Microsatellite and SNP markers for sd-1 in rice

The most important semi-dwarfing gene in rice is sd-1. This gene has been used predominantly, to increase lodging resistance, harvest index and responsiveness to nitrogen fertilisation and to improve general plant type for the development of highly productive rice cultivars. The gDNA clone RG109 has been genetically mapped close to sd-1. We have identified a microsatellite repeat within this clone and developed the microsatellite into a co-dominant PCR based marker. The marker is polymorphic and a further polymorphism (SNP) has been identified in the sequence flanking the microsatellite. The SNP did not correspond to a loss or gain of a restriction site however the polymorphism could be detected by temperature gradient gel electrophoresis. These PCR markers were found to be potentially useful for selection for sd-1 in a range of rice crosses.