Molecular Diversity Analysis of Traditional Rice Varieties of Kerala Using RAPD Markers

Abstract

Thirty traditional landraces collected from nine ecological zones of Kerala were subjected to molecular studies.
Twenty oligonucleotide primers used for the study produced 222 amplicons with a polymorphism of 82%. The
amplifi cation products derived with random primers had size ranging from 2.0 kb to less than 0.5 kb. Of the
twenty primers OPF-04 gave maximum number of polymorphic products and also produced two unique positive
products in the accession Cheruvirippu (size between 1.0 kb and 1.5 kb) and in the accession Njavara yellow
(size of less than 0.5 kb). This primer has the highest resolving power (24.52) and Effective Multiplex Ratio
(15.0) and so is selected as the best primer for distinguishing rice varieties in this study. Clustering based on
Jaccard’s similarity coeffi cient revealed the highest similarity between the accessions Chettivirippu and Pokkali
(0.825). Both these accessions are suited to the saline sodic soils of Kerala. The Njavara group of accessions
(medicinal rice), Njavara yellow and Njavara black, clustered at a similarity value of 0.707. The primer OPB-05
and OPF-01 could distinguish the Njavara accessions from others. OPB-05 produced unique product with a size
of less than 1.0 kb and OPF-01 produced product at size of less than 0.5 kb unique for the Njavara accessions.
Even though these accessions were from different ecological zones location specifi c clustering was not observed
pointing the uniqueness of the collection at the micro level