Thirteen SSR markers previously mapped in the rice
chromosomes were characterized and selected according to
the number of alleles, allelic size range and polymorphism.
Two fluorescent-based SSR multiplex marker systems
were developed for genetic analysis of rice germplasm that
allow fast and reliable DNA typing at 11 independent
hypervariable loci by automated DNA sequencers. Allelic
frequencies at the 11 loci were computed after genotyping
the 108 O. sativa RC accessions and can now be used as a
reference database for accurate genetic analysis in rice. The
multiplex systems were tested on real cases of hybrid identification
and variety identity, validating their use in the
analysis of genetic relationships in rice, such as required for
paternity testing of hybrid progeny, analysis of sample contamination
and variety protection. Polymorphism at these
loci was also used to estimate genetic distances between
four male-sterile lines of the CMS hybrid program and their
maintainers. The data indicated that some of the maintainer
lines are not as near isogenic to the male sterile lines as previously
assumed by the breeding program