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A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics

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Abstract

An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (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 map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.

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Acknowledgments

We gratefully acknowledge P. Hayes for providing the SM and OWB DH-lines, A. Seitz, M. Soffner, E. Graner for developing database support for marker data management, A. Winter for help in statistical analyses, C. Kuenzel, U. Beier, J. Pohl, S. Stegmann, M. Kretschmann, J. Perovic for excellent technical assistance, W. Weschke, V. Radchuk, E. Potokina for providing cDNA libraries for EST sequencing, and S. Meyer, B. Kersten from RZPD, Berlin (http://gabi.rzpd.de) for updating NCBI Genebank EST-accessions with marker information. This work was supported by grants of the German Ministry of Education and Research (BMBF: FKZ 0312271A, 0312271C, 0312278C, 0312706A), GRDC Australia and the state of Saxony-Anhalt.

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  1. Manoj Prasad

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

  2. Hangning Zhang

    Present address: Agronomy Department, University of Florida, IFAS, P.O. Box 11O300, Gainesville, 32611-300, USA

  3. Markus Wolf

    Present address: Trait Genetics, Am Schwabeplan 1b, 06466, Gatersleben, Germany

  4. Raja Kota

    Present address: Plant Disease Resistance Group, CSIRO—Plant , Industry, Canberra, ACT, 2601, Australia

  5. Rajeev K. Varshney

    Present address: International Crops Research Institute for Semi Arid Tropics (ICRISAT), Patancheru, 502 324, AP, India

  6. Dragan Perovic

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

Authors and Affiliations

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

    Nils Stein, Manoj Prasad, Uwe Scholz, Thomas Thiel, Hangning Zhang, Markus Wolf, Raja Kota, Rajeev K. Varshney, Dragan Perovic, Ivo Grosse & Andreas Graner

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Correspondence to Andreas Graner.

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Communicated by B. Keller.

Nils Stein and Manoj Prasad have contributed equally.

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ESM Table 1: Summary of EST-based markers (XLS 277 kb)

ESM Table 2: Summary of included anchor / reference markers (DOC 334 kb)

ESM Table 3: EST based RFLP-marker detecting multiple loci (DOC 35 kb)

ESM Table 4: EST / TC mapped by different marker systems in multiple populations (DOC 58 kb)

ESM Table 5: Distribution of anchor marker loci over the seven barley linkage groups (DOC 32 kb)

ESM Table 6: Summary of anchor markers (DOC 163 kb)

ESM Table 7: Regions of distorted segregation in the individual mapping populations (DOC 34 kb)

ESM Table 8: Summary of 1st to 3rd BLASTN match of barley EST to the rice genome (XLS 309 kb)

122_2006_480_MOESM9_ESM.tif

ESM Figure 1: Distribution along the barley consensus genetic map of mapped barley ESTs with or without sequence homology to the rice genome.Barley ESTs underlying GB and cMWG markers of this study were classified as showing homology or no homology to the rice genome (BLASTN E-value ≤ 1E-10 or > 1E-10, respectively). Based on their genetic postion they were grouped into bins of 20 cM (y-axis = number of ESTs, x-axis = genetic length given in cM). The distribution of ESTs without rice homology (upper panel of the histogram) was plotted against the distribution of ESTs showing homology to rice (lower panel of the histogram). The distribution of both classes of ESTs was following a very similar pattern along all chromosomes – no significantly different clustering to specific chromosomal regions could be observed. (TIF 1.26 mb)

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Stein, N., Prasad, M., Scholz, U. et al. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 114, 823–839 (2007). https://doi.org/10.1007/s00122-006-0480-2

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