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Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

Nature Genetics volume 44, pages 1388–1392 (2012)Cite this article

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Abstract

As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present1, domesticated crops encountered considerable ecological and environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS2 (HvCEN) as a contributor to successful environmental adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.

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Figure 1: Genetic structure and population differentiation in European barley germplasm.
Figure 2: Genome-wide and local divergent selection.
Figure 3: Flowering time of ten verified MAT-C alleles and associated mutations in HvCEN.
Figure 4: Allele mining at HvCEN.
Figure 5: Natural distribution of major haplotypes.

Accession codes

Primary accessions

NCBI Reference Sequence

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Acknowledgements

We thank A. Graner, S. Friedel, F. Blattner, R. Sharma, R.K. Pasam, R. Neef and G. Willcox for discussions, K. Mayer and M. Pfeifer for searches for conservation of synteny in sequenced model grass genomes, J. Plieske and G. Durstewitz for their assistance in mapping and development of the cluster file and C. Trautewig, M. Ziems, K. Wolf, N. Uzrek and J. Morris for excellent technical assistance. We thank H. Özkan, E. Fridman and the IPK Genebank for providing seeds and/or DNA for barley accessions. The authors would like to acknowledge the support given by the Scottish Government Rural and Environment Science and Analytical Services Division Research Programme (WP 5.2), the European Union International Research Cooperation with Mediterranean Partner Countries program ICA3-CT2002-10026 (Mapping Adaptation of Barley to Drought Environments) and Framework Programme 7 (FP7) TriticeaeGenome grant (FP7-212019), and the German Science Foundation Priority Programme SPP1530 to B.K.

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Author notes

  1. Jordi Comadran and Benjamin Kilian: These authors contributed equally to this work.

Authors and Affiliations

  1. Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie,, Dundee, UK

    Jordi Comadran, Joanne Russell, Luke Ramsay, Paul Shaw, Micha Bayer, William Thomas, David Marshall, Pete Hedley & Robbie Waugh

  2. Genebank Department Genome Diversity Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Benjamin Kilian & Nils Stein

  3. TraitGenetics, Gatersleben, Germany

    Martin Ganal

  4. Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA), Genomics Research Centre, Fiorenzuola d'Arda, Italy

    Alessandro Tondelli

  5. Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy

    Nicola Pecchioni & Enrico Francia

  6. KWS Cereals Biotechnology, KWS LOCHOW, Bergen, Germany

    Viktor Korzun

  7. Department of Earth Sciences, Regional Climate Group, University of Gothenburg, Gothenburg, Sweden

    Alexander Walther

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Contributions

J.C. conceived and executed the genome-wide divergent selection component, identified candidate genes, validated HvCEN as MAT-C and wrote the manuscript. B.K. established the diverse barley population, executed and analyzed the diversity study and wrote the manuscript. P.H., J.R. and M.B. developed the iSelect genotyping platform, wrote the Supplementary Note and edited the manuscript. N.S., L.R. and V.K. developed the Morex × Barke population and conducted iSelect linkage mapping and analyzed the data. M.G. coordinated the development of the 9K barley iSelect platform, directed the assay analysis and provided preliminary allele calls and the mapping data. W.T. advised on germplasm, P.S. developed the underlying database and online data access tools and D.M. advised on the analysis of genotypic data. A.T., N.P. and E.F. developed the Nure × Tremois population, conceived and analyzed the Nure × Tremois work, conducted the expression analysis and suggested candidate genes. A.W. created the topographical maps showing the haplotype distributions. R.W. conceived, directed and coordinated the work and wrote the manuscript.

Corresponding author

Correspondence to Robbie Waugh.

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Competing interests

M.G. has competing commercial interests as a member of TraitGenetics, which is a commercial company that performs molecular marker analysis services with the barley array. The authors maintain their agreement to the sharing of all data and materials. There are no further products in development or marketed products or patents to declare. All other authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–5 and Supplementary Tables 1–5, 7–10, 12 and 13 (PDF 1606 kb)

Supplementary Table 6

Barley 9K iSelect platform (Excel file) (XLSX 1422 kb)

Supplementary Table 11

Geo-referenced wild, landrace and cultivated lines (Excel File) (XLSX 108 kb)

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Comadran, J., Kilian, B., Russell, J. et al. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44, 1388–1392 (2012). https://doi.org/10.1038/ng.2447

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