Chromosome-scale assembly of wheat cultivar Sumai 3, a major germplasm source for Fusarium head blight resistance

Fusarium head blight (FHB) is a devastating disease that severely impacts global wheat (Triticum aestivum L.) production. Sumai 3, a wheat cultivar widely used in breeding programs for its strong FHB resistance, has not been fully resolved at the chromosome level. Here, we present a high-quality chromosome-scale assembly of Sumai 3 using PacBio HiFi reads and chromosome conformation capture sequencing. The 14.6 Gb assembly consists of 832 contigs, with the longest contig being 245.2 Mb and a contig N50 of 41.90 Mb, which were scaffolded into 21 pseudomolecules. De novo annotation identified 104,620 high-confidence protein-coding genes and found 92.67% of the genome to consist of repetitive sequences. Synteny analysis showed strong collinearity between Sumai 3 and the wheat reference sequence Chinese Spring IWGSC RefSeq v2.1 (CS). Structural variant analysis identified chromosome 2A with the highest number of deletions (2773) and insertions (2645), while chromosome 3B had the most inversions (359). Duplications were most frequent on 2A (337), and contractions on 5B (122). The gene content of the major resistance quantitative trait loci on 3B, Fhb1, largely validates previous annotations for CS, although we discovered two new genes at approximately 12.4 Mb, including an additional copy of a terpene synthase, further suggesting homology with CS 3D over 3B. Differential expression analysis highlighted up-regulation of three genes coding pore-forming toxin-like protein, sina superfamily protein, and plastid-lipid-associated proteins potentially involved in FHB resistance. This assembly provides critical insights into FHB resistance and offers a valuable genomic resource for wheat breeding programs.