Genetic diversity analysis of selected local rice varieties of Pakistan using RAPD markers

Assessment of the genetic diversity is very important for the improvement of many crop species including rice. The study was undertaken to assess the genetic diversity prevailing among ten commercially grown rice varieties of Pakistan using nine random amplified polymorphic DNA (RAPD) markers. All the nine primers were able to produce a total of 444 amplicons with an average of 49. 33 amplicon per primer. A total of 356 polymorphic amplicons were generated and showed 80.18 % polymorphism with an average number of 39.55 polymorphic bands per primer. RAPD marker, GL C-12 produced maximum number of bands (76 in all varieties) whereas GL G-14 generated minimum number of bands (26) in the genomic pool. A high level of genetic polymorphism at the DNA level was observed among the ten Oryza sativa varieties with an average genetic distance ranging from 28% to 64% on the basis of average dissimilarity coefficient matrix following UPGMA. A dendrogram constructed using the information of the average dissimilarity coefficient matrix of all the ten varieties based on the data of nine RAPD primers placed the varieties in two categories. Cluster analysis grouped six rice varieties i.e. Sarshar, TN-1, Jajai-77, JP-5, Pakhal and Shadab into one group, indicating the similarities between these varieties while the four rice varieties RI-DR-92, Shaheen Basmari, NIR-9 and Sada Hayat were found to be different from the six varieties grouped together. The cluster analysis placed RI-DR-92 and Sarshar in the different groups confirms the maximum genetic distance between the two varieties as shown by the genetic distance (64%) estimated in percent. The dendrogram indicated that the RI-DR-92 and Sarshar and JP-5 and Sada Hayat are distantly apart from one another and can be crossed to broaden the genetic base of Oryza sativa. In addition, more informative primers can be converted to sequence tagged sites (STS) and sequence characterized amplified regions (SCAR) for the amplification of specific alleles which can aid further in rice genome analysis.