ABSTRAK
Padi hitam merupakan salah satu tanaman serealia yang berpotensi sebagai pangan fungsional, karena kandungan zat gizi dan zat aktif antosianin yang bermanfaat bagi kesehatan. Tujuan penelitian karakterisasi ini adalah identifikasi profil pita DNA, keragaman genetik, dan hubungan kekerabatan beberapa varietas lokal padi hitam berdasarkan marka RAPD (Random Amplified Polymorphic DNA).
Metode penelitian meliputi isolasi DNA, penetapan kuantitas dan kemurnian DNA, seleksi primer, analisis RAPD, serta elektroforesis dan visualisasi. Data yang diperoleh dari penelitian kemudian dianalisis menggunakan program NTSYSpc versi 2.02. dengan metode pengelompokan UPGMA (Unweighted Pair Group Method of Arithmetic Means) fungsi SHAN (Sequential,Hierarchical, Agglomerative, and Nested).
Analisis RAPD pada 6 varietas padi yang diuji dengan 5 primer terpilih menghasilkan pita spesifik, seperti OPA 13-450, OPB 08-300, OPC 16-2000, OPC 16-450, OPC 20-450, dan OPC 20-800.  Selain itu, total pita DNA yang diperoleh adalah 33 pita DNA dengan 31 (93,93%) diantaranya adalah polimorfik. Dendogram pada derajat kemiripan 0,62 (62%) atau jarak genetik 0.38 memisahkan padi kontrol-putih (Ciherang) dengan kelima varietas padi hitam yang diuji.
Kata kunci: karakterisasi, keragaman genetik, padi hitam, RAPD
ABSTRACT
Black rice is one of cereal crop that has potential as a functional food, because of the content of nutrients and active substance (anthocyanin) that are beneficial to health.  The purpose of this characterization research is to identify the DNA band, the genetic diversity, and the relationship some local varieties of black rice on the strength of RAPD marker (Random Amplified Polymorphic DNA.)
Research methods include isolation of DNA, measurement of the quantity and the purity of DNA, selection of primer, RAPD analysis, than electrophoresis and DNA visualization. The data were  analyzed using NTSYS-pc version 2.02 by the clustering method of UPGMA (Unweighted Pair Group Method of Arithmetic Means) function SHAN (Sequential, Hierarchical, Agglomerative, and Nested).   
RAPD analysis on six rice varieties were tested using five selected primers produced spesific bands, such as OPA 13-450, OPB 08-300, OPC 16-2000, OPC 16-450, OPC 20-450, and OPC 20-800. In addition, the total DNA obtained was 33 bands in which 31 (90%) of them were polymorphic. Dendogram at the similarity coeficient of 0,62 (62%) was separated the control rice-white (Ciherang) with five varieties of black rice tested.
Key word: characterization, diversity genetic, black rice, RAPD