Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding.

High-quality genome information is essential for efficiently deciphering and improving crop traits. Here we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against yellow rust (YR) disease. By integrating HiFi and Hi-C sequencing reads, a 14.75 Gb genome assembly, with contig N50 and scaffold N50 reaching 70.94 and 735.11 Mb, respectively, was developed for Zhou8425B. Comparison with previously sequenced common wheat cultivars shed light on the structural changes of 1RS chromosome arm extensively used in wheat improvement. Interestingly, Zhou8425B 1RS carried more genes encoding AP2/ERF-ERF or B3 transcription factors (TFs) than its counterparts in the four wheat and rye genotypes sequenced to date. Zhou8425B genome assembly aided the fine mapping of a new APR locus (YrZH3BS) that significantly decreased YR disease severity and promoted grain yield under field conditions. Notably, pyramiding YrZH3BS with two previously characterized APR loci (YrZH22 and YrZH84) could further reduce YR severity and enhance grain yield, with triple combination (YrZH3B+YrZH22+YrZH84) having the highest effect. Finally, the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data, which uncovered important Zhou8425B genomic blocks in its derivative cultivars. Our data demonstrate the value of Zhou8425B assembly for further studying the structural and functional characteristics of 1RS, genetic basis of durable resistance against YR disease, and founder genotype effects in wheat breeding. Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.