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Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers

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Abstract

Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in ‘nr’ database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms “Fatty acid metabolic process” and “Fatty acid biosynthetic process” were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.

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Author notes

  1. Pankaj Pandey

    Present address: National Agri-Food Biotechnology Institute, C-127 Industrial Area, SAS Nagar Phase 8, Mohali, 160071, Punjab, India

  2. Devender Kumar

    Present address: RVC Center and College, c/o 56 APO, Meerut Cantt, 900468, India

Authors and Affiliations

  1. Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139, India

    Atul Grover, Maya Kumari, Sadhana Singh, Shivender Singh Rathode, Sanjay Mohan Gupta, Pankaj Pandey, Devender Kumar, Mohommad Arif & Zakwan Ahmed

  2. Department of Biotechnology, Indian Institute of Technology, Guwahati, India

    Sween Gilotra

  3. Directorate of Management Services, Defence Research and Development Organization, DRDO Bhawan, New Delhi, 110011, India

    Zakwan Ahmed

Authors
  1. Atul Grover
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  2. Maya Kumari
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  3. Sadhana Singh
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  4. Shivender Singh Rathode
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  5. Sanjay Mohan Gupta
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  9. Mohommad Arif
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  10. Zakwan Ahmed
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Correspondence to Atul Grover.

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Grover, A., Kumari, M., Singh, S. et al. Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers. Physiol Mol Biol Plants 20, 139–142 (2014). https://doi.org/10.1007/s12298-013-0204-4

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  • DOI: https://doi.org/10.1007/s12298-013-0204-4

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