Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan sorghum core collection

Authors: Cuevas, Hugo; PROM, LOUIS - US Department Of Agriculture (USDA)

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/13/2020
Publication Date: 1/28/2020
Citation: Cuevas, H.E., Prom, L.K. 2020. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan sorghum core collection. BMC Genomics. 21, 28. https://doi.org/10.1186/s12864-020-6489-0.
DOI: https://doi.org/10.1186/s12864-020-6489-0

Interpretive Summary: The USDA-ARS National Plant Germplasm System (NPGS) Sudanese sorghum core collection includes 352 accessions that have not been evaluated for potential use in breeding programs. To access the genetic diversity of the Sudan core set, we genetically characterized these accessions with the genotyping-by-sequencing (GBS) platform previously used to characterize the sorghum association panel and NPGS Ethiopian core collection. The genomic characterization, phylogenetic and population structure analyses of the Sudan core set provided novel critical information necessary to exploit its genetic diversity in breeding programs. Population structure of the Sudan core set was associated with phenotypic variation for six agronomic traits and a total of 75 accessions were resistant to anthracnose. The genotypic and phenotypic analysis of the Sudan core set allows selection by breeding programs of genetically diverse accessions for adaptation to temperate regions.

Technical Abstract: The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3,011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response at two locations. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 75 accessions were resistant to anthracnose; these accessions could represent up to five different resistance sources. Genome-wide association analysis of the midrib color demonstrated that the genotypic data and population structure could be used for the genomic dissection of agronomically important traits. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. Population genomic analysis of the NPGS Sudan core collection could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.