An inter-specific Amaranthus pangenome captures genetic variation potentially underlying key leafy vegetable traits in this underutilised crop
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Wiley
Abstract
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.
Description
DATA AVAILABILITY : Data presented in this paper can be found in the National Center for Biotechnology Information under Bioproject PRJNA1193012 (genome sequencing, assembly and RNA sequencing data) and in the MASSIVE database under datasets MSV000096703, MSV000096711, MSV000096712, MSV000096713, MSV000096714 and MSV000096870 (as outlined in the Supporting Information). All genome assemblies, annotations, protein-coding genes, sequence and structural variants, and the graphical pangenome are deposited in the ORCAE database at https://bioinformatics.psb.ugent.be/gdb/Amranthus/.
SUPPLEMENTARY FIGURES
FIG. S1 Leaf trait data from the irrigated field trial of the eight MAGIC parent accessions.
FIG. S2 Accession and metabolite sample clustering based on normalised data for 3256 redundant detected features.
FIG. S3 Clustering of 122 annotated metabolites based on their abundance across samples from the 8 Amaranth MAGIC population founder lines.
FIG. S4 Amaranthus MAGIC population parent accession genome assembly and annotation.
FIG. S5 Co-linearity and phylogenetic relationships between the eight Amaranth MAGIC population parent genomes.
FIG. S6 Analysis of pangenome components.
FIG. S7 Structural variants in the eight MAGIC population founder lines.
FIG. S8 Density of structural variants in the eight MAGIC population founder accession genomes.
FIG. S9 Genes contained within deletion regions (or containing deleted regions) of the MAGIC parent genomes compared with the A. cruentus reference genome.
FIG. S10 Linear reference vs pangenome mapping statistics.
SUPPLEMENTARY METHOD AND TABLE
METHODS S1 Detailed metabolite profiling methodology.
TABLE S1 Statistical significance of trait variation in the eight MAGIC population founder lines from irrigated field trials.
SUPPLEMENTARY DATASETS
DATASET S1 MAGIC population parent accession field trial information and data.
DATASET S2 Custom metabolite database for annotation.
DATASET S3 Data from Lin et al. (2022) for the eight MAGIC parent accessions.
DATASET S4 Features detected from metabolome profiling of the eight amaranth MAGIC parent accessions.
DATASET S5 Sequencing statistics for the eight Amaranthus accessions.
DATASET S6 Repetitive element content of the eight Amaranth MAGIC population parent genomes and the Amaranthus cruentus and Amaranthus hypochondriacus reference genomes.
DATASET S7 Orthologous gene families and single-copy genes (orthogroups) within the 8 amaranth MAGIC population parent lines and the reference Amaranthus cruentus, Amaranthus hypochondriacus and Amaranthus tricolor genomes.
DATASET S8 Gene Ontology terms showing significant enrichment in genes from the core, dispensable and private pangenome components.
DATASET S9 Genes within the Amaranthus cruentus reference genome which are missing in one or more MAGIC population parent lines.
DATASET S10 Mapping statistics for alignment of the 121 amaranth whole genome sequences from Stetter et al. (2020) to the Amaranthus cruentus linear reference genome (bams) and to the graphical pangenome generated in this study (gams).
Keywords
Amaranthus, Field trial, MAGIC population, Metabolomics, Pangenome, Structural variants
Sustainable Development Goals
SDG-15: Life on land
Citation
De Kinderen, M.A.J., Ma, X., Vaistij, F.E. et al. 2026, 'An inter-specific Amaranthus pangenome captures genetic variation potentially underlying key leafy vegetable traits in this underutilised crop', New Phytologist, vol. 250, no. 6, pp. 3540-3558. https://doi.org/10.1111/nph.71183https://doi.org/10.1111/nph.71183.