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

BackgroundThe 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.ResultsUsing 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 F ST values 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3475-7) contains supplementary material, which is available to authorized users.

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal

“…In the USDA-NPGS Ethiopian sorghum collection, similar patterns of MAF were found where 60% of detected SNPs had MAF < 0.05 (Cuevas, Rosa-Valentin, Hayes, Rooney, & Hoffmann, 2017). High rates of SNPs with low frequency minor alleles (about 60% of the data had MAF < 0.05) were detected.…”

“…One possible explanation may be related to the fact that these accessions are mostly landraces grown in their center of origin; thus high number of rare polymorphisms might be segregating at intermediate frequency in the germplasm. In the USDA-NPGS Ethiopian sorghum collection, similar patterns of MAF were found where 60% of detected SNPs had MAF < 0.05 (Cuevas, Rosa-Valentin, Hayes, Rooney, & Hoffmann, 2017). Overall, the Senegalese sorghum landraces represent a useful genetic resource, harboring useful variation for maturity and inflorescence morphology, as well as resistant sources to grain mold and anthracnose (Cuevas, Prom, & Rosa-Valentin, 2018).…”

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

“…Previous studies showed that core collections based on either genotypic profiles or random selection could represent the genetic diversity of the entire collection [3]. The number of rare alleles (MAF < 0.05) in the Sudan core set (22%) was lower than that observed in the NPGS Ethiopia core set (60% [22]; and NPGS Senegal collection (32% [40];. Thus, the high frequency of the Durra genetic background and high frequency of rare alleles in Sudanese populations 1 and 2 suggests that both of these populations originated from Ethiopia.…”

“…Nevertheless, most of the accession in the NPGS sorghum core collection lack phenotypic and genotypic information. To access the genetic diversity of the Sudan core set, we genetically characterized these accessions with the GBS platform previously used to genetically characterize the SAP [8] and the NPGS Ethiopian collection [22]. Both the genomic characterization and population structure analysis of Sudan core set provided critical information that was absent during its development but necessary to exploit its genetic diversity in breeding programs.…”

“…Nevertheless, these panels comprise converted sorghum lines (i.e., lines adapted to temperate regions) that represent most of the genetic diversity in breeding programs. Genomic characterization of the NPGS Ethiopia core set and Niger collection revealed that a limited portion of the sorghum genetic diversity is present in the association panels [22,23]. Thus, the characterization of other NPGS core sets is necessary to create a valuable genomic resource for in-depth phenotypic analysis and to expand the genetic diversity of association panels.…”