Authentication, Genetic fingerprinting and assessing relatedness of rice (Oryza Sativa) genotypes by SSR molecular markers

Rice (Oryza sativa L.), is a staple food and cash crop in many countries and studies on genetic structure and differentiation patterns of rice landraces along with the cultivated rice, provide important data for future rice breeding. Therefore, the aims of present investigation were 1-To study the genetic diversity present within Iranian rice genotypes, 2-To study genetic relatedness of these rice genotypes, and 3-To provide barcoding of the rice genotypes based on SSR molecular markers and produce data for rice varieties authentication.  In total, 201 rice samples originated from 10 geographical regions of Iran were studied in this project. All rice samples underwent fragment analysis in every 64 SSR loci and different clustering and ordination methods performed. In general, four major clusters were formed. Both landraces as well as rice cultivars were distributed in different clusters due to their genetic difference. STRUCTURE analysis of the studied genotypes followed by Evanno test produced the optimal number of genetic groups K = 2. The mean Nm = 13.6, for the studied genotypes indicates that a high degree of gene flow/ ancestral common alleles are present in the rice genotypes studied. Mantel test indicated a significant positive association between genetic distance and geographic distance of the rice genotype studied and presence of an overall isolation by distance (IBD) model of differentiation across the geographical regions of Iran. Overall, the significant genetic difference observed between rice landraces and rice cultivars of the country may be used in future hybridization and breeding of rice in the country. The landrace rice genotypes may contain useful genes to be transferred to the popular rice cultivars. Moreover, SSR loci that can differentiate rice genotypes are identified and can be used in rice cultivars authentication.