Pan-genomic and genetic dissection of drought tolerance in a resilient wheat germplasm JIN50

Global climate change intensifies drought threats to wheat productivity, necessitating genetic enhancement of drought resistance. We present a high-quality genome assembly of drought-resistant wheat genotype JIN50 (contig N50 = 50.63 Mb) and conduct pan-genomic analyses across 14 wheat genomes and 196 germplasms, revealing 430,739 structural variants (SVs). Integrated SV-, SNP-, and Indel-based GWAS identified 46 drought-resistance loci enriched in JIN50. Notably, the structural variation in promoter of root development regulator TaLBD1 and functional haplotypes of methylglyoxal detoxification enzyme TaGLYI7, both contributing to drought adaptation through distinct mechanisms. The JIN50 genome and pan-genomic resources provide critical tools for deciphering drought-resistance networks and accelerating molecular breeding. These findings advance understanding of wheat's multigenic drought response system and offer strategic genomic solutions to bolster food security under climate challenges.