Molecular Biology Reports

, Volume 46, Issue 1, pp 41–49 | Cite as

Microsatellite marker set for genetic diversity assessment of primitive Chitala chitala (Hamilton, 1822) derived through SMRT sequencing technology

  • Nimisha Dutta
  • Rajeev K. SinghEmail author
  • Vindhya Mohindra
  • Abhinav Pathak
  • Raj Kumar
  • Priyanka Sah
  • Sangeeta Mandal
  • Gurjeet Kaur
  • Kuldeep K. Lal
Original Article


In present study, single molecule-real time sequencing technology was used to obtain a validated set of microsatellite markers for application in population genetics of the primitive fish, Chitala chitala. Assembly of circular consensus sequencing reads resulted into 1164 sequences which contained 2005 repetitive motifs. A total of 100 sequences were used for primer designing and amplification yielded a set of 28 validated polymorphic markers. These loci were used to genotype n = 72 samples from three distant riverine populations of India, namely Son, Satluj and Brahmaputra, for determining intraspecific genetic variation. The microsatellite loci exhibited high level of polymorphism with PIC values ranging from 0.281 to 0.901. The genetic parameters revealed that mean heterozygosity ranged from 0.6802 to 0.6826 and the populations were found to be genetically diverse (Fst 0.03–0.06). This indicated the potential application of these microsatellite marker set that can used for stock characterization of C. chitala, in the wild. These newly developed loci were assayed for cross transferability in another notopterid fish, Notopterus notopterus.


PacBio RSII Contigs NGS Population genetics Genotype Cross species amplification 



The authors are grateful to the consistent support of the Director, ICAR-NBFGR, Lucknow during this work. The work was a part of ICAR plan funded project entitled, Outreach Activity on Fish Genetic Stocks, Phase II. We are thankful to Sh R.S. Sah and Sh Rajesh Kumar for their excellent technical assistance.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Informed consent

Informed consent was obtained from all individual participants included in the study.


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.National Bureau of Fish Genetic ResourcesLucknowIndia
  2. 2.Amity Institute of BiotechnologyAmity University, Lucknow CampusLucknowIndia

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