Theoretical and Applied Genetics

, Volume 126, Issue 12, pp 2969–2982 | Cite as

Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.)

  • Johanna Acevedo-Garcia
  • Nicholas C. Collins
  • Nahal Ahmadinejad
  • Lu Ma
  • Andreas Houben
  • Pawel Bednarek
  • Mariam Benjdia
  • Andreas Freialdenhoven
  • Janine Altmüller
  • Peter Nürnberg
  • Richard Reinhardt
  • Paul Schulze-Lefert
  • Ralph Panstruga
Original Paper

Abstract

Key message

TheRor1gene was fine-mapped to the pericentric region of barley chromosome 1HL.

Abstract

Recessively inherited loss-of-function alleles of the barley (Hordeum vulgare) Mildew resistance locus o (Mlo) gene confer durable broad-spectrum disease resistance against the obligate biotrophic fungal powdery mildew pathogen Blumeria graminis f.sp. hordei. Previous genetic analyses revealed two barley genes, Ror1 and Ror2, that are Required formlo-specifiedresistance and basal defence. While Ror2 was cloned and shown to encode a t-SNARE protein (syntaxin), the molecular nature or Ror1 remained elusive. Ror1 was previously mapped to the centromeric region of the long arm of barley chromosome 1H. Here, we narrowed the barley Ror1 interval to 0.18 cM and initiated a chromosome walk using barley yeast artificial chromosome (YAC) clones, next-generation DNA sequencing and fluorescence in situ hybridization. Two non-overlapping YAC contigs containing Ror1 flanking genes were identified. Despite a high degree of synteny observed between barley and the sequenced genomes of the grasses rice (Oryza sativa), Brachypodium distachyon and Sorghum bicolor across the wider chromosomal area, the genes in the YAC contigs showed extensive interspecific rearrangements in orientation and order. Consequently, the position of a Ror1 homolog in these species could not be precisely predicted, nor was a barley gene co-segregating with Ror1 identified. These factors have prevented the molecular identification of the Ror1 gene for the time being.

Supplementary material

122_2013_2186_MOESM1_ESM.pdf (68 kb)
Supplementary material 1 (PDF 68 kb) File S1 Non-coding sequences derived from de novo assembly of YAC sequence reads
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Supplementary material 2 (PNG 1536 kb) Fig. S1 Micrographs of multicolor FISH on barley metaphase chromosomes of cv. Ingrid. Shown in white (in merged) is the signal of the chromosome 1H long arm-specific probe pHv-1112 (Kato 2011); the arrows indicate the position of the signals for the genic probes in green and red; the insets show a magnification of the chromosomes with the FISH signals in black and white and after pseudo-coloring (in part rotated to suit the Figure format, arrow head indicates the pHv-1112-specific signal). Scale bar = 20 µm. a Probes for Con (red) + Pol (green) + pHv-1112. bCon (red) + Unk (green) + pHv-1112. Note that only results for combinations 1 and 2 (see main text) are shown and that the different chromosome background colors in Fig. 3 (blue) and Fig. S1 (greenish) are due to the fact that results shown in Fig. S1 are multicolor overlays of three differently labeled probes, lacking a dedicated color for the chromosomes
122_2013_2186_MOESM3_ESM.png (545 kb)
Supplementary material 3 (PNG 544 kb) Fig. S2 Accumulation of selected secondary metabolites in first leaves of the indicated barley genotypes at 24 and 48 hours after inoculation with Blumeria graminis f. sp. hordei spores. Compounds with retention time (RT) 10.9, 12.3, 14.1 and 16.2 minutes are shown as the ones representing the most striking induction after pathogen inoculation. Error bars indicate standard deviations of one experiment
122_2013_2186_MOESM4_ESM.png (148 kb)
Supplementary material 4 (PNG 148 kb) Fig. S3 UV spectra for four UPLC-PDA metabolite peaks showing induction by Blumeria graminis f. sp. hordei inoculation in primary barley leaves. Representative UV spectra of compounds eluted at retention time (RT) 14.1 and 16.2 resemble those reported for hordatines, their precursors and derivatives (Stoessl and Unwin 1970; von Röpenack et al. 1998). AU, absorbance units
122_2013_2186_MOESM5_ESM.xlsx (15 kb)
Supplementary material 5 (XLSX 15 kb) Table S1 Primer pairs used to amplify the Pol and Con genes and selected YAC ends
122_2013_2186_MOESM6_ESM.xlsx (18 kb)
Supplementary material 6 (XLSX 17 kb) Table S2 Detail of primer pairs used to investigate the genes from the YAC clones and the genomic DNA sequence obtained for each gene fragment in the parents Ingrid and Malteria Heda
122_2013_2186_MOESM7_ESM.xlsx (12 kb)
Supplementary material 7 (XLSX 11 kb) Table S3 Primer pairs used to amplify unique probes for barley FISH
122_2013_2186_MOESM8_ESM.xls (119 kb)
Supplementary material 8 (XLS 119 kb) Table S4 Details of DNA sequence polymorphism survey across three barley mapping parent genotypes
122_2013_2186_MOESM9_ESM.xls (52 kb)
Supplementary material 9 (XLS 52 kb) Table S5 Polymorphisms, haplotypes and marker details for the three barley mapping parent genotypes
122_2013_2186_MOESM10_ESM.xls (50 kb)
Supplementary material 10 (XLS 50 kb) Table S6 Genotypes of F2 recombinants for the Ror1 interval, used for fine mapping
122_2013_2186_MOESM11_ESM.xlsx (14 kb)
Supplementary material 11 (XLSX 13 kb) Table S7 Genotype in a panel of recombinants for the Ror1 interval for the genes identified in the sequenced YAC clones
122_2013_2186_MOESM12_ESM.xlsx (16 kb)
Supplementary material 12 (XLSX 16 kb) Table S8 Anchoring option, position coordinates and contigs in the barley genome for the genes present in the sequenced YAC clones close to the Ror1 locus. The analysis is based on the International Barley Sequencing Consortium (2012) genome draft release ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/ and http://webblast.ipk-gatersleben.de/barley

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Johanna Acevedo-Garcia
    • 1
    • 3
  • Nicholas C. Collins
    • 2
    • 7
  • Nahal Ahmadinejad
    • 1
    • 8
  • Lu Ma
    • 4
  • Andreas Houben
    • 4
  • Pawel Bednarek
    • 10
  • Mariam Benjdia
    • 1
    • 9
  • Andreas Freialdenhoven
    • 6
  • Janine Altmüller
    • 5
  • Peter Nürnberg
    • 5
  • Richard Reinhardt
    • 1
  • Paul Schulze-Lefert
    • 1
  • Ralph Panstruga
    • 1
    • 3
  1. 1.Department of Plant-Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
  2. 2.Sainsbury LaboratoryJohn Innes CentreNorwichUK
  3. 3.Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
  4. 4.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
  5. 5.Cologne Center for Genomics (CCG)University of CologneCologneGermany
  6. 6.Institute for Biology IRWTH Aachen UniversityAachenGermany
  7. 7.Australian Centre for Plant Functional Genomics, School of Agriculture Food and WineUniversity of AdelaideGlen OsmondAustralia
  8. 8.INRES, Crop BioinformaticsUniversity of BonnBonnGermany
  9. 9.European Commission ERC Executive Agency, COV2BrusselsBelgium
  10. 10.Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland

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