Identifikasi dan Aplikasi Marka Berbasis PCR untuk Identifikasi Varietas Padi dengan Palatabilitas Tinggi

To date, there has been no DNA fingerprint profile as unique identity of rice variety that has a high palatability (overall eating quality) in Indonesia, thus identification of premium varieties using molecular markers is considered to be important. This study aimed to establish DNA fingerprint profiles of indica and japonica rice varieties, and unique identities of rice varieties with high palatability using molecular markers associated with palatability. Total of 22 japonica and 24 indica rice varieties were evaluated their overall eating quality and tested using 20 molecular markers STS (sequence-tagged site) which were designed on the basis of japonica rice genome. To identify the genes functions, all these markers amplicons were cloned, transformed, sequenced and the sequences results were analyzed their homologous against the genome database. Ilpum (japonica) and Rojolele (indica) were identified to have the highest palatability compared to other varieties. DNA fingerprint profiles identified with the total STS markers were not able to differentiate each variety, however premium varieties of japonica and indica showed specific identities. A unique identity of Indonesian indica variety possessing high palatability, Rojolele was successfully developed using a markers set. DNA fingerprint profile in digital value system facilitates the identification of premium rice from other varieties. The fragments of the STS primers showed no any known-genes functions related to rice eating quality, therefore these markers are preferentially used for identification of premium rice with high palatability than differentiation of rice varieties based on the palatability. In this study, the unique identity of rice variety with high palatability is very usefull to evaluate the purity for germplasm protection.