Leveraging Sorghum Biofortification: Grain Color as a Proxy for Carotenoid-Rich Varieties to Combat Vitamin A Deficiency

  • SorghumBase Team
  • 7 July 2025

Developing carotenoid-rich sorghum varieties using grain color as a proxy for carotenoid levels, combined with marker-assisted selection, offers a promising strategy to combat vitamin A deficiency in vulnerable populations.

Keywords: Biofortification, Carotenoids, Cereals, GWAS, Grain color, Provitamin-A

By linking grain color with genetic markers for carotenoid biosynthesis, this research advances a practical, cost-effective strategy to accelerate sorghum biofortification, offering new hope in the global fight against vitamin A deficiency. – McDowell

 

Vitamin A deficiency (VAD) is a pervasive health issue, particularly in regions where access to vitamin A-rich foods is limited, contributing to blindness, immune deficiencies, and increased mortality among children under five. Sorghum, a staple crop for millions, presents an opportunity for biofortification due to its genetic diversity and ability to produce carotenoids—plant compounds that can be converted into vitamin A. However, sorghum’s carotenoid levels are typically low, necessitating the development of varieties with higher concentrations. High-performance liquid chromatography (HPLC), the standard method for carotenoid quantification, is costly and labor-intensive, creating a demand for accessible, high-throughput phenotyping approaches. Grain color has shown promise as a proxy for carotenoid levels, with yellow grain often indicating higher carotenoid content. Despite challenges like environmental variability and subjective visual assessment, preliminary studies suggest that colorimetric analysis and grain color-based selection could streamline biofortification efforts.

Leveraging genebank resources, researchers from Colorado State University and the Center for Grain and Animal Health Research, USDA-ARS, Manhattan, KS, identified sorghum accessions with potentially high carotenoid levels and analyzed genetic markers associated with grain color and carotenoid concentration. Genome-wide association studies (GWAS) revealed overlaps between genetic loci controlling grain yellowness and carotenoid biosynthesis genes ZEP, PDS, CYP97A, NCED, CCD, and LycE, supporting the use of marker-assisted selection (MAS) for breeding. However, significant variation in carotenoid composition and concentration within yellow grain accessions indicates the need for precise phenotyping and genetic validation. Challenges, including distinguishing carotenoid-induced yellowness from other pigments and environmental influences, underscore the importance of integrating color-based screening with advanced genetic tools. These findings suggest a phased breeding strategy: rapid selection based on grain color during early breeding cycles, followed by MAS for specific carotenoid traits, offering a pathway to alleviate vitamin A deficiency through biofortified sorghum.

SorghumBase examples: 

This study identified promising candidates for Marker-Assisted Selection by highlighting their dual role in the genetic regulation of carotenoid concentration and grain color variation in global sorghum germplasm. SorghumBase provides an integrated platform to explore their genomic context, genetic and phenotypic information, as well as additional functional evidence. For example, ZEP (SORBI_3006G097500 or Sobic.006G097500) is a major gene underlying sorghum carotenoid variation that is orthologous to maize zeaxanthin epoxidase. ZEP was found to be significantly associated with total carotenoids and zeaxanthin content. Moreover, a meaningful marker-trait association for qualitative grain color (just below the 5% FDR threshold) was also identified in the proximity of ZEP.

Figure 1: Querying SorghumBase for genes in the “Carotenoid biosynthesis” pathway from Plant Reactome returns a list of candidate carotenoid genes including the ZEP gene, which encodes a zeaxanthin epoxidase.
Figure 2: The Pathways tab of the ZEP gene in the SorghumBase search interface shows the gene’s epoxidase activity catalyzing the conversion of antheraxanthin to violaxanthin.
Figure 3: The genomic context (Gene View) of the ZEP gene in the SorghumBase Ensembl genome browser can be reached from the Location tab of the search results for ZEP. The image shown can be configured to display all the QTLs and GWAS aggregated by OZ Sorghum (Sorghum QTL Atlas). Note that a “grain color” QTL is in close proximity to the 3’-end of the gene.
Figure 4: By clicking on the name of a phenotype (for example, “grain color”), it is possible to get a list of all the loci associated with the trait.
Figure 5: The Variant Image of the ZEP gene shows all the genetic variants (color-coded by predicted functional effect) and protein domains overlaid on the gene’s structure. By clicking on a variant (color-coded square with alternative alleles at that position), an inset window is displayed with additional information. For example, the synonymous variant (green square with G/A alleles) at position chr6:46717975 is also known as rs5437506202 with both alleles encoding an Arginine when part of a gene’s coding sequence. This variant corresponds to S6_46717975 within the ZEP and antisense SORBI_3006G097600 genes (see also Figures 3 and 6), which this study found to have significant GWAS associations (P < 10−11) with total carotenoids and zeaxanthin.

Figure 6: S6_46717975 is the most significant marker-trait association within the ZEP gene and corresponds to rs5437506202. This variant maps to an intron within the ZEP gene, and a synonymous variant relative to the co-localized antisense SORBI_3006G097600 gene. In addition to a summary of the available information for this variant, allele and genotype frequencies in four population studies, as well as the genotypes of 3436 accessions at this variant locus are accessible.

Reference:

McDowell R, Banda L, Bean SR, Morris GP, Rhodes DH. Grain yellowness is an effective predictor of carotenoid content in global sorghum populations. Sci Rep. 2024 Oct 24;14(1):25132. PMID: 39448715. doi: 10.1038/s41598-024-75451-9. Read more

Related Project Websites: 

Rhodes lab members and collaborators from CERAAS holding yellow sorghum grain in Senegal. Photo Credit Davina Rhodes.
Rae McDowell holding sorghum in Manhattan, Kansas in August 2022. Photo Credit Gina Cerimele.