Planta Med 2007; 73(3): 262-266
DOI: 10.1055/s-2007-967121
Original Paper
Biochemistry and Molecular Biology
© Georg Thieme Verlag KG Stuttgart · New York

Development of Simple Sequence Repeat Markers in Cymbopogon Species

Jitendra Kumar1 , 3 , Vijeshwar Verma1 , Ashok Kumar Shahi2 , Gulam Nab Qazi1 , Harindra Singh Balyan3
  • 1Division of Biotechnology, Regional Research Laboratory, Jammu, India
  • 2Division of Botany, Regional Research Laboratory, Jammu, India
  • 3Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, India
Further Information

Publication History

Received: December 5, 2005

Accepted: December 22, 2006

Publication Date:
22 February 2007 (online)


The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8 %) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8 %) and other higher order repeat motifs. Eighteen (81.8 %) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2 %) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1 - 18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding.


SSR: Simple sequence repeat

DNA: Deoxyribonucleic acid

PCR: Polymerase chain reaction

dNTP: Deoxynucleotide triphosphate

EST: Express sequence tag

QTL: Quantitative trait loci

PIC: Polymorphic information content

MAB: Marker assisted selection

LB: Luria-Bertani


Dr. Jitendra Kumar

Department of Genetics & Plant Breeding

Ch. Charan Singh University