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

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.