Genetic diversity and environmental adaptation in Ethiopian tef

Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000-1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis (RDA), complemented by single-site differentiation and LD-based methods. We identified 145 loci associated with abiotic environmental factors, with minimal geographic influence observed in the genetic structure of the sample population. Overall, this work contributes to the broader understanding of local adaptation and its genetic basis in tef, providing insights that support efforts to develop elite germplasms with improved environmental resilience.

Methods
The Ethiopian Biodiversity Institute provided the genetic materials for this study and granted access to passport information for environmental data curation. Bioclimatic (bio1-bio19) and altitudinal data were obtained using latitude and longitude coordinates from each site, with WorldClim version 2.1 layers at 10-minute resolution based on long-term averages for 1970-2000 (Fick & Hijmans, 2017). Researchers at the Ethiopian Institute of Agricultural Research, including Tadelech Bizuneh, Adanech Teshome, and Doni Hinsene, prepared DNA samples from young leaf samples for each greenhouse-grown tef accession. DNA concentration and quality were determined using a 1.5% agarose gel and a NanoDrop Spectrophotometer. The extracted DNA was sent to the BioFrontiers Sequencing Core at the University of Colorado Boulder for unique dual indexing 10 bp library preparation. Genomic libraries of the Ethiopian tef accessions were then sent to the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus for paired-end whole genome sequencing (2 × 150 bp at ~10× coverage) using an Illumina NovaSeq 6000 platform. Details regarding the variant calling pipeline and downstream analyses are provided in the manuscript.