Location: Tropical Crops and Germplasm ResearchTitle: Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement Author
|Rosa-valentin, Giseiry - Former ARS Employee|
|Rooney, William - Texas A&M University|
|Hoffmann, Leo - Texas A&M University|
Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/26/2016
Publication Date: 1/26/2017
Citation: Cuevas, H.E., Rosa-Valentin, G., Hayes, C.M., Rooney, W.L., Hoffmann, L. 2017. Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement. BMC Genomics. 18:108. doi:10.1186/s12864-016-3475-7.
Interpretive Summary: 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. The genome analysis for a representative core subset of 374 accessions reflects the collection is constituted by three subpopulations, which are also defined by unique agronomic and seed compositional traits. This population structure can be exploited to identify and screen novel exotic germplasm, and to preserve the genetic diversity of the collection. The genotypic data of these accessions is a valuable tool to for sorghum breeders and geneticists worldwide to accelerate the utilization of the Ethiopian genetic diversity present in the NPGS collection for the improvement of sorghum cultivars.
Technical Abstract: 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 at two locations for agronomic traits and characterized at the genomic level through genotyping-by-sequencing (GBS). Genotyping-by-sequencing identified 148,476 single-nucleotide polymorphism (SNPs) markers distributed across the entire genome. Fifty eight percent of the alleles had frequency < 0.05 (i.e. rare alleles). 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 (FST = 0.15). Phenotypic analysis indicated that these subpopulations were also defined by unique 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. Genome-wide association studies for plant height and tannin content demonstrated that the GBS-SNPs could be employed for the genomic dissection of important phenotypes in this important core set of Ehtiopian sorghum germplasm. The USDA-NPGS Ethiopian sorghum germplasm collection is highly genetically and phenotypically diverse core set of germplasm composed of three main subpopulations, two of which are not adequately represented within the primary sorghum association panel. This population structure can be exploited to identify and screen novel exotic germplasm by phenotyping particular subpopulations of interest. The large number of rare alleles indicates that this germplasm may possess potentially valuable undiscovered alleles, but their discovery and characterization will require much additional effort. The genotypic data now available for these accessions is a valuable resource for sorghum breeders and geneticists to further explore the potential of this highly diverse germplasm for sorghum improvement.