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Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH

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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.

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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

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Acknowledgments

We are grateful to Martina Kühne and Katrin Kumke (IPK, Gatersleben) for excellent technical assistance. We thank Glyn Jenkins (IBERS, Aberystwyth, UK) and Robert Hasterok (Silesian University, Katowice, Poland) for providing B. distachyon seeds and BACs. This project was supported by the Leibniz Association (WGL).

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Author notes

  1. Giang T. H. Vu

    Present address: Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Edward Llwyd Building, Ceredigion, SY23 3DA, UK

Authors and Affiliations

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

    Lu Ma, Giang T. H. Vu, Veit Schubert, Koichi Watanabe, Nils Stein, Andreas Houben & Ingo Schubert

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  1. Lu Ma
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Correspondence to Ingo Schubert.

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Ma, L., Vu, G.T.H., Schubert, V. et al. Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18, 841–850 (2010). https://doi.org/10.1007/s10577-010-9166-3

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  • DOI: https://doi.org/10.1007/s10577-010-9166-3

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