Selection of ssr markers for assembling tungro-resistant rice varieties adaptive to swampland
Rini Ismayanti, Effi Alfiani Siddik, Firmansyah Firmansyah, Khaerana Khaerana, Nur Rosida, Wasis Senoaji, Elisurya Ibrahim

Food Crop Research Centre, BRIN

Abstract

Tungro disease is found in several swamps in Indonesia, but adaptive tungro-resistant varieties in swamps to prevent the spread of tungro disease are not yet available. Therefore, it is necessary to assemble new varieties that are specific to swamps by utilizing SSR molecular markers as a tool to facilitate selection. The purpose of this study was to determine the SSR primer that can distinguish resistant and susceptible varieties to tungro disease which is used as the parent of the cross. The parents used in the crosses were Inpara 2 as swamp adaptive elders, Tukad Petanu, Utri Merah 16680, and Utri Merah 16682 as tungro resistant parents. Thus, three cross combinations were obtained, namely Inpara 2 with Tukad Petanu, Inpara 2 with Utri Merah 16680, and Inpara 2 with Utri Merah 16682. A total of 14 pairs of SSR primers were used in this study. The CTAB method is used to isolate the total DNA of plant that were 4 weeks old. Master mix PCR components are created using the protocol^s composition, with some MgCl2 usage modifications. DNA amplification was visualized by electrophoresis on 2% agarose gel. There are seven polymorphic SSR primers, namely RM 8213, RM335, RM20, RM336, RM16425, RM3471, and RM16428. However, only three of them could distinguish four parents, namely RM8213, RM16425, and RM16428, while the other four primers could only distinguish two or three parents.

Keywords: R optimation, polymorphism, SSR primer

Topic: Plant breeding and biotechnology