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Whole-genome analysis with SNPs from BOPA1 shows clearly defined groupings of Western Mediterranean, Ethiopian, and Fertile Crescent barleys

Abstract

The discovery of Hordeum spontaneum C. Koch, a wild ancestor of cultivated barley, in Morocco in 1978 led to the proposal of a multicentric origin for this crop, as an alternative to the widely accepted theory of a single centre of domestication in the Fertile Crescent. Since this discovery, we have tested this hypothesis using the most advanced genetic techniques available at the time, from CM-proteins to RFLP and DNA-chloroplast markers. Nowadays, the availability of single nucleotide polymorphism (SNP) markers that are spread densely over the barley genome provides us with another powerful tool to give further support for the above. We have used 1,536 SNPs from the Barley Oligo Pool Assay 1 (BOPA1) of Illumina to characterize 107 wild and cultivated barley accessions from the Western Mediterranean, Fertile Crescent, Ethiopia, and Tibet. The results have confirmed that each location of the above-mentioned germplasm groups clusters separately. Analysis of molecular variance enabled us to focus on the chromosomal regions and loci that differentiated these groups of barley germplasm. Some of these regions contain vernalization and photoperiod response genes, some of the so-called domestication genes, as well as the most important quantitative trait locus for flowering time in the Mediterranean region. We have combined these results with other genetic evidence, and interpreted them in the framework of current theories on the onset of the Neolithic revolution in the Mediterranean region, to conclude that neither Ethiopia nor the Western Mediterranean can be ruled out as centres of barley domestication, together with the Fertile Crescent.

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Acknowledgments

We want to thank INIA (MICINN) for partially funding this work through different grants. The Centre UdL-IRTA forms part of the Centre CONSOLIDER on Agrigenomics funded by the Spanish Ministry of Education and Science and acknowledges partial funding from grant AGL2005-07195-C02-02. Genotyping of the RIL population with BOPA1 was funded by the Spanish Ministry of Science and Innovation; project GEN2006-28560-E. We thank Prof. Nicolás Jouve Universidad de Alcalá de Henares, Spain) for supplying us with interesting information regarding mutation frequencies. We also thank Dr. Helmut Knüpffer (IPK, Gatersleben, Germany), who kindly supplied us with the Hordeum agriochrithon accessions.

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Correspondence to Ernesto Igartua.

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Lluís Torres: Deceased.

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Igartua, E., Moralejo, M., Casas, A.M. et al. Whole-genome analysis with SNPs from BOPA1 shows clearly defined groupings of Western Mediterranean, Ethiopian, and Fertile Crescent barleys. Genet Resour Crop Evol 60, 251–264 (2013). https://doi.org/10.1007/s10722-012-9831-9

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  • DOI: https://doi.org/10.1007/s10722-012-9831-9

Keywords

  • Barley
  • Domestication
  • Phylogeny
  • Western Mediterranean
  • Whole-genome scan