title: Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement.
abstract: The USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes.
  
  
  
  Using genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise FSTvalues ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm.
  
  
  
  The NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare alleles, suggesting that this germplasm contains potentially useful undiscovered alleles, but their discovery and characterization will require extensive effort. The genotypic data available for these accessions provide a valuable resource for sorghum breeders and geneticists to effectively improve crops.
authors.affiliation: USDA-ARS, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Avenue, Mayaguez, 00680, Puerto Rico. hugo.cuevas@ars.usda.gov.
authors.forename: Hugo E
authors.initials: HE
authors.lastname: Cuevas
authors.affiliation: USDA-ARS, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Avenue, Mayaguez, 00680, Puerto Rico.
authors.forename: Giseiry
authors.initials: G
authors.lastname: Rosa-Valentin
authors.affiliation: USDA-ARS, Cropping Systems Research Laboratory, 3810 4th Street, Lubbock, TX, 79415, USA.
authors.forename: Chad M
authors.initials: CM
authors.lastname: Hayes
authors.affiliation: Departments of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
authors.forename: William L
authors.initials: WL
authors.lastname: Rooney
authors.affiliation: Departments of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
authors.forename: Leo
authors.initials: L
authors.lastname: Hoffmann
mesh_terms: D000483:Alleles; D005002:Ethiopia; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D000068098:Seed Bank; D012639:Seeds / Q000235:genetics*; D012641:Selection, Genetic; D045868:Sorghum / Q000145:classification / Q000235:genetics*; D014481:United States; D016885:United States Department of Agriculture
keywords: Exotic germplasm; Genome-wide association study; Genotyping-by-sequencing; Population structure; Sorghum bicolor