Location: Agricultural Genetic Resources Preservation Research
Project Number: 3012-21000-017-026-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 5, 2025
End Date: Sep 30, 2026
Objective:
Hordeum pusillum ("little barley") is a compelling study species because it is a CWR of an important crop with extensive genomic information; NPGS’s collection under-represents extant populations; and it possibly represents the third independent domestication of barley, which began in North America 3800 years ago. Archaeological evidence suggests past human use of this CWR was followed by loss of domestication traits [1, 131]. The species is widespread and locally common across the continental United States, but like other New World diploid Hordeum species, H. pusillum is poorly represented in the NPGS Develop the genomic characterization of Assess the scale and identity of genetic structure within a large national collection of Hordeum pusillum with emphasis on genomic signatures of selection across its range in the US. This effort will support utility of this wild relative as a source of novel variation for agronomic traits for US barley breeding.
Approach:
The ARS investigator has developed a substantial set of population collections (seed, tissue and vouchers specimens) from 120 collection sites within the range of Hordeum pusillum. In addition, seed from most of these collections have been grown and self-pollinated and harvested. The PI has also developed a set of low coverage genotyping data on the majority (95) of the collections sites and 8 medium coverage (12x) assemblies used as a reference for variant calling. The hierarchical work plan begins with finishing the remaining poo-seq data collection from the 2025 collection sites. The cooperator is provided funds for DNA extraction, library construction and sequencing of the remaining 22 bulk samples (~$3000K). Pipelines for variant calling and SNP frequency determination has been developed by the PI and will be shared with cooperator. The sequencing data will be analyzed for genetic structure and demographic history jointly using admixture analysis and ordination. PI will defer to cooperators experience with coalescent modelling approaches to estimate demographic history. This step is important to differentiate adaptive signals from neutral demographic patterns (drift) that confound signatures of adaptive selection. The PI and the cooperator will jointly conduct genome scans among these samples for signatures of local or regional selection (outlier methods and site frequency spectrum analysis). The PI and cooperator will jointly explore methods for environmental association analysis across the range of this species. Additional genotyping individual S1 seed from wild collected seed (identified in pool-seq survey) will provide additional resolution to help support validation of loci under selection.