A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding
Abstract Tetraploid wheat ( Triticum turgidum L., BBAA), a key pasta crop, serves as an untapped genetic resource with rich genomic diversity for hexaploid bread wheat improvement. Here we de novo assembled 12 genomes spanning all 10 recognized tetraploid wheat (genome BBAA) subspecies, and a graph-based pangenome was constructed. Chromosome rearrangements drove subgenome asymmetry and shaped genomic divergence, with an average of 0.25 million structural variations per accession, predominantly attributable to transposon activity. Using 736 globally distributed tetraploid wheat accessions, we identified locally adapted subgroups with untapped breeding potential and discovered a novel retrotransposon‑induced loss‑of‑function Btr1-A allele responsible for convergent adaptation of non-brittle rachis. Genome-wide association studies identified 287 loci associated with 32 traits. A homeodomain-leucine zipper transcription factor HAT14-B that enhances both spikelet number and grain size was identified. This subspecies-wide pangenome enriches Triticeae AB subgenome resources and facilitates the discovery and application of agronomically important genetic variations.
Authors
- Xing Wang Deng (ORCID: https://orcid.org/0000-0001-8709-1467)
- S S Wang
- Yang Gh
- Yongming Chen (ORCID: https://orcid.org/0000-0002-2143-3134)
- Hude Mao (ORCID: https://orcid.org/0000-0002-2484-9952)
- Shuangxing Zhang
- Hang He (ORCID: https://orcid.org/0000-0003-3165-283X)
- Xiaojun Nie (ORCID: https://orcid.org/0000-0002-4787-7550)
- Qing Sang (ORCID: https://orcid.org/0000-0003-1163-1521)
- Jianxin Bian (ORCID: https://orcid.org/0000-0001-6443-7218)
- Yan Pan (ORCID: https://orcid.org/0000-0002-6870-3015)
- Baoxing Song (ORCID: https://orcid.org/0000-0003-1478-9228)
- Qidi Zhu
- Zhen Qin (ORCID: https://orcid.org/0000-0001-7185-3965)
- Shoucheng Liu (ORCID: https://orcid.org/0000-0002-0138-0995)
- Bin Chen (ORCID: https://orcid.org/0000-0001-9745-6546)
- Yiqiao Wang (ORCID: https://orcid.org/0000-0001-8179-5797)
- Shuai Ding (ORCID: https://orcid.org/0009-0008-9803-3754)
- Shisheng Chen (ORCID: https://orcid.org/0000-0002-8617-4356)
- Yi-Xiang Wang (ORCID: https://orcid.org/0000-0002-4021-4228)
- Yanzhe Jia
- Dong Xu
- Yan Zhang
- Mengmeng Jiang
- Guifen Zhang
- Fangyu Liu
- Yuqing Lu
- Can Yuan
Institutions
- Guangzhou University (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Tea Research Institute (CN)
- Chongqing Academy of Agricultural Sciences (CN)
- Institute of Crop Sciences (CN)
- Center for Life Sciences (CN)
- Henan Institute of Science and Technology (CN)
- Southwest Minzu University (CN)
- Northwest A&F University (CN)
Publication Details
- Journal
- Nature Genetics
- Published
- 2026-07-22
- DOI
- https://doi.org/10.1038/s41588-026-02678-9
- Primary Topic
- Wheat and Barley Genetics and Pathology
- Type
- article
- Field-Weighted Citation Impact
- 0.00