Abstract Microsatellites or simple sequence repeats
(SSRs) markers are very informative for various
applications in genetics and breeding. Information
obtained with these markers has contributed to a better
understanding of evolution and the complexity of the
sugarcane genome.With the objective of identifying a
large set of polymorphic microsatellite markers
designated as Unigene derived Sugarcane Microsat-
ellite (UGSM) and Sugarcane Enriched Genomic
Microsatellite (SEGMS), 351 UGSM and 36 SEGMS
were tested to find out informative SSRs marker for
sugar content. These markers were screened and
validated for their use in genetic diversity, cross
transferability and comparative linkage potential in
high and low sugar bulk of two segregating progenies
and twenty each, cultivated high and low sugar
cultivars. 158 (40.83%) of the microsatellite markers
(144-UGSM: 14-SEGMS) were found to be highly
robust and polymorphic. Cross amplification was
estimated among nineteen accessions of six sugarcane
cultivars, one inter specific hybrids, five related
species, four related genera, and three divergent
genera by using 27 UGSM primers. Analysis of 388
alleles, amplified by these markers, indicated the high