Sunday, October 14, 2018

Transcriptome mining for EST-INDELs and development of EST-SSR markers in turmeric

Sabu K. K., M. D. Shehenaz and J. Amrutha. 2018. Transcriptome mining for EST-INDELs and development of EST-SSR markers in turmeric (Curcuma longa L.). International Journal of Agriculture, Environment and Biotechnology 11(3): 487-492.

Curcuma longa L. commonly known as turmeric is used as a culinary spice in India and many Asian countries. Turmeric has anti-fungal, anti-bacterial, anti-malarial and anti-cancer properties to mention a few. We have analyzed the transcriptome of C. longa retrieved from NCBI SRA database (SRR495223) for the development and validation of EST-SSR markers and identification of EST-InDels to be used for C. longa and related genera. A total of 337 primers were developed and 20 primers having the rating of 100% with the help of NetPrimer were selected and used for PCR validation in C. longa, Amomum subulatum Roxb. (large cardamom) and Elettaria cardamomum (L.) Maton (small cardamom). It was found that around 50% primers generated PCR products in both types of cardamom and 85% in C. longa. The developed primers worked with curcuma, large cardamom and small cardamom plants at varying levels. Besides, the transcriptome analysis detected high amount of deletion and 18 addition of bases which could be screened through the development of CAPS markers using the tool SNP2CAPS and it was found that 93 restriction enzyme can be used for screening these InDels.

  • Transcriptome sequence of Curcuma longa was used for the development of EST-SSR markers.
  • The EST-SSR primers were validated in Curcuma longa and its related taxa such as Amomum subulatum and Elettaria cardamomum
  • EST-InDels were also successfully identified in the transcriptome sequences of Curcuma longa.

Keywords: Curcuma longa, EST-SSR, EST-InDel, PCR, ClustalW, WebSat, NetPrimer, SNP2CAPS

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