A total of 141 polymorphic DNA marker comprising RAPD(48/275), SSRs (28/410) and  gSSRs (65/533 ) were used to assign for linkage groups using MAPMAKER/EXP version 3.0 b, of which 63 gene based marker could be mapped to different linkage groups. The linked markers in the present study were assigned to linkage group, with an average interlocus distance of 20 cM with a total genetic map length of 2905cM. The number of markers mapped per linkage group ranged from six in LG G and LG J to 33 in LG B. Out of 63 EST-SSR mapped on to different linkage group the functional annotation was available only for 27 (42.1%) EST-SSR while for remaining 38 (60.3%) EST-SSR no putative function could be assigned.