The teff (Eragrostis tef) pangenome reveals haplotypic diversity and targets for molecular improvement

Modern genomic tools can accelerate molecular breeding of underutilized crops such as teff (Eragrostis tef), a gluten-free cereal that is a staple in the Horn of Africa. Here, we report the development of a pangenome comprising chromosome-scale assemblies of 26 teff accessions, including both landraces and improved cultivars, and representing the species’ gene pool. The teff pangenome reveals a highly conserved genome architecture characterized by structural stability across different accessions, with a content of repetitive elements increased by 8% with respect to previous annotations. We describe the features of the pangenome and use it to advance teff biology, targeting seed color, a priority trait for breeding. By defining k-mer-based haplotypes at genomic loci previously known to be associated with the trait, we build a prediction model capable of accurately predicting the color of the seed. Our supervised classification analysis shows that seed color determination cannot be explained by less than four haplotype combinations at loci on chromosomes 4B and 6A. Our results represent a key resource to advance teff breeding and demonstrate that a pangenomic dimension can expand association studies to fully dissect the determination of complex traits.