Variant, Metabolite and Source Data for: Population genomics uncover loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

These files contain the variant and metabolome for a collection of 220 tef (Eragrsotis tef) accessions from an ethiopian diversity panel. The accessions were assembled and managed by the Ethiopian Institute of Agricultural Research (EIAR, Ethiopia). The variant data was produced at the John Innes Centre (UK). The metabolome data was produced at Aberystwyth University (UK). These dataset are described in Jones et al. (2024), bioRxiv, https://doi.org/10.1101/2024.09.30.615331. The source data for main figures in the publication are also included.

The submission contains

1. EIAR_filtered.vcf.gz: This is the variant data obtained from alignment of Illumina reads from all 220 teff accessions to the reference assembly of tef (Dabbi).  Low quality variants were filtered out. This variant data was used for constructing the phylogenetic relationship between the accessions. The samples names corresponds to the DNA code in Supplementary Table S10 (Jones et al, 2024).
2. pooled_EIAR_filtered.vcf.gz: After the phylogentic analysis described above, reads from accessions that were found to be genetically redundant were pooled before variant calling. This file was used for the SNP GWAS analysis. The samples names corresponds to the DNA code in Supplementary Table S10 (Jones et al, 2024).
3.  Metabolite_Profile.xlxs (source data for Figure 5): This file contains m/z feature intensities from untargeted metabolite fingerprinting using Flow Infusion Electrospray High-resolution Mass Spectrometry (FIE-HRMS). The sample names contains a combination of Location code and Plot number in Supplementary Table S10 e.g AT plot 1, CD plot 1, DZ plot 1, where AT, CD and DZ represent Alem Tena, Chefe Donsa and Debre Zeit, respectively. The data was used for the partial least squares discriminant analysis and differentially accumulated metabolites analysis presented in Figure 5.
4. Source data: Numerical source data for graphs and charts in Figures 3 - 7.
5. Tsedey TT2 Sequence from Improved Assembly: The 4A and 4B sequences around the TT2 orthologue in tef from the improved PacBio-based chromosome-scale assembly of tef. These sequences were used for plotting the LTR Copia alignments presented in Supplementary Figure 9. We thank Corteva for pre-publication access to this improved Tsedey genome assembly.