A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

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Abstract

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world’s most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 bc in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130–1000 bc. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

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Fig. 1: Emmer wheat husks in accession UC10164 and the sequenced specimens.
Fig. 2: The relationship between UC10164 and modern emmer wheat.
Fig. 3: Phylogenetic analysis of UC10164 and 64 modern emmer wheats.
Fig. 4: Haplotype sharing between UC10164 and modern emmer wheat within loci associated with selection under domestication.

Data availability

Sequence data are deposited in the ENA with study accession number PRJEB31103. The genotype calls are also provided as the source data for Fig. 2. The database of archaeobotanical observations is provided as the source data for Extended Data Fig. 1. Source data are available for Figs. 24 and Extended Data Figs. 15.

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Acknowledgements

We thank Y. Diekmann, D. O’Rourke and A. Garnett for helpful discussions. M.F.S. and R.M. are supported by RCUK BBSRC grant BB/M011585/1. R.M. is also supported by RCUK BBSRC grant BB/P024726/1; L.R.B. by the Spanish Ministry of Economy and Competitiveness Severo Ochoa Programme for Centres of Excellence in R&D 2016-2019 (SEV-2015-0533) and CERCA Programme, Generalitat de Catalunya; M.G.T. and S.B. by a Wellcome Trust Senior Research Fellowship, grant 100719/Z/12/Z. D.Q.F. and C.S. are supported by the ERC ComPag project, grant number 323842. V.E.M. and S.B. are partially supported by the RCUK NERC grant NE/P012574/1. UCL computing infrastructure was supported by BBSRC grant BB/R01356X/1.

Author information

L.R.B., M.F.S., R.M., D.Q.F., C.S., A.S. and M.G.T. designed and coordinated the study. M.F.S. designed and performed data analysis. L.R.B., S.B. and V.E.M. performed experiments. C.S. obtained image data. M.F.S. and R.M. coordinated the sequencing. D.Q.F. coordinated the carbon dating. M.G.T. supervised access to the ancient DNA laboratory. D.Q.F., A.S. and C.S. collated archaeobotanical data. M.F.S. and R.M. wrote the manuscript. All of the authors edited and approved the manuscript.

Correspondence to Michael F. Scott or Richard Mott.

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The authors declare no competing interests.

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Peer Review Information Nature Plants thanks Thomas Gilbert, James Breen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Map showing archaeobotanical observations of emmer wheat from 9000 – 1000 BCE in Northeast Africa and South West Asia.

Map showing archaeobotanical observations of emmer wheat from 9000 – 1000 BCE in Northeast Africa and South West Asia. The collection location for the sequenced accession (UC10164) is labelled.

Extended Data Fig. 2 Summary of sequencing data from UC10164 samples S1 and S2.

Summary of sequencing data from UC10164 samples S1 and S2. Panel A shows the C to T and G to A misincorporations of alignments against the emmer wheat reference genome as output by MapDamage. Both samples show a small excess of these misincorporations in the 2 bp at each fragment end, as expected for partially UDG treated aDNA libraries. Panel B shows the distribution of fragment sizes after the overlapping paired-end reads were collapsed and adapter sequence was removed using AdapterRemoval. Panel C shows coverage and subgenome representation for different minimum mapping quality scores after these fragments were aligned to the hexaploid bread wheat reference genome. Panel D shows the coverage obtained from alignment to the emmer wheat reference genome, split by minimum mapping quality filters. The exonic SNP sites (at which genotypes are called) have a much lower percentage of ambiguous alignments with low mapping quality scores.

Extended Data Fig. 3 (a) phylogeny of modern emmer wheat accessions and (b) source population proportions inferred by the ADMIXTURE model for various number of source populations (K parameter).

(a) phylogeny of modern emmer wheat accessions and (b) Source population proportions inferred by the ADMIXTURE model for various number of source populations (K parameter). The maximum likelihood phylogeny in (a) was constructed from the full set of SNPs called among modern accessions, excluding UC10164. Bootstrap support for each node is shown where it is less than 100 (based on 1000 bootstraps). In (b), the majority of the ancestry proportion inferred for the ancient Egyptian accession (UC10164) across K values is from the same population that predominates among the “Indian Ocean” subgroup (green accession names). Furthermore, the ancient Egyptian accession has a relatively high proportion of ancestry inferred to come from population groups that are common among modern wild Southern Levant emmer wheats (light blue accession names).

Extended Data Fig. 4 Heatmap of the genotypic similarity between each pair of accessions across 86,594 SNP sites that were called in the ancient Egyptian accession (UC10164).

Heatmap of the genotypic similarity between each pair of accessions across 86,594 SNP sites that were called in the ancient Egyptian accession (UC10164). Below the diagonal, we plot similarity using identity by state. Above the diagonal, we plot haplotypic similarity, which is defined as the fraction of sliding windows of 50 SNP sites that are more than 95% concordant.

Extended Data Fig. 5 Differences between each modern accession and the ancient Egyptian accession (UC10164) across the genome.

Differences between each modern accession and the ancient Egyptian accession (UC10164) across the genome. The fraction of genotypic differences from UC10164 is calculated within sliding windows of 50 SNPs (moved in intervals of 25 SNPs). Each modern accession is plotted as a line and coloured according to its subgroup membership. Below zero we plot the ancestry mosaic inferred for each SNP site called in UC10164. The dissimilarity within sliding windows is plotted against the median physical map position of the SNPs in the sliding window. Each chromosome has a large region around the centromere that has low exonic SNP density and low recombination rate, resulting in long haplotypes.

Supplementary information

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Supplementary Tables 1–5

Supplementary Table 1: table of alignment statistics for S1 and S2 after various filters have been applied. Supplementary Table 2: concordances between UC10164 and modern accessions, split by chromosome and accession subgroup. Supplementary Table 3: D statistics calculated for the phylogeny (outgroup, (Southern Levant Accession, (Indian Ocean, UC10164))). Supplementary Table 4: raw radiocarbon dating results. Supplementary Table 5: at SNP genotype sites called in UC10164, the proportion of substitutions that are C to T and G to A, relative to the outgroup genotype, and the ratio of transitions to transversions.

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Scott, M.F., Botigué, L.R., Brace, S. et al. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat. Plants 5, 1120–1128 (2019) doi:10.1038/s41477-019-0534-5

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