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Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

Abstract

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture1. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

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Figure 1: Ancient plant remains excavated at Yoram Cave.
Figure 2: Ancient barley samples are closely related to present-day landraces from the Levant.
Figure 3: Relationship between genetic similarity and geographical distance.
Figure 4: Gene flow between wild and domesticated barleys in the Levant.

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Acknowledgements

We gratefully acknowledge B. Schäfer for providing photographs of barley spikes and A. Fiebig for sequence data submission. This work was supported by a grant of the Israel Science Foundation (1179/13) to E.W., funding from the Endowed Chair in Molecular Genetics Applied to Crop Improvement at the University of Minnesota and the Triticeae Coordinated Agricultural Project, USDA-NIFA 2011-68002-30029 to G.J.M., and core funding of IPK Gatersleben to N.S. and M.M. R.W., J.R. and I.K.D. were supported by Research Programme funding from the Scottish government and the University of Dundee (R.W.). N.M. and U.D. acknowledge a grant from the Irene Levi Sela CARE Foundation.

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Authors and Affiliations

Authors

Contributions

E.W., T.F., N.S. and J.K. conceived the study. E.W., T.F., N.S., J.K., V.J.S. and M.M. designed experiments. N.M., U.D., M.D., S.R. and E.W. performed excavations and archaeobotanical analyses. V.J.S., A.H. and E.R. performed the ancient DNA experiments. M.M., S.H., A.K., M.S., S.H.V. and R.E.G. analyzed data. J.R., M.M., I.K.D., B.K., G.J.M., N.S. and R.W. provided exome capture data. M.M., V.J.S., A.H., S.R., T.F., J.K., E.W. and N.S. wrote the manuscript with input from all co-authors. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Tzion Fahima, Johannes Krause, Ehud Weiss or Nils Stein.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Plan of Yoram Cave—top plan and sections.

The arrow indicates the entrance to the cave and the human-made wall across it. Note the boulders in the northern room and the relatively horizontal surface in the southern room. Gray shaded borders indicate that the edge of the cave is cut into rock.

Supplementary Figure 2 Photographs from the excavation.

(a) Masada Southern Cave complex, with three caves located in the southeastern cliff of the Masada Horst. The dotted red line marks the easiest trail giving access to the caves. (b) The entrance of Yoram Cave, facing southeast, in an almost vertical cliff, some 4 m above the trail leading to the cave. (c) The south room during excavation of locus 3.

Supplementary Figure 3 Photographs of ancient barley grains used for DNA extraction.

Supplementary Figure 4 Length distribution of sequence fragments.

Supplementary Figure 5 Nucleotide misincorporation profiles in reads mapped to the whole-genome shotgun assembly of barley cv. Morex.

The proportion of C>T misincorporation sites (red) is compared to the G>A baseline (black).

Supplementary Figure 6 Nucleotide misincorporation profiles in reads mapped to the barley chloroplast genome assembly.

The proportion of C>T substitutions (red) is compared to the G>A baseline (black).

Supplementary Figure 7 Haplotype of Btr1, Btr2 and Vrs1.

The contigs of the Morex whole-genome sequencing assembly harboring these genes were identified by BLAST searches. Read depth in the deeply sequenced sample JK3014 is shown in black. Position on the respective whole-genome sequencing contig is indicated along the upper axis. Distance (in genomic sequence) from the start codon of each gene is shown along the bottom axis. Btr1 and Btr2 are single-exon genes. Gray bars indicate the positions of the three exons of Vrs1. The positions of SNPs are highlighted by vertical lines. The Morex allele is shown above and the JK3014 allele is shown below the lines. SNPs with a previously reported functional effect are shown in red. JK3014 carries a loss-of-function allele of Btr1, whereas Btr2 and Vrs1 have wild-type alleles. The coding sequences of Btr1 and Btr2 are identical to those in the haplotype of cv. Haruna Nijo as reported by Komatsuda et al. (NCBI GenBank accession KR813337.1). The sequence of Vrs1 matches the Vrs1.b2 allele as designated by Komatsuda et al.22.

Supplementary Figure 8 Relationship between genetic similarity and geographical distance.

(af) Scatterplots of genetic similarity and geographical distance between 91 extant wild barley accessions sampled across the Fertile Crescent and archaeological sample JK3014 found at Yoram Cave and sequenced to higher depth using all SNPs (a), a two-rowed cultivated landrace from Israel (b), a two-rowed cultivated landrace from Egypt (c), the ancient sample JK3014 found at Yoram Cave and sequenced to higher depth excluding transition SNPs (d), two-rowed cultivated landraces from Israel excluding transition SNPs (e) and two-rowed cultivated landraces from Egypt excluding transition SNPs (f). The geographical position attributed to each sample is as follows: 31.3141° N, 35.353° E for a and d, 31.7156° N, 35.1871° E for b and e, and 31.193° N, 29.904° E for c and f. Correlation coefficients and P values for the geographically proximate and distant subsets are indicated in blue and red, respectively.

Supplementary Figure 9 Cross-validation error of ADMIXTURE analysis.

Box plots were calculated from 20 replicate runs for each K value.

Supplementary Figure 10 ADMIXTURE analysis with K = 5 for domesticated and wild samples.

Top, domesticated samples; bottom, wild samples. Colors in both panels correspond to the same ancestral populations. Sample names and countries of origin are indicated above and below the plots, respectively. Ancient samples are highlighted by blue borders.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 1, 2 and 4. (PDF 1168 kb)

Supplementary Table 3

Identity-by-state matrix. (XLSX 26 kb)

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Mascher, M., Schuenemann, V., Davidovich, U. et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet 48, 1089–1093 (2016). https://doi.org/10.1038/ng.3611

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