Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)
Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free "superfood" with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited "omics" resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1-a transcription factor regulating inflorescence morphology in cereals. We also observe a previously unknown relationship between grain size, colour, and fatty acids. These traits are highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.
Authors
- Kebebew Assefa (ORCID: https://orcid.org/0000-0002-2734-2436)
- Brande B. H. Wulff (ORCID: https://orcid.org/0000-0003-4044-4346)
- Oluwaseyi Shorinola (ORCID: https://orcid.org/0000-0003-3516-303X)
- Maximillian R. W. Jones (ORCID: https://orcid.org/0000-0002-4887-591X)
- Chris S. Jones (ORCID: https://orcid.org/0000-0001-9096-9728)
- Jesús Quiroz-Chávez (ORCID: https://orcid.org/0000-0001-5935-2578)
- Abel Teshome (ORCID: https://orcid.org/0000-0001-7137-5991)
- Zerihun Tadele (ORCID: https://orcid.org/0000-0002-3686-3698)
- Luis A. J. Mur (ORCID: https://orcid.org/0000-0002-0961-9817)
- Aiswarya Girija (ORCID: https://orcid.org/0000-0002-7802-7145)
- Cristóbal Uauy (ORCID: https://orcid.org/0000-0002-9814-1770)
- Solomon Chanyalew (ORCID: https://orcid.org/0000-0003-3117-5383)
- James K. M. Brown (ORCID: https://orcid.org/0000-0001-8719-2268)
- Dejene Girma
- Adanech Teshome
- Worku Kebede
Institutions
- John Innes Centre (GB)
- University of Bern (CH)
- Aberystwyth University (GB)
- Scuola Superiore Sant'Anna (IT)
- Norwich Research Park (GB)
- Institute of Biological, Environmental and Rural Sciences (GB)
- Ethiopian Institute of Agricultural Research (ET)
- International Livestock Research Institute (KE)
- King Abdullah University of Science and Technology (SA)
- University of Birmingham (GB)
Publication Details
- Journal
- Communications Biology
- Published
- 2025-05-26
- DOI
- https://doi.org/10.1038/s42003-025-08206-5
- Citations
- 1
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- Aberystwyth University
- European Commission
- Consejo Nacional de Ciencia y Tecnología
- Consortium of International Agricultural Research Centers
- Directorate for Biological Sciences
- Horizon 2020 Framework Programme
- Biotechnology and Biological Sciences Research Council