New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags

Genome. 2001 Jun;44(3):361-7.


To provide improved access to the wealth of resources and genomic information that is presently being developed for rice a set of 88 rice expressed sequence tags (ESTs) previously mapped on rice chromosome I in the cross 'Nipponbare' x 'Kasalath' was used for comparative mapping in a cross of the barley cultivars 'Igri' and 'Franka'. As expected. most (89%) of the clones gave distinct banding patterns in barley of which about one-third was polymorphic between 'Igri' and 'Franka'. These polymorphisms were mapped, and most of these (56%) confirmed that rice chromosome 1 and barley chromosome 3H are syntenous. All single-copy markers identified conserved collinear positions, while markers with multiple copies did so in a few cases only. The markers that were not fitting in the collinear order were distributed randomly across the barley genome. The comparative maps of barley chromosome 3H and rice chromosome 1 comprise in total 26 common markers covering more than 95% of the genetic length of both chromosomes. A 30-fold reduction of recombination is seen around the barley centromere, and synteny may be interrupted in this region. However, the good overall synteny on a mesoscale (1-10 cM) justifies the use of rice as a platform for map-based cloning in barley.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • Chromosomes / genetics*
  • Cloning, Molecular
  • Conserved Sequence
  • Crosses, Genetic
  • DNA Probes
  • Expressed Sequence Tags*
  • Gene Order / genetics*
  • Genetic Markers
  • Hordeum / genetics*
  • Hybridization, Genetic
  • Oryza / genetics*
  • Polymorphism, Genetic / genetics
  • Sequence Alignment
  • Synteny / genetics*


  • DNA Probes
  • Genetic Markers