Assessing genetic diversity of rice genotypes using microsatellite markers and their relationship with morphological characteristics of seedling stage under non- and drought-stress conditions

Marker assisted selection is one of the important applications molecular markers especially in creation of tolerant genotypes to environmental stresses in crop plants. In this research, seedlings of twenty two rice genotypes were investigated under two culture conditions (normal and drought stress via Manitol) on the basis of completely randomized factorial experiment with three replications at growth chamber of Faculty of Agriculture and Natural Resources, Gonbad Kavous University, Iran, in 2012, and root and shoot length and dry weight were measured. Analysis of variance showed that genotype×culture condition interactions were significant for all measured traits. This result revealed different reaction of the studied genotypes under two culture conditions and genetic diversity among the genotypes in seedling stage. To investigate the molecular diversity among the genotypes, genomic DNA was extracted amplified using 22 microsatellite markers linked to drought tolerance. In total, 106 alleles were detected with the number of 2-7 alleles and the average of 4.28 alleles per locus. The polymorphic information content (PIC) varied from 0.29 to 0.82 with the average of 0.64 and the gene diversity ranged from 0.351 to 0.840 with the average of 0.686. Genetic distance among the studied genotypes was also calculated in the range of 0.23 to 0.99. Cluster analysis using microsatellite data grouped the genotypes in two clusters. Result of principal component analysis showed that the first 10 principal components explained 98.51% of the total variation. Grouping of the genotypes according to first and second principal components assigned the studied genotypes into four groups. Results of these grouping methods demonstrate the suitability of the microsatellite markers to assess the genetic diversity among the rice genotypes. To identify the informative (positive) markers affecting the morphological characteristics, regression analysis was performed. A total of 16 informative markers were detected under both culture conditions which are recommended for drought tolerance in the breeding programs.