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Exploiting EST databases for the development and characterisation of 3425 gene-tagged CISP markers in biofuel crop sugarcane and their transferability in cereals and orphan tropical grasses

Amaresh Chandra1*, Radha Jain1, Sushil Solomon1, Shiksha Shrivastava2 and Ajoy K Roy2

Author Affiliations

1 Division of Plant Physiology and Biochemistry, Indian Institute of Sugarcane Research, Rae Bareli Road, 226002, Lucknow, Uttar Pradesh, India

2 Indian Grassland and Fodder Research Institute, Gwalior Road, 284003, Jhansi, Uttar Pradesh, India

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BMC Research Notes 2013, 6:47  doi:10.1186/1756-0500-6-47

Published: 4 February 2013



Sugarcane is an important cash crop, providing 70% of the global raw sugar as well as raw material for biofuel production. Genetic analysis is hindered in sugarcane because of its large and complex polyploid genome and lack of sufficiently informative gene-tagged markers. Modern genomics has produced large amount of ESTs, which can be exploited to develop molecular markers based on comparative analysis with EST datasets of related crops and whole rice genome sequence, and accentuate their cross-technical functionality in orphan crops like tropical grasses.


Utilising 246,180 Saccharum officinarum EST sequences vis-à-vis its comparative analysis with ESTs of sorghum and barley and the whole rice genome sequence, we have developed 3425 novel gene-tagged markers — namely, conserved-intron scanning primers (CISP) — using the web program GeMprospector. Rice orthologue annotation results indicated homology of 1096 sequences with expressed proteins, 491 with hypothetical proteins. The remaining 1838 were miscellaneous in nature. A total of 367 primer-pairs were tested in diverse panel of samples. The data indicate amplification of 41% polymorphic bands leading to 0.52 PIC and 3.50 MI with a set of sugarcane varieties and Saccharum species. In addition, a moderate technical functionality of a set of such markers with orphan tropical grasses (22%) and fodder cum cereal oat (33%) is observed.


Developed gene-tagged CISP markers exhibited considerable technical functionality with varieties of sugarcane and unexplored species of tropical grasses. These markers would thus be particularly useful in identifying the economical traits in sugarcane and developing conservation strategies for orphan tropical grasses.

Conserved-intron scanning primers; Sugarcane; Tropical grasses; Oat; Gene annotation; Gene-tagged markers