A genetic toolkit to reduce wheat immunogenicity and incidence of celiac disease

In this study, we generated Triticum aestivum lines carrying fast neutron–induced deletions spanning prolamin gene clusters. Because most of these lines were derived from the cultivar Summit, we produced a de novo genome assembly for Summit using ~398 Gb of PacBio HiFi sequencing data. The resulting contigs were scaffolded into 21 pseudomolecules (totaling 14.52 Gb) using the Kariega cultivar genome as a reference. An additional 79 Mb of unplaced scaffolds were grouped into Chr_Un. Gene models were transferred from the high-confidence Chinese Spring reference genome (version 2.1, CS2.1), and new consecutive Summit-specific gene IDs were assigned across all pseudomolecules. Manual curation of prolamin loci identified 78 complete genes, including 5 HMW-GS (Ax1, Bx17, By18, Dx5, and Dy10), 13 LMW-GS, 11 γ-gliadins, 2 δ-gliadins, 12 ω-gliadins, and 35 α-gliadins. In addition, 67 putative prolamin pseudogenes were annotated. The Summit genome assembly and raw reads have been deposited in NCBI under BioProject PRJNA1438777. This represents the first genome assembly for this wheat variety and provides a reference framework for characterizing the deletions described here, as well as for future breeding efforts aimed at improving wheat quality and gluten composition.