Full Length Research Paper

Estimation of genetic diversity in rice (Oryza sativa L.) genotypes using SSR markers and morphological characters

K. Seetharam, S. Thirumeni* and K. Paramasivam

Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, U.T. of Puducherry, India.

*Corresponding author. E-mail: s_thirumeni@rediffmail.com.

Abbreviations: PCR, Polymerase Chain Reaction; SSR, Simple Sequence Repeats.

Accepted 25 July, 2008

Thirty rice genotypes comprising land races, pure lines, somaclones, breeding lines and varieties specifically adapted to costal saline environments were characterized by SSR markers and morphological characters in this study. Out of 35 primers of SSR markers, 28 were found to be polymorphic. The PIC value ranged from 0.064 (RM 274) to 0.72 (RM 580) with an average of 0.46. The Jaccard’s similarity coefficient ranged from 0.42 to 0.90. At the genetic similarity of 56% the genotypes were grouped into five clusters. PCA components explained 41.6% of variation. There was overlapping of tolerant genotypes and susceptible genotypes within the cluster. Morphological traits of each genotype were measured on five randomly chosen plants. The matrix of average taxonomic distance was estimated using Euclidian distance. The average taxonomic distance ranged from 1.5 to 7.78. At a Euclidean distance of 3.49, the 30 genotypes were grouped into IV clusters. The clustering pattern clearly grouped the genotypes based on their response to salinity and clustering was not based on their geographical origin. PCA components explained 38.4% of variation.

Key words: Rice, salt tolerance, SSR markers, cluster analysis.