%0 Journal Article
%T 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
%A Amaresh Chandra
%A Radha Jain
%A Sushil Solomon
%A Shiksha Shrivastava
%A Ajoy K Roy
%J BMC Research Notes
%D 2013
%I BioMed Central
%R 10.1186/1756-0500-6-47
%X Findings: Utilising 246,180 Saccharum officinarum EST sequences vis-a-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.
%U http://www.biomedcentral.com/1756-0500/6/47/abstract