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Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping

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Abstract

Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat–H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2Hch, 3Hch and 5Hch in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.

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Acknowledgments

This research was supported by grants (to S.G. Atienza) AGL2008-03720, 200840I137 and P09-AGR-4817 from the Spanish Ministry of Science and Innovation (MSI), CSIC, Junta de Andalucía and FEDER. We are grateful to E. León for her technical assistance. C. Rodríguez-Suárez acknowledges financial support from CSIC (JAE-Doc program). The authors thank Prof. Tsujimoto (Tottori University, Japan), for providing barley EST primers.

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Authors and Affiliations

  1. Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, 14080, Córdoba, Spain

    C. Rodríguez-Suárez, M. J. Giménez, N. Gutiérrez, M. C. Ramírez, A. C. Martín, A. Castillo, A. Martín & S. G. Atienza

  2. Área Mejora y Biotecnología, IFAPA-Centro Alameda del Obispo, Córdoba, Spain

    C. M. Ávila

  3. Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla, ACT, 2600, Australia

    A. Machado, E. Huttner & A. Kilian

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  1. C. Rodríguez-Suárez
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  2. M. J. Giménez
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  4. C. M. Ávila
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Correspondence to S. G. Atienza.

Additional information

Communicated by M. Xu.

Electronic supplementary material

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Supplementary File 1. Set of COS and EST markers used in this work. (XLS 61 kb)

122_2011_1741_MOESM2_ESM.xls

Supplementary File 2. Physical mapping of 287 DArT markers using H. chilense (H1)-wheat (Chinese Spring) chromosome and telosomic addition lines. (XLS 146 kb)

122_2011_1741_MOESM3_ESM.xls

Supplementary File 3. Features of loci of the linkage map. Excel spreadsheet containing a list of all mapped loci and their features. Data include locus position (in both Kosambi and Haldane), physical mapping when available and segregation in the RIL population. (XLS 2946 kb)

122_2011_1741_MOESM4_ESM.pdf

Supplementary Fig. 1. Genetic linkage map of the cross H1 × H7 containing 2,032 loci. Loci with physical mapping are indicated with a chromosome-code. The estimated centromere position is indicated as a green segment. For chromosomes 6Hch and 7Hch, where the centromere was positioned in a single map position, markers mapping to the centromere are shown in red color. (PDF 56 kb)

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Rodríguez-Suárez, C., Giménez, M.J., Gutiérrez, N. et al. Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping. Theor Appl Genet 124, 713–722 (2012). https://doi.org/10.1007/s00122-011-1741-2

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