Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)
2025
Jones, M.R.W. | Kebede, W. | Teshome, Abel | Girija, A. | Teshome, A. | Girma, D. | Brown, J.K.M. | Quiroz-Chavez, J. | Jones, Christopher S. | Wulff, B.B.H. | Assefa, K. | Tadele, Z. | Mur, L.A.J. | Chanyalew, S. | Uauy, C. | Shorinola, Oluwaseyi
Tef (<i>Eragrostis tef</i>) 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 <i>qSH1</i>—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 <i>TRANSPARENT TESTA 2</i>, 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.
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