Genetic resource optimization: a core collection of tetraploid wheat from 2,254 NBRP-wheat accessions

Tetraploid wheat, comprising both Emmer wheat (Triticum turgidum, AABB genome) and Timopheevii wheat (T. timopheevii, AAGG genome), harbors rich genetic diversity that remains underutilized in modern breeding. The National Bioresource Project-Wheat (NBRP-Wheat) conserves over 2,000 wild and landrace accessions of tetraploid wheat. To enhance the accessibility and application of these resources, we aimed to develop a representative core collection and explore its potential in genetic analysis and breeding.

We first assessed the genetic diversity of all tetraploid wheat accessions in the NBRP-Wheat gene bank using Diversity Arrays Technology (DArT), and selected 179 representative accessions to establish a core collection. This core set and T. durum cv. Kronos were further genotyped using genotyping by random amplicon sequencing-direct (GRAS-Di). Population structure and diversity analyses revealed clear genetic differentiation among Timopheevii, wild emmer, and domesticated emmer wheat. A significant reduction in genetic diversity was observed in domesticated emmer compared to its wild counterpart. Selective sweep analysis identified several differentiated loci between wild and free-threshing emmer, some of which correspond to known domestication-related genes. Additionally, k-mer-based genome-wide association studies (GWAS) have identified both known and novel loci associated with important agronomic traits, including glume hairiness, anthocyanin pigmentation in cotyledons and coleoptiles, hundred-grain weight, and culm length.

Our study provides a valuable core collection that captures the genetic diversity of tetraploid wheat conserved in NBRP-Wheat. The identified genomic regions and trait-associated loci demonstrate the utility of this core set for trait dissection and highlight its potential in future wheat improvement programs.