Kaixuan Zhang, Yuqi He, Hao Lin, Jiayue He, Zhirong Wang, Wei Li, Yanhua Chen, Jing Li, Yaliang Shi, Xu Huang, Mengqi Ding, Pu Yang, Zhiqiang Chen, Annapurna Chitikineni, Jiguang Li, Jinfeng Gao, Baili Feng, Zongwen Zhang, Ming Hao, Reyazul Rouf Mir, Dengcai Liu, Sun-Hee Woo, Dagmar Janovská, Muriel Quinet, Alisdair R. Fernie, Wenhua Liao, Xibo Feng, Dhurva Prasad Gauchan, Namraj Dhami, Ivan Kreft, Artur Piński, Alexander Betekhtin, Manuel Spannag, Xu Liu, Rajeev K. Varshney, Jianquan Liu, Meiliang Zhou

Cell; 2026; IF: 45.1‌

DOI: 10.1016/j.cell.2026.07.035

Abstract

Tartary buckwheat is a nutritionally important crop of the Himalayas and is crucial for local economies and food security. However, key genes and superior alleles for high-altitude adaptability and yield remain poorly defined, constraining the breeding of high-altitude buckwheat varieties. Here, we generated a telomere-to-telomere reference genome and a 16-accession pangenome spanning Himalayan wild populations and globally distributed landraces. We identified 123,131 non-redundant structural variations in 16 accessions, including gene copy-number variations. The graph-based pangenome revealed FtRNH, a wild-specific gene enhancing high-altitude adaptability. We also identified a copy-number variation at the FtPLATZ locus and a 28-bp insertion in FtPLATZ3 promoter that together contribute to seed-size variation across wild buckwheat and landraces. Leveraging these superior FtRNH and FtPLATZ alleles, we developed buckwheat lines with enhanced high-altitude adaptability and improved yields across sites. These findings establish a pangenome-guided strategy for recovering wild alleles and combining stress adaptation with yield improvement in crops.