African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12487

Full Length Research Paper

Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes

Himanshu Aggarwal
  • Himanshu Aggarwal
  • Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-125001(Haryana), India: Department of Biotechnology, Maharishi Markandeshwar University, Mullana-133207 (Haryana), India.
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Alka Rao1, Anil Kumar
  • Alka Rao1, Anil Kumar
  • Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-125001(Haryana), India.
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Jasbir Singh
  • Jasbir Singh
  • Department of Biochemistry, Kurukshetra University, Kurukshetra-136119(Haryana), India.
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Jogender Singh Rana
  • Jogender Singh Rana
  • Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-125001(Haryana), India.
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Pradeep Kumar Naik
  • Pradeep Kumar Naik
  • Department of Biotechnology, Guru Ghasidas Central University, Koni Bilaspur- 495009 (Chhattisgarh), India.
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Vinod Chhokar*
  • Vinod Chhokar*
  • Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-125001(Haryana), India.
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  •  Received: 30 June 2015
  •  Accepted: 20 August 2015
  •  Published: 11 November 2015

Abstract

The current investigation was carried out to analyse the genetic diversity estimates between 125 chickpea genotypes using sequence-tagged microsatellite (STMS) markers. Thirty one STMS primers generated a total of 153 loci (an average of 4.94 loci per primer) out of which 129 loci were found to be polymorphic and 24 loci were monomorphic. The value of PIC varied from 0.128 to 0.783 while the resolving power varied from 0.912 to 4.768. The UPGMA generated dendrogram showed the grouping of all the 125 chickpea cultivars into two major clusters and one small cluster. An unbiased clustering of genotypes based on STRUCTURE program, without prior knowledge about the populations, clustered all the 125 genotypes into three major groups. Percentage of polymorphic loci using POPGENE analysis was 50.98, 58.82 and 96.73 for susceptible, resistant and miscellaneous genotypes, respectively. Genetic diversity analysis in terms of Shannon’s index and Nei’s gene diversity for resistant, susceptible, and miscellaneous cultivars revealed higher values for miscellaneous cultivars, indicating more variability among these cultivars in comparison to resistant and susceptible cultivars. AMOVA results among groups and among cultivars were 10 and 90%, respectively, while the estimated gene flow was 6.117. The overall Nei’s gene diversity (0.238) and Shannon’s information index (0.372) indicated high degree of genetic polymorphism revealed by the STMS molecular markers. So, genetic divergence in chickpea can provide useful indications in understanding species relationships and may help in developing effective breeding programs.

Keywords: Cicer arietinum, genetic polymorphism, molecular markers, analysis of molecular variance, gene flow.

Abbreviation

STMS, Sequence-tagged microsatellite; MAS, maker-assisted selection; RAPD, random amplified polymorphic DNA; ISSR, inter simple sequence repeats; RFLP, restriction fragment length polymorphism; AFLP, amplified fragment length polymorphism; ITS, internal transcribed spacer; SSR, simple sequence repeats; CTAB, cetyltrimethyl ammonium bromide; NPL, number of polymorphic loci; PPL, percentage polymorphic loci; PIC, polymorphism information content; DI, diversity index; EMR, effective multiplex ratio; MI, marker index.

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This article is published under the terms of the Creative Commons Attribution License 4.0

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