Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing

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• Open access
• Published: 27 October 2026

• Khalid Sedeek^1,2,
• Andrea Zuccolo^2,3,
• Umair Ali Toor²,
• Krishnaveni Sanikommu^1,2,
• Sunitha Kantharajappa^1,2,
• Luis Rivera-Serna²,
• Rod A. Wing^2,4 &
• …
• Magdy M. Mahfouz^1,2 

Scientific Reports (2026) Cite this article

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Abstract

Amaranth (Amaranthus spp.) is an emerging crop that combines outstanding nutritional value in both edible grain and leaves with strong agronomic resilience, positioning it as an attractive candidate for sustainable food systems. Comprehensive metabolomic and genomic resources are, however, still lacking for many cultivated amaranths, limiting targeted breeding and genome-editing efforts. Here we combine non-targeted ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) metabolome profiling with PacBio HiFi whole-genome sequencing to characterise five widely grown grain amaranth cultivars: coral fountain (CF), emerald tassels (ET), golden giant (GG), hopi red dye (HR) and New Mexico (NM). Metabolite profiling identified 426 and 420 structurally known compounds in grain and leaf tissues, respectively, revealing cultivar-specific differences in sulfur amino acids, vitamins, chlorogenic acids, and potentially anti-nutritive compounds such as oxalate and raffinose-family oligosaccharides; on average, CF and ET showed the most favourable nutritional profiles. De novo assembly using PacBio HiFi data produced reference genomes of 465–484 Mb per cultivar (46.9–48.7% repetitive elements), with gene models supported by Iso-seq transcript evidence. Together, these resources accelerate trait discovery, marker-assisted breeding, and genome-editing-based improvement of amaranth as a future nutritional crop.

Acknowledgements

We thank Nahed Mohamed and members of the Laboratory for Genome Engineering and Synthetic Biology at KAUST for critical discussions and technical support. We also thank Hudson Valley Seed Company, USA, for providing the seeds and panicle images. This work was funded by KAUST baseline funding to M.M.M.

Funding

This work was funded by KAUST baseline funding to M.M.M.

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Authors and Affiliations

1. Laboratory for Genome Engineering and Synthetic Biology, Division of Biomedical Sciences, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia

   Khalid Sedeek, Krishnaveni Sanikommu, Sunitha Kantharajappa & Magdy M. Mahfouz

2. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia

   Khalid Sedeek, Andrea Zuccolo, Umair Ali Toor, Krishnaveni Sanikommu, Sunitha Kantharajappa, Luis Rivera-Serna, Rod A. Wing & Magdy M. Mahfouz

3. Manash Kozybayev North Kazakhstan University, International Campus, Petropavlovsk, 150000, Kazakhstan

   Andrea Zuccolo

4. Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA

   Rod A. Wing

Authors

1. Khalid Sedeek
2. Andrea Zuccolo
3. Umair Ali Toor
4. Krishnaveni Sanikommu
5. Sunitha Kantharajappa
6. Luis Rivera-Serna
7. Rod A. Wing
8. Magdy M. Mahfouz

Corresponding author

Correspondence to Magdy M. Mahfouz.

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The authors declare no competing interests.

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Sedeek, K., Zuccolo, A., Toor, U.A. et al. Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing. Sci Rep (2026). https://doi.org/10.1038/s41598-026-76657-9

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• Received: 26 April 2026

• Accepted: 14 October 2026

• Published: 27 October 2026

• DOI: https://doi.org/10.1038/s41598-026-76657-9

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