The effect of gamma ray re-irradiation on genetic variations in black rice based on RAPD and Bph gene resistance location based on SSR markers

Abstract

Abstract The black rice variety Cempo Ireng M8 generation already has morphologically uniform characteristics and good productivity values. However, the black rice M8 generation is still susceptible to planthopper pests. Therefore, a re-irradiation process was carried out on M8 using 200 Gy gamma rays to obtain a black rice variety resistant to planthopper pests. This re-radiation treatment has produced the M2 generation. To determine the genetic variations between M8 black rice plants and the M2 generation that are formed, this research conducted molecular methods using six RAPD markers and three SSR markers to determine genes in the sample related to the Bph resistance gene. The sequenced SSR amplicons were analyzed using BLAST in NCBI. The results of the RAPD marker showed genetic variation in the seven black rice samples with an average polymorphism percentage of 92.85% and the Polymorphic Information Content (PIC) value for the six primers was between 0.25-0.5, which means the RAPD primers is informative. The analysis and sequence results of the RM5953 primer show that the primer is located in the Bph resistance gene (chromosome 4) and produces an amplicon at a band size of 129 bp.