DOI: 10.5061/dryad.9w0vt4bkg
title: Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies

description: 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-performance liquid chromatography, finding high carotenoid
 accessions not previously identified. Genome-wide association studies
 confirmed that zeaxanthin epoxidase is a major gene underlying variation
 for not only zeaxanthin but also lutein and β-carotene. High carotenoid
 lines were found to have limited genetic diversity and originated
 predominantly from only one country. Potential novel genetic diversity for
 carotenoid content was identified through genomic predictions in 2,495
 accessions of unexplored germplasm. Oligogenic variation of carotenoids
 was confirmed, as well as evidence for polygenic variation, suggesting
 both marker-assisted selection and genomic selection can facilitate
 breeding efforts. Conclusions Sorghum vitamin A biofortification could be
 beneficial for millions of people who rely on it as a dietary staple.
 Carotenoid content in sorghum is low, but high heritability suggests that
 increasing concentrations through breeding is possible. Low genetic
 diversity among high carotenoid lines might be the main limitation for
 breeding efforts, therefore further germplasm characterization is needed
 to assess the feasibility of biofortification breeding. Based on germplasm
 here evaluated, most countries’ germplasm lacks high carotenoid alleles,
 thus prebreeding will be needed. An SNP marker within the zeaxanthin
 epoxidase gene was identified as a good candidate for use in
 marker-assisted selection. Due to the oligogenic and polygenic variation
 of sorghum grain carotenoids, both marker-assisted selection and genomic
 selection can be employed to accelerate breeding efforts.
description: 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.