Chromosome Research

, Volume 18, Issue 7, pp 841–850

Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH

Authors

  • Lu Ma
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
  • Giang T. H. Vu
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
    • Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth University
  • Veit Schubert
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
  • Koichi Watanabe
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
  • Nils Stein
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
  • Andreas Houben
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Article

DOI: 10.1007/s10577-010-9166-3

Cite this article as:
Ma, L., Vu, G.T.H., Schubert, V. et al. Chromosome Res (2010) 18: 841. doi:10.1007/s10577-010-9166-3

Abstract

We investigated by fluorescence in situ hybridization (FISH) the synteny between Brachypodium distachyon with a small genome (1C = 320 Mb) and barley with a large genome (1C = 5,100 Mb) at the chromosome level. Reciprocal genomic in situ hybridization (GISH) between B. distachyon and barley labeled mainly 45S ribosomal DNA loci, indicating that most high copy DNA is weakly conserved between both grasses. Of 13 BAC clones with inserts from different B. distachyon chromosomes, only two belonging to chromosome 1 yielded hybridization signals on a barley metaphase chromosome (on 7HS and 7HL, respectively), confirming synteny between both chromosomes. FISH experiments to characterize the synteny of single-copy loci were performed. Two of four Brachypodium sylvaticum BACs spanning a 223-kb interval homologous to the region of barley that harbors a gibberellic-acid-insensitive semi-dwarfing gene, sdw3, hybridized specifically to a central position of B. distachyon chromosome 1 short arm but not to the homologous region of the barley genome. Repeat-free sequences PCR amplified from four non-overlapping barley BACs linked to the core of Sdw3 region yielded signals at distinct positions in the middle of barley chromosome arm 2HS. Together, these results (1) confirmed the synteny between B. distachyon chromosome 1 and barley chromosomes 2H and 7H at the cytological level, (2) indicated mid-arm position for the Sdw3 locus genetically mapped at the centromere of barley chromosome 2H, and (3) proved that the sdw3 core interval of <100 kb in B. distachyon corresponds to a megabase-sized syntenic region in barley.

Keywords

Brachypodium distachyonHordeum vulgareFISHsingle-copy sequencesSdw3 region

Abbreviations

BAC

Bacterial artificial chromosome

CCD

Charge-coupled device

cM

CentiMorgan

dUTP

2’-deoxyuridine-5’-triphosphate

FISH

Fluorescence in situ hybridization

GISH

Genomic in situ hybridization

HCl

Hydrogen chloride

kb

Kilo-base pairs

Mb

Mega-base pairs

MDR

Mathematically defined repeat

PCR

Polymerase chain reaction

sdw

Semi-dwarfing

SSC

Saline sodium citrate

TE

Tris-EDTA buffer

Copyright information

© Springer Science+Business Media B.V. 2010