Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies

Background
Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene—the main provitamin A carotenoid—is below the target concentration in sorghum grain, therefore, biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors.
Results
In this study, we characterized carotenoids in 447 accessions from the sorghum association panel and carotenoid panel using high-performan..., 1- Ethiopia_NGPS_renamed.vcf
Accessions and SNP dataset from the NPGS Ethiopian collection were obtained from Cuevas, H. E. via personal communication. The dataset consists of 367 accessions and 215,741 SNPs on version 3.1 of the sorghum genome.
Original data is from: Cuevas, H.E., Rosa-Valentin, G., Hayes, C.M., Rooney, W.L. and Hoffman, L. 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. 2017. 
2- Sudan_NGPS_renamed.vcf
Accessions and SNP dataset from the NPGS Sudan core collection were obtained from Cuevas, H. E. via personal communication. The dataset consists of 319 accessions and 215,741 SNPs on version 3.1 of the sorghum genome.
Original data is from: Cuevas, H.E. and Prom, L.K. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan sorghum core collection. BMC Genomics 21:88. 2020.,