Marker identification and phylogenetic analysis of saline tolerant rice varieties

Abstract

Selection for saline tolerant rice genotypes has been based on morphological or physiological character. These two characters are phenotypically affected by environmental factors, such that, their reliabilities for selection criteria are obscure. Molecular marker assisted selection has been reported to be an effective and efficient selection method as molecular markers are not influenced by environmental factors. The objectives of this study were: (1) to describe the phylogenetic relationship of rice genotypes based on SSR markers, and (2) to know the reliability of microsatellite markers for phylogenetic analysis of rice genotypes in relation to salinity tolerance. The research was conducted from July to October 2020 at Plant Breeding and Biotechnology Laboratory, Faculty of Agriculture, Jenderal Soedirman University, Purwokerto, Indonesia. DNA extraction was carried out using CTAB method. Agarose gel electrophoresis was used for determination of genomic DNA quality and concentration. PCR was performed using 2720 Applied Biosystems Thermal Cycler. Seventeen microsatellite primers, namely: RM129, RM156, RM222, RM223, RM224, RM241, RM292, RM342B, RM444, RM426, RM493, RM519, RM528, RM1287, RM3412, RM8094, and Wn11463, were analyzed on eight rice genotypes, namely: Inpari Unsoed-79 Agritan, Cisadane, Atomita-2, Pelopor, Dendang, Lambur, Siak Raya, and IR 29. Extraction of genomic DNA has resulted in high quality DNA of 100 ng/µL concentration. Phylogenetic analysis demonstrated that the eight genotypes could be grouped into two clusters. Tolerant variety of Inpari Unsoed-79 Agritan was distantly apart from the susceptible variety IR29.