Genome-wide knowledge about the nature and extent of genetic diversity present in tef (Eragrostis tef), the most consumed food grain in Ethiopia is limited. Adopting next generation sequencing (NGS) protocols to enhance its genomics and breeding is essential. Here, we applied the Restriction Site Associated DNA (RAD) sequencing protocol and surveyed the genomes of 43 tef landraces, one mutant line and two wild Eragrostis species. After mapping sequencing reads to the de novo assembled unitag and the tef reference genome, a total of 9,024 and 58,735 high quality single nucleotide polymorphisms (SNPs) were identified, respectively. We identified greater number of SNPs and greater nucleotide diversity in the two wild Eragrostis species than in the tef landraces. The tef landrace populations in this study were poorly differentiated with FST values of 0.015. In the phylogenetic analysis, grouping of the landraces was not consistent with the area of collection, but few localized grouping of the landraces was evident, probably showing the communality of tef seed use across geographical boundaries. The improved tef varieties show reduced genetic diversity compared to the landraces and were all grouped into one cluster reflecting the nature of tef breeding which largely targets common genomic regions. We suggest that future work needs to aim beyond common genomic regions. The work presented here is a valuable addition to the growing molecular resources developed for tef genetic improvement.
