Location: Plant Science Research
Project Number: 6070-22000-019-043-A
Project Type: Cooperative Agreement
Start Date: Aug 1, 2026
End Date: Jul 31, 2030
Objective:
Our goal is improvement of genomic resources of US winter wheat germplasm to accelerate genetic discovery and breeding improved cultivars. We will develop high-quality genomic resources for Soft Red Winter Wheat cultivars. Sequenced lines are selected based on genetic diversity and traits of interest and analyses will use a combination of de novo assembly, RagTag scaffolding, pan-genome graph construction, candidate gene testing and genotyping assay development.
Approach:
1. Reference quality De Novo Assemblies will be developed for two widely adapted cultivars (Hilliard and AGS2000) using PacBio HiFi, Hi-C scaffolding, and Iso-Seq annotation.
2. RagTag-based Scaffolding of PacBio HiFi sequences will be done for six additional winter wheat lines with annotation liftover.
3. Pan-genome Graph will be constructed for improved variant calling and genotype imputation.
4. Trait QTL/gene mining will be done across the pan set and other diverse germplasm to nominate causal variants. Appropriate technologies will be used for causal variant validation.
5. Marker development is done, including gene specific assays and targeted amplicon sequencing panels.