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Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley

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Abstract

The barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. Towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cM interval in a “cold spot” of recombination of the proximal region of the short arm of barley chromosome 2H. Extensive synteny between the barley Sdw3 locus (Hvu_sdw3) and the orthologous regions (Osa_sdw3, Sbi_sdw3, Bsy_sdw3) of three other grass species (Oryza sativa, Sorghum bicolor, Brachypodium sylvaticum) allowed for efficient synteny-based marker saturation in the target interval. Comparative sequence analysis revealed colinearity for 23 out of the 38, 35, and 29 genes identified in Brachypodium, rice, and Sorghum, respectively. Markers co-segregating with Hvu_sdw3 were generated from two of these genes. Initial attempts at chromosome walking in barley were performed with seven orthologous gene probes which were delimiting physical distances of 223, 123, and 127 kb in Brachypodium, rice, and Sorghum, respectively. Six non-overlapping small bacterial artificial chromosome (BAC) clone contigs (cumulative length of 670 kb) were obtained, which indicated a considerably larger physical size of Hvu_sdw3. Low-pass sequencing of selected BAC clones from these barley contigs exhibited a substantially lower gene frequency per physical distance and the presence of additional non-colinear genes. Four candidate genes for sdw3 were identified within barley BAC sequences that either co-segregated with the gene sdw3 or were located adjacent to these co-segregating genes. Identification of genic sequences in the sdw3 context provides tools for marker-assisted selection. Eventual identification of the actual gene will contribute new information for a basic understanding of the mechanisms underlying growth regulation in barley.

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Acknowledgements

GTHV was supported by the Vietnamese Ministry of Education and Training (MOET) and core funding of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK, Germany). We thank Dr. A. Börner (IPK) for providing seed material, Dr. D. Schulte (IPK) for the high-information content fingerprinting support.

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  1. Giang T. H. Vu

    Present address: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK

Authors and Affiliations

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

    Giang T. H. Vu, Andreas Graner & Nils Stein

  2. Institute of Plant Biology, University Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland

    Thomas Wicker & Jan P. Buchmann

  3. CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia

    Peter M. Chandler

  4. National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Takashi Matsumoto

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Supplemental Table 1

List of primers for PCR-based markers at the Sdw3 locus (DOC 39 kb)

Supplemental Table 2

The mapping status of 29 coding sequences of rice within the Hv_sdw3 interval between the mapped markers TC142185 and TC149567 (DOC 44 kb)

Supplemental Table 3

Screening results after probing the B. sylvaticum and Morex BAC libraries with eight probes of the Sdw3 region (DOC 32 kb)

Supplemental Table 4

Genes identified in the sdw3 regions from Brachypodium, rice, and Sorghum. Gene numbers correspond to those in Fig. 2. Highlighted are those genes which were also found on barley BAC clones from the Sdw3 region. Positions indicate the start positions of the gene on the respective sequence. In rice and Sorghum, the positions are relative to the chromosomal positions given in Fig. 2. (DOC 98 kb)

Supplemental Table 5

Summary of SNPs found of the barley cigr2-ortholog in the wild-type cultivars Himalaya and Monte Cristo, in the allelic mutants Hv287 = sdw3 (derived from cv. MC), M12, M13, M102, M107, M119, M127, M130, M651, M671, M680 (derived from cv. Himalaya) and in the non-allelic GA-sensitive mutant line Hv288 (DOC 49 kb)

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Vu, G.T.H., Wicker, T., Buchmann, J.P. et al. Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct Integr Genomics 10, 509–521 (2010). https://doi.org/10.1007/s10142-010-0173-4

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