Molecular Breeding

, Volume 27, Issue 1, pp 1–9 | Cite as

Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding

  • Xiao-Qi Zhang
  • Chengdao LiEmail author
  • Joe Panozzo
  • Sharon Westcott
  • Guoping Zhang
  • Amy Tay
  • Rudi Appels
  • Mike Jones
  • Reg Lance


The terminal region of barley chromosome 5HL controls malt extract, diastatic power, free amino acid nitrogen, alpha-amylase activity, seed dormancy and pre-harvest sprouting. Comparative analysis of the barley and rice maps has established that the terminal region of barley chromosome 5HL is syntenic to rice chromosome 3L near the telomere end. The rice BAC (Bacterial Artificial Chromosome) sequences covering the region of chromosome 3L were used to search barley expressed sequenced tags database. Thirty-three genes were amplified by PCR (polymerase chain reaction) with the primers designed from barley ESTs (expressed sequence tag). Comparison of the sequences of the PCR generated DNA fragments revealed polymorphisms including single nucleotide polymorphism (SNP), insertions or deletions between the barley varieties. Seven new PCR based molecular markers were developed and mapped within 10 cM in three doubled haploid barley populations (Stirling × Harrington, Baudin × AC Metcalfe and Chebec × Harrington). The mapped genes maintain the micro-syntenic relationship between barley and rice. These gene specific markers provide simple and efficient tools for germplasm characterization and marker-assisted selection for barley malting quality, and ultimately lead to isolation and identification of the major gene(s) controlling multiple quality traits on barley chromosome 5HL.


Malting quality Comparative mapping Micro-synteny Rice Hordeum vulgare Marker-assisted selection 



This research was supported by Molecular Plant Breeding CRC, Australian Grain Research and Development Corporation and Natural Science Foundation of China (30828023).


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Xiao-Qi Zhang
    • 1
  • Chengdao Li
    • 1
    • 2
    Email author
  • Joe Panozzo
    • 3
  • Sharon Westcott
    • 2
  • Guoping Zhang
    • 4
  • Amy Tay
    • 2
  • Rudi Appels
    • 5
  • Mike Jones
    • 1
  • Reg Lance
    • 2
  1. 1.State Agricultural Biotechnology CenterMurdoch UniversityPerthAustralia
  2. 2.Department of Agriculture and Food, Western AustraliaSouth PerthAustralia
  3. 3.Department of Primary IndustryDPI Horsham CentreHorshamAustralia
  4. 4.Department of AgronomyZhejiang UniversityHangzhouChina
  5. 5.Centre of Comparative GenomicsMurdoch UniversityPerthAustralia

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