Genomic insights into the NPGS intermediate wheatgrass germplasm collection

Authors: CRAIN, JARED - Kansas State University; Larson, Steven; STHAPIT, SAJAL - The Land Institute; Jensen, Kevin; POLAND, JESSE - King Abdullah University Of Science And Technology; Dorn, Kevin; THOMAS, AARON - Utah State University; DEHAAN, L - The Land Institute

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2023
Publication Date: 2/22/2023
Citation: Crain, J.L., Larson, S.R., Sthapit, S., Jensen, K.B., Poland, J.A., Dorn, K.M., Thomas, A., DeHaan, L. 2023. Genomic insights into the NPGS intermediate wheatgrass germplasm collection. Crop Science. 63(3):1381-1396. https://doi.org/10.1002/csc2.20944.
DOI: https://doi.org/10.1002/csc2.20944

Interpretive Summary: The USDA National Plant Germplasm System (NPGS) is a vital resource for genetic diversity, yet efficient utilization of this resource requires descriptive and reliable information for each collection. Intermediate wheatgrass (IWG) is a perennial grass species that has been improved through breeding with the NPGS collection for forage and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data (‘old’) with agronomic and genomic data (‘new’). A total of 331 NPGS accessions were profiled by DNA sequencing and field evaluations and to evaluate population structure and the genetic architecture of traits. This DNA analysis revealed two subpopulations, which were defined as Asian and European groups, and are differentiated around the Black Sea region. While there were many statistically significant differences between the trait values for the two groups, greater than 70% of the genetic variance was partitioned within accessions. Finally, 260 DNA variants were associated for five agronomic and four forage traits. For IWG breeding, these results suggest that breeding within accessions should lead to genetic gains for both forage and grain breeding. More broadly, the methods we applied could be applicable to low-resourced species, leveraging existing and new data, to enhance genetic characterization and breeding efficiency.

Technical Abstract: The national plant germplasm system (NPGS) is a vital resource for genetic diversity, yet efficient utilization of this resource requires adequate passport data. Intermediate wheatgrass (IWG, Thinopyrum intermedium) is a perennial grass species that has been improved through breeding with the NPGS collection for forage and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data (‘old’) with agronomic and genomic data (‘new’). A total of 331 NPGS accessions were genomically profiled with genotyping-by-sequencing (GBS) and a genome-wide association study (GWAS) was used to evaluate trait architecture. Along with the GWAS, in silico bulk samples were profiled by recoding GBS data to conduct association mapping through allele counting with extreme-phenotype (XP)-GWAS. Population structure was assessed by geography, molecular markers, and analysis of molecular variation (AMOVA). Genomic analysis consistently revealed two subpopulations, which were defined as Asian and European groups, and are differentiated around the Black Sea region. While there were often significant differences (p < 0.05) between the trait values for the two groups, greater than 70% of the genetic variance was partitioned within accessions. Finally, XP-GWAS revealed 260 marker trait associations for five agronomic and four forage traits. For IWG breeding, these results suggest that breeding within accessions should lead to genetic gains for both forage and grain breeding. More broadly, the methods we applied could be applicable to low-resourced species, leveraging existing and new data, to enhance genetic characterization and breeding efficiency.