Genetic diversity analysis of recombinant inbred lines of rice (Oryza sativa L.) using microsatellite markers

Estimation of genetic diversity is an important factor in germplasm conservation and characterization. In rice breeding programs, genetic diversity information on specific regions of genome can be very useful for the application of marker assisted selection (MAS) and for gene mapping. A total of ۱۵۲ rice lines were considered for breeding programs using microsatellites (SSR) technique. The total number of polymorphic alleles was ۲۰۶ with an average of ۲ alleles per SSR locus. The PIC value for the SSR loci ranged from ۰.۴۷۹ to ۰.۵ with an average of ۰.۴۹۸. The highest PIC value was observed for primers RM۶۰, RM۶۸۳۲, RM۳۸۳۸ and RM۵۹۲. RM۱, RM۲۳۷, RM۱۵۴ and RM۸۴ had the lowest PIC values in a decreasing order. Nei’s gene diversity ranged from ۰.۴۷۹ to ۰.۵ with an average of ۰.۴۹۸. Using Shannon’s diversity index, a mean genetic diversity of ۰.۶۹۱ was obtained. The lowest diversity was found for RM۱, RM۲۳۷, RM۲۴۶, RM۱۵۴ and RM۲۷۹ in an ascending order and ۲۷ SSR markers had the highest value (۰.۶۹۳). Cluster analysis using the UPGMA method based on Jaccard’s similarity coefficient classified all lines into three clusters. Association analysis by general linear model (GLM) method revealed that ۶۲ SSR markers showed a significant association with ۱۰ studied morphological traits. Twenty eight markers were associated with more than one trait. These may be further investigated in rice breeding programs to be introduced as informative and useful markers. Results showed the potential of SSR markers to identify rice lines at the DNA level. The information will help the selection of lines to serve for efficient rice breeding programs.

Keywords:

Association analysis , Cluster analysis , Genetic Variation , Rice , SSR