For hybrid rice breeding, the nuclear genome diversity of 22 cytoplasmic malesterile
(CMS) lines used as female parents for breeding hybrids in the Philippines were
assayed at loci amplified by 20 microsatellite or simple-sequence repeat (SSR), 25
RAPD, and !O amplified fragment length polymorphism (AFLP) primers or primer
combinations. A high degree of polymorphism was detected in the CMS lines.
Microsatellites and AFLPs appeared to be the most suited for DNA fingerprinting.
Cluster analysis based on 222 molecular markers classified the CMS lines into nine
groups. The groupings could guide hybrid rice breeders in developing genetically
diverse and heterotic rice hybrids.