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Population genomics of the wild wheat Aegilops tauschii (Open wild wheat consortium phase II)

Cavalet-Giorsa, Emile1; Gonzalez-Munoz, Andrea1; Athiyannan, Naveenkumar1; Wulff, Brande B. H.1; Krattinger, Simon G.1

Published Jun 12, 2024; Updated Aug 13, 2024 on Dryad. https://doi.org/10.5061/dryad.vmcvdnd0d

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Jun 12, 2024 version files 158.48 GB
Aug 13, 2024 version files 158.76 GB

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Abstract

Wild wheat relatives of bread wheat represent genetic diversity that can be used for wheat crop improvement. Here, we establish and analyse genomic resources for Tausch’s goatgrass, Aegilops tauschii, the donor of the bread wheat D genome. We determined 493 genetically non-redundant accessions from a diversity panel of over 900 sequenced accessions. We generated high-quality assemblies for 46 accessions, including annotated chromosome-scale assemblies for one accession from each of the three lineages of Ae. tauschii to serve a reference assemblies to anchor the genomic resources. This dataset was generated under the aegis of the Open Wild Wheat Consortium (www.openwildwheat.org). We also resequenced and analysed 60 wheat landraces and generated a chromosome-scale genome assembly for one of these to study the genetic composition and history of the bread wheat D genome. We determined the complexity and origin of the D genome across 17 hexaploid wheat lines by dividing the wheat genomes into 50-kb windows and assigned each window to an Ae. tauschii subpopulation based on identity-by-state.

This dataset provides:

  1. Pseudo-chromosome level genome assemblies, Hi-C contact maps and genome annotations for the Ae. tauschii lineage-reference accessions TA10171 (L1), TA1675 (L2) and TA2576 (L3),
  2. Contig-level and lineage reference-scaffolded assemblies for 43 Ae. tauschii accessions sequenced with PacBIO CCS
  3. Pseudo-chromosome level genome assembly, Omni-C contact map and genome annotation for bread wheat landrace accession CWI 86942,
  4. Variant call (SNP) vcf file for the Ae. tauschii diversity panel. SNP were called against the TA1675 (L2) reference assembly,
  5. Phylogenetic newick tree file for the non-redundant Ae. tauschii accessions,
  6. Structural variants (SV) vcf files for Ae. tauschii accessions sequenced with PacBIO CCS. SV were called against the TA1675 (L2) reference assembly,
  7. IBSpy variations across 17 hexaploid wheat genomes using Ae. tauschii k-mer sets