Analysing South Sumatra red rice polymorphism using random amplified polymorphic DNA (RAPD) markers

Abstract

this research aims to determine genetic variation based on polymorphism bands and the relationship between red rice in south sumatra based on PCR- RAPD (Polymerase Chain Reaction- Random Amplified Polymorphic DNA) tecnique using the mathematical modeling application NTSys 2.1. Collecting data using observation methods where samples are collected genetic variation and presented in quantitative form. Research instruments include tools and laboratory materials that facilitate the research process such as electrophoresis, thermal cycle machines, gel documentation and others. DNA bands obtained electrophoresized PCR sample is converted into binary data which is stated by the presence or absence of DNA bands, if there is a DNA band then marked with (1), whereas if the DNA band does not appear then marked with (0). Data were analysed using the NTSys version program. 2.1. Dendrogram created using unweighted pair-group with arithmetic average with genetic similarity coefficient using Jaccard Coefficient of Similarity and presented in the form of dendrogram. Based on the DNA band profile of RAPD results which 43 DNA bands show polymorphism (93.47%). Based on the analysis using the NTSys 2.1 program, a dendogram was obtained where red rice in South Sumatra was divided into two main clusters at a genetic similarity coefficient level of 0.19, namely cluster A consisting of red rice with CT code (Cahya Tani) and cluster B consisting of red rice SJ code (Sumber Jaya), SP (Sp Padang), and K (Kelirejo). The four red rice individuals taken from different places have a low genetic similarity coefficient of 0.15-0.37, meaning that the fourth genetic variation of red rice is very high.