Genomic Characterization of a Core Set of the USDA-NPGS Ethiopian Sorghum Germplasm Collection

The USDA-ARS National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world and includes 7,217 accessions from the center of diversity located in Ethiopia. This exotic germplasm has not been characterized on a genome-wide basis to better inform its conservation and utilization in research and breeding programs. Therefore, a representative core set of 374 Ethiopian accessions were phenotyped and characterized at the genomic level through genotyping-by-sequencing (GBS).  A total of 148,476 single-nucleotide polymorphism (SNPs) markers distributed across the entire genome were identified, which over half of the SNPs were rare (frequency < 0.05).  The genetic profile of each accession was unique (i.e. no duplicates), and 93% of the pairwise genetic distance among them ranged from 0.60 to 0.79. Population structure and cluster analysis separated the collection into three subpopulations with a high differentiation index (F_ST = 0.15).  Phenotypic analysis confirmed these subpopulations based on agronomic and seed compositional traits. Cluster analysis with the sorghum association panel based on 60,962 SNPs determined that two of the Ethiopian subpopulations were not adequately represented in this panel. Indeed, the population structure of the NPGS Ethiopian collection can be exploited to screen this exotic germplasm. The large numbers of rare alleles indicates that this germplasm contains undiscovered and potentially useful alleles, but their discovery and characterization will require much additional effort. This genomic characterization provide a valuable resource for sorghum breeders and geneticists to effectively explore the potential of this highly diverse germplasm for sorghum improvement