Theoretical and Applied Genetics

, Volume 112, Issue 5, pp 808–817 | Cite as

Unigene derived microsatellite markers for the cereal genomes

  • Swarup K. Parida
  • K. Anand Raj Kumar
  • Vivek Dalal
  • Nagendra K. Singh
  • Trilochan Mohapatra
Original Paper


Unigene derived microsatellite (UGMS) markers have the advantage of assaying variation in the expressed component of the genome with unique identity and positions. We characterized the microsatellite motifs present in the unigenes of five cereal species namely, rice, wheat, maize, Sorghum and barley and compared with those in Arabidopsis. The overall UGMS frequency in the five cereal species was 1/7.6 kb. The maximum UGMS frequency was in rice (1/3.6 kb) and the lowest in wheat (1/10.6 kb). GC-rich trinucleotide repeat motifs coding for alanine followed by arginine and the dinucleotide repeat motif GA were found to be abundant UGMS classes across all the five cereal species. Primers could be designed for 95% (wheat and barley) to 97% (rice) of the identified microsatellites. The proportion and frequency of occurrence of long hypervariable class I (≥20 nucleotides) and potentially variable class II (12–20 nucleotides) UGMS across five cereal species were characterized. The class I UGMS markers were physically mapped in silico on to the finished rice genome and bin-mapped in wheat. Comparative mapping based on class I UGMS markers in rice and wheat revealed syntenic relationships between the two genomes. High degree of conservation and cross-transferability of the class I UGMS markers were evident among the five cereal species, which was validated experimentally. The class I UGMS-conserved orthologous set (COS) markers identified in this study would be useful for understanding the evolution of genes and genomes in cereals.


Sorghum Rice Chromosome Cereal Species Microsatellite Motif International Rice Genome Sequencing Project 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The work presented in the manuscript was partly carried out under the Sugarcane Genomics Project and National Bioscience Project awarded to the corresponding author (TM) by the Department of Biotechnology (DBT), Government of India. We are thankful to NCBI and RGP for making their databases available and Institute of Plant Genetics and Crop Research (IPK) for the availability of microsatellite search tool MISA.

Supplementary material


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Swarup K. Parida
    • 1
  • K. Anand Raj Kumar
    • 1
  • Vivek Dalal
    • 1
  • Nagendra K. Singh
    • 1
  • Trilochan Mohapatra
    • 1
  1. 1.National Research Centre on Plant BiotechnologyIndian Agricultural Research InstituteNew DelhiIndia

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