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The original publication is available at http://www.springerlink.com under the DOI:10.1007/s00122-006-0480-2.

A 1000 loci transcript map of the barley genome – new anchoring points for integrative grass genomics


Nils Stein1+, Manoj Prasad1,2+, Uwe Scholz1, Thomas Thiel1, Hangning Zhang1,3, Markus Wolf1,4, Raja Kota1,5, Rajeev K. Varshney1,6, Dragan Perovic1,7, Andreas Graner1*


1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany

2 Present Address: National Centre for Plant Genome Research (NCPGR), JNU Campus, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi-110067, India

3 Present Address: Agronomy Department, University of Florida, IFAS, PO Box 11O300, Gainesville, FL32611-300, USA

4 Present Address: Present Address: Trait Genetics, Am Schwabeplan 1b, D-06466 Gatersleben, Germany

5 Present Address: Plant Disease Resistance Group, CSIRO – Plant Industry, Canberra, ACT 2601, Australia

6 Present Address: International Crops Research Institute for Semi Arid Tropics (ICRISAT), Patancheru-502 324, Andhra Pradesh, India

7 Present Address: Federal Centre for Breeding Research on Cultivated Plants, Institute of Epidemiology and Resistance Resources, Theodor-Roemer-Weg 4, 06449 Aschersleben, Germany

* Address for correspondence:
    Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
    e-mail: graner@ipk-gatersleben.de
    Tel.: ++49-(0)39482 5521
    Fax: ++49-(0)39482 5155

+= authors contributed equally


An integrated barley transcript map (consensus map) comprising 1,032 EST-based markers (total 1,055 loci: 607 RFLP, 190 SSR and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The consensus map covers 1118.3 cM with individual linkage groups extending over 130 (chromosome 4H) and 199 cM (chromosome 3H), respectively, yielding an average marker interval distance of 0.90 cM. Four-hundred and seventy-five EST-based markers exhibited a syntenic organisation to known colinear linkage groups of the rice genome thus providing an extended insight into the status of barley / rice genome collinearity. A new aspect of previously unobserved colinearity between barley chromosome 2H and rice Os03 was determined. The presented barley transcript map is a valuable resource for (i) targeted marker saturation and identification of candidate genes at agronomically important loci, is providing (ii) new anchor points for detailed studies in comparative grass genomics and will (iii) support any attempt of linking genetic map information to a future physical map of the barley genome.