Molecular Characterization of Selected Landraces of Rice for Salt Tolerance Using SSR Markers

Salinity stress is the major constraint in rice production. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In this study three selected SSR markers viz. RM336, RM510 and RM3412 were used to screen the germplasm for salt tolerance. For genotyping rice germplasm, DNA was extracted from leaf samples using CTAB mini-prep method. The number of allele per locus was 10, with an average number of 10 per locus. The average gene diversity of overall SSR loci for the 25 genotypes was 0.8693, ranging from 0.8608 to 0.8768. The PIC values for 3 SSR markers varied from 0.8456 (RM336) to 0.8645 (RM510) with an average PIC of 0.8556. Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram, constructed from Nei's genetic distance produced three distinct clusters of 25 rice genotypes which is very much similar to Principal Component Analysis (PCA). It can be concluded that Jamai naru, Kajol shail, Hogla, Khak shail, Tal mugur, BINA dhan8 were salt tolerant compared to FL 478 because they showed a lower similarity value with FL 478. Marker RM510 showed the highest level of diversity due to high PIC value. This scientific information could be used for selection of suitable parents and development of salt tolerant rice varieties as well.