de Kinderen, Maud Allegonda Johanna
ORCID: 0000-0002-9439-7314
(2025)
Exploiting an Amaranth MAGIC population and diversity set for improvement of leafy vegetable traits.
PhD thesis, University of York.
Abstract
Amaranths are traditional nutritious underutilised crops with potential to contribute to sustainable, healthy food systems, although unfortunately research and breeding is often neglected. Hence improvement of vegetable amaranth through understanding genomics underlaying agronomic traits and selecting preferred lines for cultivation could greatly benefit African smallholders.
Most of this work focussed on a Multi-parent Advanced Generation Inter-Cross (MAGIC) population created for linking phenotypic with genetic variation and developing new amaranth lines. Using MAGIC founder plus existing reference genomes, an inter-specific Amaranthus pan-genome has been made as a novel genetic resource to be used by scientists. Additionally, a 90-accession diversity set has been exploited both to aid species demarcation and to conduct the first metabolite-based genome-wide association study (mGWAS) with amaranths. Lastly, genomic and transcriptomic data of both sets (MAGIC and diversity) were used to identify putative biosynthetic gene clusters (BGC) aiding prediction of nutritional metabolite profiles.
The Amaranthus pan-genome showed the MAGIC founders to be phenotypically metabolically and genomically variable, with a graphical pan-genome based on structural variants developed for read alignment. 51 offspring accessions are selected as best due to consistent performance. Phenotypic variation of the founders segregates in the MAGIC offspring indicating a sufficient quality mapping population. This was confirmed by the ability to map genome associations with leaf yield as a relevant agronomic trait at two loci (chromosome 9 and 10). Phylogenetic analysis and mGWAS using the diversity set was successful, classifying 38 of 90 accessions, questioning existence of the A. hybridus species and revealing 81 metabolite-genome associations. 43 putative BGC are identified with 11 selected as of interest due to gene co-expression.
Both exploited amaranth sets contain lines useful for direct farming or further breeding practices. Additional trials are suggested incorporating more phenotypes and to identify candidate genes, however, current association results can already benefit amaranth improvement.
Metadata
| Supervisors: | Denby, Katherine and Jeffares, Daniel |
|---|---|
| Keywords: | Amaranthus, MAGIC population, QTL mapping, leaf yield, pan-genomes, metabolomics |
| Awarding institution: | University of York |
| Academic Units: | The University of York > Biology (York) |
| Date Deposited: | 16 Feb 2026 11:20 |
| Last Modified: | 16 Feb 2026 11:20 |
| Open Archives Initiative ID (OAI ID): | oai:etheses.whiterose.ac.uk:38163 |
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