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Construction of a Microsatellite Database Containing 325 Rice Varieties (Oryza sativa L.)
Microsatellite marker is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. The suitability of simple sequence repeat (SSR) markers for varietal identification and genetic diversity were evaluated for 325 rice varieties. Four hundred thirty six pairs of SSR primers were screened against 11 rice varieties. Twenty six primer pairs were highly polymorphic and reproducible. These primer sets were used to construct a DNA profile database containing 325 rice varieties grown in Korea through automatic detection system (ABI 3130XL). Microsatellite polymorphism was showed to be high. A total of 331 polymorphic amplified fragments were obtained by using 26 microsatellite markers. The number of alleles per locus ranged from 9 to 18 with an average of 12.73 alleles per locus. The average polymorphism information content (PIC) was 0.734 ranging from 0.555 to 0.880. Three hundred thirty one SSR loci were used to calculate Jaccard’s distance coefficients for UPGMA cluster analysis. These varieties were separated into several distinctive groups corresponding to varietal types. Almost all of the varieties were discriminated by SSR marker genotypes. This information may be useful to select comparative variety through comparison of genetic relationship analysis between existing variety and candidate varieties in distinctive tests.
