TY - JOUR
T1 - Genomic insights into the NPGS intermediate wheatgrass germplasm collection
AU - Crain, Jared
AU - Larson, Steve
AU - Sthapit, Sajal
AU - Jensen, Kevin
AU - Poland, Jesse
AU - Dorn, Kevin
AU - Thomas, Aaron
AU - DeHaan, Lee
N1 - KAUST Repository Item: Exported on 2023-04-03
Acknowledgements: The high-performance computing for this project was performed on the Beocat Research Cluster at Kansas State University, which was funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109. Keygene N.V. owns patents and patent applications protecting its Sequence Based Genotyping technologies. Contribution no. (23-018-J) from the Kansas Agricultural Experiment Station. We appreciate the constructive comments by two anonymous reviewers that improved the manuscript.
PY - 2023/2/22
Y1 - 2023/2/22
N2 - The National Plant Germplasm System (NPGS) is a vital resource for genetic diversity, yet utilization of this resource requires a thorough understanding of the germplasm and genetic diversity. Intermediate wheatgrass (IWG, Thinopyrum intermedium) is a perennial grass species that has been improved for forage production through breeding utilizing the NPGS collection and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data with new agronomic and genomic data. 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. Genomic analysis revealed two subpopulations, which were defined as European and Asian groups, and are differentiated around the Black Sea region. Phenotypic observations for forage and agronomic traits differed between the two groups (p < 0.05), even though greater than 70% of the genetic variance was partitioned within individual accessions. Finally, XP-GWAS revealed 303 marker–trait associations for five agronomic and four forage traits. These results suggest that genetic diversity within the NPGS collection should lead to genetic gains for both forage and grain breeding as well as opportunities for breeding programs to enhance genetic diversity. More broadly, the methods we applied could be applicable to low-resourced species, leveraging existing, and new data, to strengthen genetic characterization and breeding efficiency.
AB - The National Plant Germplasm System (NPGS) is a vital resource for genetic diversity, yet utilization of this resource requires a thorough understanding of the germplasm and genetic diversity. Intermediate wheatgrass (IWG, Thinopyrum intermedium) is a perennial grass species that has been improved for forage production through breeding utilizing the NPGS collection and has also been targeted for domestication as a perennial grain crop. To better characterize the IWG collection, we combined previously published forage data with new agronomic and genomic data. 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. Genomic analysis revealed two subpopulations, which were defined as European and Asian groups, and are differentiated around the Black Sea region. Phenotypic observations for forage and agronomic traits differed between the two groups (p < 0.05), even though greater than 70% of the genetic variance was partitioned within individual accessions. Finally, XP-GWAS revealed 303 marker–trait associations for five agronomic and four forage traits. These results suggest that genetic diversity within the NPGS collection should lead to genetic gains for both forage and grain breeding as well as opportunities for breeding programs to enhance genetic diversity. More broadly, the methods we applied could be applicable to low-resourced species, leveraging existing, and new data, to strengthen genetic characterization and breeding efficiency.
UR - http://hdl.handle.net/10754/690777
UR - https://onlinelibrary.wiley.com/doi/10.1002/csc2.20944
UR - http://www.scopus.com/inward/record.url?scp=85150830500&partnerID=8YFLogxK
U2 - 10.1002/csc2.20944
DO - 10.1002/csc2.20944
M3 - Article
SN - 1435-0653
JO - Crop Science
JF - Crop Science
ER -