Conservation Genetics Resources

, Volume 5, Issue 1, pp 133–136 | Cite as

Development of polymorphic EST-SSR markers in Macrobrachium rosenbergii by data mining

  • P. Mohanty
  • L. Sahoo
  • K. Parida
  • P. DasEmail author
Technical Note


Expressed sequence tags (EST) provide a valuable and cost effective source of developing simple sequence repeat (SSR) markers. In the present study, genic microsatellite markers were developed for Macrobrachium rosenbergii through mining of EST databases. Twenty-three polymorphic EST-SSR loci were found with number of alleles ranging from 3 to 10, observed and expected heterozygosity per locus ranged from 0.1481 to 0.9565 and from 0.2655 to 0.8741, respectively. Of these SSRs, 7 showed significant homology to known genes by BLASTx (basic local alignment search tool x) search. In cross-species amplification, out of 23 polymorphic loci, there were 21 positive amplifications in M. malcolmsonii, 22 in M. gangeticum and 18 in M. lamarrei. These new EST-SSR markers will be useful for genetic studies and genome mapping of M. rosenbergii and closely related macrobrachium species.


M. rosenbergii EST-SSRs Data mining Cross-species amplification 



This work was supported by the Department of Science and Technology, New Delhi. We are thankful to the Director, CIFA for providing laboratory facilities to work.


  1. Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F, Quillet EA (2006) Type I and Type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7:302PubMedCrossRefGoogle Scholar
  2. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefGoogle Scholar
  3. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for analysis of allelic data, Ver 1.0.Free program distributed by the authors over the internet available at
  4. Ma HY, Bi JZ, Shao CW, Chen Y, Miao GD, Chen SL (2009) Development of 40 microsatellite markers in spotted halibut (Verasper variegatus) and the cross-species amplification in barfin flounder (Verasper moseri). Anim Genet 40:576–578PubMedCrossRefGoogle Scholar
  5. McDonald GJ, Danzmann RG, Ferguson MM (2004) Relatedness determination in the absence of pedigree information in three cultured strains of rainbow trout (Oncorhynchus mykiss). Aquaculture 233:65–78CrossRefGoogle Scholar
  6. Mian MA, Saha MC, Hopkins AA, Wang ZY (2005) Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48:637–647PubMedCrossRefGoogle Scholar
  7. New MB (2000) History and global status of freshwater prawn farming. In: New MB, Valenti WC (eds) Freshwater prawn culture; the farming of Macrobrachium rosenbergii. Blackwell Science, Oxford, pp 1–11CrossRefGoogle Scholar
  8. Ng PKL (1997) The conservation status of freshwater prawns and crabs in Singapore with emphasis on the Nature Reserves. Proc Nat Res Surv Sem Garden’s Bull Singap 49:267–272Google Scholar
  9. Pettay DT, LaJeunesse TC (2009) Microsatellite loci for assessing genetic diversity, dispersal and clonality of coral symbionts in “stress-tolerant” Clade D Symbiodinium. Mol Ecol Resour 9:1022–1025PubMedCrossRefGoogle Scholar
  10. You F, Huo N, Gu Y, Luo M, Ma Y, Hane D, Lazo G, Dvorak J, Anderson O (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253PubMedCrossRefGoogle Scholar
  11. Zhang T, Kong J, Wang W, Wang Q (2010) Genetic variability assessed by microsatellites in the breeding populations of the shrimp Penaeus (Fenneropenaeus) chinensis in China. Aquaculture 310:229–233CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Fish Genetics and Biotechnology DivisionCentral Institute of Freshwater AquacultureKausalyaganga, BhubaneswarIndia

Personalised recommendations