing Wang Deng, Dr. Hang He and Dr. Bosheng Li. Co-first authors: Dr. Shoucheng Liu, Associate Researcher Kui Li, Assistant Researcher Xiuru Dai (now a faculty member at Shandong Agricultural University) and Researcher Guochen Qin.

 

We thank Prof. Hongqing Ling (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS)) for providing wheat seeds, and Prof. Zuojun Liu (Lanzhou University of Technology), Prof. Songnian Hu (Institute of Microbiology, CAS), and Sen Wang (Beijing University of Agriculture) for insightful comments. Funding was provided by the Shandong Provincial Scientific and Technological Innovation Development Fund, the Shandong Natural Science Foundation, the President’s Fund of Peking University Institute of Advanced Agricultural Sciences, the National Key Talent Programs, and the National Key R&D Program of China.