Pangenome-guided breeding restores high-altitude adaptation and improves yield in Tartary buckwheat

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 that enhances high-altitude adaptability. We also identified a copy-number variation at the FtPLATZ locus and a 28-bp insertion in the 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.