Over the last few decades, the use of molecular markers has played an
increasing role in rice breeding and genetics. Of the different types of molecular markers,
microsatellites have been utilized most extensively, because they can be readily amplified
by PCR and the large amount of allelic variation at each locus. Microsatellites are also
known as simple sequence repeats (SSR), and they are typically composed of 1–6 nucleotide
repeats. These markers are abundant, distributed throughout the genome and are highly
polymorphic compared with other genetic markers, as well as being species-specific and
co-dominant. For these reasons, they have become increasingly important genetic markers
in rice breeding programs. The evolution of new biotypes of pests and diseases as well as
the pressures of climate change pose serious challenges to rice breeders, who would like to
increase rice production by introducing resistance to multiple biotic and abiotic stresses.