Genotyping of rice accessions using SSR markers

Abstract

Molecular characterization of germplasm accessions of rice revealed genetic polymorphism and ensured unambiguous identification. A total of 24 SSR markers were used covering all the chromosomes of rice for their molecular characterization and discrimination. After analysis of the data generated, a total of 69 alleles were detected in 24 accessions of rice. The number of alleles per locus generated by each marker ranged from 1 to 6 alleles with an average number of 2.87 alleles per locus. The highest number of alleles (6) was detected in the locus RM 22565 while, lowest number of alleles (1) detected on each of locus OSR 13, RM 431, RM 454 and Xa5s. The PIC value ranged from 0.00 (OSR 13, RM 431, RM 454 and Xa5s) to 0.76 (RM 12146). Microsatellite markers (SSR) are also used to detect the genetic similarity of germplasm accessions of rice. The genetic similarity coefficient ranged from 0.24 to 1.00 as revealed by UPGMA cluster analysis using the 24 SSR markers. A total of five distinct groups resulted at a cut-off similarity coefficient of 0.46 among the 24 rice accessions, below which the similarity values narrowed conspicuously. Coefficient of similarity revealed that the rice accessions of cluster I were genetically distant from cluster IV. Thus, Peeleeluchai (135131) and Mahuwadeta Lal of cluster I; whereas, Kadamphool and Ram Karoni of cluster IV seems to be promising and should be utilized in hybridization programme. Molecular markers like RM 1, RM 12146, RM 215, RM 22710 RM 154 and RM 25 could potentially be used for molecular characterization of rice germplasm accessions from various sources on the basis of polymorphic reactions and high PIC values.