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

Scott, Michael F., Botigué, Laura R., Brace, Selina, Stevens, Chris J., Mullin, Victoria E., Stevenson, Alice, Thomas, Mark G., Fuller, Dorian Q., Mott, Richard·2019·Nature Plants
DOI 10.1038/s41477-019-0534-5PMC PMC6858886
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  1. Arranz-Otaegui, A., Colledge, S., Zapata, L., Teira-Mayolini, L. C. & Ibáñez, J. J. Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia. Proc. Natl Acad. Sci. USA 113, 14001–14006 (2016). · DOI
  2. Fuller, D. Q., Willcox, G. & Allaby, R. G. Early agricultural pathways: moving outside the ‘core area’ hypothesis in southwest Asia. J. Exp. Bot. 63, 617–633 (2012). · DOI
  3. Fuller, D. Q. & Lucas, L. in Encyclopedia of Global Archaeology (Ed. Smith, C.) 7812–7817 (Springer, 2014). · DOI
  4. McClatchie, M. et al. Neolithic farming in north-western Europe: archaeobotanical evidence from Ireland. J. Archaeol. Sci. 51, 206–215 (2014). · DOI
  5. Mascher, M. et al. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat. Genet. 48, 1089–1093 (2016). · DOI
  6. Ramos-Madrigal, J. et al. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr. Biol. 26, 3195–3201 (2016). · DOI
  7. Vallebueno-Estrada, M. et al. The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. Proc. Natl Acad. Sci. USA 113, 14151–14156 (2016). · DOI
  8. Kistler, L. et al. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362, 1309–1313 (2018). · DOI
  9. Smith, O. et al. A domestication history of dynamic adaptation and genomic deterioration in sorghum. Nat. Plants 5, 369–379 (2018). · DOI · Paper page
  10. Palmer, S. A., Smith, O. & Allaby, R. G. The blossoming of plant archaeogenetics. Ann. Anat. 194, 146–156 (2012). · DOI
  11. Bilgic, H., Hakki, E. E., Pandey, A., Khan, M. K. & Akkaya, M. S. Ancient DNA from 8400 year-old Çatalhöyük wheat: implications for the origin of neolithic agriculture. PLoS ONE 11, e0151974 (2016). · DOI
  12. Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009). · DOI
  13. Avni, R. et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357, 93–97 (2017). · DOI
  14. Nalam, V. J., Vales, M. I., Watson, C. J. W., Kianian, S. F. & Riera-Lizarazu, O. Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.). Theor. Appl. Genet. 112, 373–381 (2006). · DOI
  15. Pourkheirandish, M. et al. Evolution of the grain dispersal system in barley. Cell 162, 527–539 (2015). · DOI
  16. Fuller, D. Q. Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann. Bot. 100, 903–924 (2007). · DOI
  17. Harlan, J. R., de Wet, J. M. J. & Price, E. G. Comparative evolution of cereals. Evolution 27, 311–325 (1973). · DOI
  18. Salamini, F., Özkan, H., Brandolini, A., Schäfer-Pregl, R. & Martin, W. Genetics and geography of wild cereal domestication in the near east. Nat. Rev. Genet. 3, 429–441 (2002). · DOI
  19. Horovitz, A. The soil seed bank of wild emmer. In Proc. International Symposium on In situ Conservation of Plant Genetic Diversity (eds Zencirci, N. et al.) 185–188 (Central Research Institute for Field Crops, 1998).
  20. Nave, M., Avni, R., Ben-Zvi, B., Hale, I. & Distelfeld, A. QTLs for uniform grain dimensions and germination selected during wheat domestication are co-located on chromosome 4B. Theor. Appl. Genet. 129, 1303–1315 (2016). · DOI
  21. Allaby, R. G., Stevens, C., Lucas, L., Maeda, O. & Fuller, D. Q. Geographic mosaics and changing rates of cereal domestication. Proc. R. Soc. B 372, 20160429 (2017).
  22. Crawford, D. J. Food: tradition and change in Hellenistic Egypt. World Archaeol. 11, 136–146 (1979). · DOI
  23. Nesbitt, M. & Samuel, D. From stable crop to extinction? The archaeology and history of the hulled wheats. In Proc. First International Workshop on Hulled Wheats (eds Padulosi, S. et al.) 41–100 (International Plant Genetic Resources Institute, 1996).
  24. Wetterstrom, W. in The Archaeology of Africa (eds Andah, B., Okpoko, A., Shaw, T. & Sinclair, P.) 165–226 (Routledge, 1993).
  25. Zaharieva, M., Ayana, N. G., Al Hakimi, A., Misra, S. C. & Monneveux, P. Cultivated emmer wheat (Triticum dicoccon Schrank), an old crop with promising future: a review. Genet. Resour. Crop Evol. 57, 937–962 (2010). · DOI
  26. IWGSC. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018). · DOI
  27. Golenberg, E. M. Outcrossing rates and their relationship to phenology in Triticum dicoccoides. Theor. Appl. Genet. 75, 937–944 (1988). · DOI
  28. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009). · DOI · Paper page
  29. Murray, M. A. in Ancient Egyptian Materials and Technology (eds Nicholson, P. T. & Shaw, I.) 505–536 (Cambridge Univ. Press, 2000).
  30. Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345, 1250092 (2014). · DOI
  31. Olsen, K. M. et al. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 173, 975–983 (2006). · DOI
  32. Walsh, B. & Lynch, M. Evolution and Selection of Quantitative Traits (Oxford Univ. Press, 2018). · DOI
  33. Fuller, D. Q., Lucas, L., Gonzalez Carretero, L. & Stevens, C. From intermediate economies to agriculture: trends in wild food use, domestication and cultivation among early villages in southwest Asia. Paleorient 44, 59–74 (2018).
  34. Badaeva, E. D. et al. Chromosomal passports provide new insights into diffusion of emmer wheat. PLoS ONE 10, e0128556 (2015). · DOI
  35. Luo, M. C. et al. The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication. Theor. Appl. Genet. 114, 947–959 (2007). · DOI
  36. Wengrow, D., Dee, M., Foster, S., Stevenson, A. & Ramsey, C. B. Cultural convergence in the neolithic of the Nile Valley: a prehistoric perspective on Egypt’s place in Africa. Antiquity 88, 95–111 (2014). · DOI
  37. Fuller, D. & Hildebrand, E. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 507–525 (Oxford Univ. Press, 2013).
  38. Civáň, P., Ivaničová, Z. & Brown, T. A. Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent. PLoS ONE 8, e81955 (2013). · DOI
  39. He, F. et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat. Genet. 51, 896–904 (2019). · DOI
  40. Di Donato, A., Filippone, E., Ercolano, M. R. & Frusciante, L. Genome sequencing of ancient plant remains: findings, uses and potential applications for the study and improvement of modern crops. Front. Plant Sci. 9, 441 (2018). · DOI
  41. Zohary, D., Hopf, M. & Weiss, E. Domestication of Plants in the Old World (Oxford Univ. Press, 2012). · DOI
  42. Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009). · DOI · Paper page
  43. Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887 (2013). · DOI · Paper page
  44. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 6, pdb.prot5448 (2010). · DOI
  45. Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016). · DOI
  46. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). · DOI · Paper page
  47. Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007). · DOI · Paper page
  48. McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010). · DOI · Paper page
  49. Jordan, K. W. et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 16, 48 (2015). · DOI
  50. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011). · DOI
  51. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011). · DOI
  52. Vavilov, N. I. Origin and Geography of Cultivated Plants (Cambridge Univ. Press, 1989).
  53. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007). · DOI · Paper page
  54. Lee, T. H., Guo, H., Wang, X., Kim, C. & Paterson, A. H. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genom. 15, 162 (2014). · DOI
  55. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009). · DOI · Paper page
  56. Kaplan, N. L., Hudson, R. R. & Langley, C. H. The hitchhiking effect revisited. Genetics 123, 887–899 (1989). · DOI · Paper page
  57. Haldane, J. B. S. The combination of linkage values and the calculation of distances between the loci of linked factors. J. Genet. 8, 299–309 (1919).
  58. Cabrera, C. P. et al. Uncovering networks from genome-wide association studies via circular genomic permutation. G3 2, 1067–1075 (2012). · DOI

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    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Scott, M. F., Botigué, L. R., Brace, S., Stevens, C. J., Mullin, V. E., Stevenson, A., Thomas, M. G., Fuller, D. Q., & Mott, R.
ORCID
Venue
Nature Plants
Publisher
Springer Science and Business Media LLC
Published
2019-11-04
Volume
5
Issue
11
Pages
1120-1128
ISSN
2055-0278
DOI
10.1038/s41477-019-0534-5
PMC
PMC6858886
Cited by
77
References
8
Language
en
Licence

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