Genome-wide association study identifies genomic regions under selection for domestication and agronomic traits in Intermediate Wheatgrass

Authors: STOLL, HANNAH - University Of Minnesota; Bajgain, Prabin; ANDERSON, JAMES - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2026
Publication Date: 6/4/2026
Citation: Stoll, H., Bajgain, P., Anderson, J.A. 2026. Genome-wide association study identifies genomic regions under selection for domestication and agronomic traits in Intermediate Wheatgrass. The Plant Genome. Volume 19, Issue 2, e70258. https://doi.org/10.1002/tpg2.70258.
DOI: https://doi.org/10.1002/tpg2.70258

Interpretive Summary: Intermediate wheatgrass (also called Kernza) is a long-lived forage grass being turned into a grain crop. Breeding it for grain use began only a few decades ago and therefore important traits like yield, seed size, seed shatter, and plant height need significant improvements. In this research, materials representing multiple old and new breeding cycles were evaluated in a common garden experiment to discover genes controlling the important traits and learn if they are under active selection. Several genes - some previously discovered and some new - controlling the traits were discovered. The research also identified that the frequency of yield-related gene variants increased across breeding cycles, indicating positive selection. Overall, the results highlight specific parts of the genome that breeders can target to speed up improvement of Kernza as a reliable grain crop for the Midwest.

Technical Abstract: Intermediate wheatgrass (Thinopyrum intermedium, IWG, Kernza) is a perennial forage grass undergoing neo-domestication as a grain crop. IWG provides numerous ecosystem services and has the potential to benefit rural communities by providing an alternative crop option with a high market value. However, IWG has only been under development as a perennial grain crop for the past few decades, and at the University of Minnesota (UMN) since 2011. Thus, improvements in grain-related traits, market development, and agronomic management are key to the long-term viability of IWG as a Midwestern grain crop. In this study, 223 parent genets (genetically unique individuals) from UMN IWG breeding cycles 2, 3, 4, and 5 were cloned, planted, and evaluated over 2 years (2021 & 2022) in 2 locations (St. Paul & Lamberton, MN). Plants were genotyped using genotyping-by-sequencing to get single nucleotide polymorphisms (SNPs), and phenotyped for key domestication and agronomic traits. A genome-wide association study (GWAS) identified 33 quantitative trait loci (QTL) for shattering, seed size, and yield traits, which individually explained 13% of phenotypic variation in the population, on average. Some of the identified QTL were also identified in previous IWG studies, and some were novel, but appeared to be in close proximity to previously identified domestication traits. Moreover, changes in allele frequencies for significant QTL across breeding cycles were examined to identify any alleles which appeared to be under selection. These findings may be used to inform IWG breeding programs of key regions of the genome which should be targeted for selection improvements.