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Conserved synteny-based anchoring of the barley genome physical map

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Abstract

Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map (“genome zipper”) for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene locations obtained from the maps constructed in other grass species, was evaluated here both at the genome-wide level and at the fine scale in a representative segment of the genome. Comparing the whole genome “genome zipper” maps with a genetic map developed by using transcript-derived markers, yielded an accuracy of >94 %. The fine-scale comparison involved a 14 cM segment of chromosome arm 2HL. One hundred twenty-eight genes of the “genome zipper” interval were analysed. Over 95 % (45/47) of the polymorphic markers were genetically mapped and allocated to the expected region of 2HL, following the predicted order. A further 80 of the 128 genes were assigned to the correct chromosome arm 2HL by analysis of wheat-barley addition lines. All 128 gene-based markers developed were used to probe a barley bacterial artificial chromosome (BAC) library, delivering 26 BAC contigs from which all except two were anchored to the targeted zipper interval. The results demonstrate that the gene order predicted by the “genome zipper” is remarkably accurate and that the “genome zipper” represents a highly efficient informational resource for the systematic identification of gene-based markers and subsequent physical map anchoring of the barley genome.

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Acknowledgements

We greatly acknowledge the excellent technical help of Jelena Perovic and Jenny Knibbiche. The work was financially supported by a grant of the German Ministry of Education and Research (BMBF) in frame of the GABI-FUTURE program (FKZ0314000, BARLEX) to NS.

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Author notes

  1. Daniela Schulte

    Present address: KWS SAAT AG, Grimsehlstr. 31, 37555, Einbeck, Germany

  2. Burkhard Steuernagel

    Present address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland (OT), Gatersleben, Germany

    Naser Poursarebani, Ruvini Ariyadasa, Ruonan Zhou, Daniela Schulte, Burkhard Steuernagel, Andreas Graner, Patrick Schweizer, Uwe Scholz & Nils Stein

  2. Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany

    Mihaela Maria Martis & Klaus Mayer

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  1. Naser Poursarebani
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Correspondence to Nils Stein.

Electronic supplementary material

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Supplementary data Table 1

Barley genome zipper of chromosome 2H (Mayer et al., 2011) for which additional information containing gene model IDs along with highlighted 2HL region selected have been provided (XLSX 1058 kb)

Supplementary data Table 2

Comparison of representativeness of the 14 cM interval to the entire chromosome 2H genome zipper (DOCX 11 kb)

Supplementary data Table 3

Genotyping data of the genome zipper-based genetic markers on a population comprising 93 doubled haploid progeny derived from the cross cv. ‘Morex’ × cv. ‘Barke’ (Close et al. 2009) (XLSX 454 kb)

Supplementary data Table 4

All genetic markers developed and their respective information including primer sequences, annealing temperature, polymorphism types and the restriction enzyme utilised to develop CAPS and dCAPS markers (XLSX 17.8 kb)

Supplementary data Table 5

Markers commonly mapped in TDMs map (Potokina et al., 2008) and the barley genome zippers that were utilised for genome-wide assessment of order prediction in barley genome zippers (XLSX 54.4 kb)

Supplementary data Table 6

Primers that were developed on the basis of barley chromosome 2H genome zipper (14 cM interval), their respective BAC clone and physical map contigs identified by PCR-based BAC library screening (XLSX 41.5 kb)

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Poursarebani, N., Ariyadasa, R., Zhou, R. et al. Conserved synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 13, 339–350 (2013). https://doi.org/10.1007/s10142-013-0327-2

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