An inter-specific Amaranthus pangenome captures genetic variation potentially underlying key leafy vegetable traits in this underutilised crop

Amaranthus species (particularly Amaranthus cruentus, Amaranthus hypochondriacus, Amaranthus tricolor and Amaranthus caudatus) are traditional underutilised crops with the potential to contribute to sustainable, healthy food systems. We focus on amaranth as a leafy vegetable aiming to develop improved lines for cultivation by smallholder farmers in Sub-Saharan Africa. We demonstrate differences in leaf yield and metabolites relevant to human nutrition across eight amaranth accessions: four A. cruentus and four A. hypochondriacus. These accessions are founders of an inter-specific multi-parent advanced generation inter-cross population. We generated high-quality genome assemblies and annotations for these founder lines and identified sequence and structural variants (SVs) compared with a reference A. cruentus genome. Pangenome analysis (also including A. cruentus, A. hypochondriacus and A. tricolor reference genomes) identified core, dispensable and private gene families. Fifty per cent of gene families were core, highlighting the value, in terms of gene discovery, of sequencing additional accessions and the inclusion of three Amaranthus species. A graphical pangenome was constructed using SVs and demonstrated variation in copy number of genes with a likely role in disease resistance. This inter-specific pangenome will be highly valuable for future research on amaranth and facilitate usage of SVs in trait mapping and causal gene discovery.