Quantitative high resolution mapping of HvMLH3 foci in barley pachytene nuclei reveals a strong distal bias and weak interference

Dylan Wyn Phillips, Joanna Wnetrzak, Candida Sofia Nibau, Abdellah Barakate, Luke Ramsay, Frank Wright, James D. Higgins, Ruth M. Perry, Glyn Jenkins

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In barley (Hordeum vulgare L.), chiasmata (the physical sites of genetic crossovers) are skewed towards the distal ends of chromosomes, effectively consigning a large proportion of genes to recombination coldspots. This has the effect of limiting potential genetic variability, and of reducing the efficiency of map-based cloning and breeding approaches for this crop. Shifting the sites of recombination to more proximal chromosome regions by forward and reverse genetic means may be profitable in terms of realizing the genetic potential of the species, but is predicated upon a better understanding of the mechanisms governing the sites of these events, and upon the ability to recognize real changes in recombination patterns. The barley MutL Homologue (HvMLH3), a marker for class I interfering crossovers, has been isolated and a specific antibody has been raised. Immunolocalization of HvMLH3 along with the synaptonemal complex transverse filament protein ZYP1, used in conjunction with fluorescence in situ hybridization (FISH) tagging of specific barley chromosomes, has enabled access to the physical recombination landscape of the barley cultivars Morex and Bowman. Consistent distal localization of HvMLH3 foci throughout the genome, and similar patterns of HvMLH3 foci within bivalents 2H and 3H have been observed. A difference in total numbers of HvMLH3 foci between these two cultivars has been quantified, which is interpreted as representing genotypic variation in class I crossover frequency. Discrepancies between the frequencies of HvMLH3 foci and crossover frequencies derived from linkage analysis point to the existence of at least two crossover pathways in barley. It is also shown that interference of HvMLH3 foci is relatively weak compared with other plant species.

Original languageEnglish
Pages (from-to)2139-2154
Number of pages16
JournalJournal of Experimental Botany
Issue number8
Early online date03 Apr 2013
Publication statusPublished - May 2013


  • barley
  • chiasma
  • crossover
  • Hordeum vulgare
  • interference
  • MLH3
  • Barley
  • Synaptonemal Complex/genetics
  • Arabidopsis/genetics
  • Molecular Sequence Data
  • Pachytene Stage/genetics
  • In Situ Hybridization, Fluorescence
  • Chromosome Mapping
  • Phylogeny
  • Crossing Over, Genetic/genetics
  • Genome, Plant/genetics
  • Chromosomes, Plant/genetics
  • Sequence Alignment
  • Hordeum/genetics
  • Base Sequence
  • Genetic Loci/genetics
  • Genetic Linkage/genetics


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