Genome analysis of traditional rice varieties of Kerala using ISSR and RAPD markers
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Date
2006
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Department of Plant Breeding and Genetics, College of Agriculture, Vellayani
Abstract
The research project “Genome analysis of traditional rice varieties of Kerala using ISSR and RAPD markers” was carried out in the Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Thiruvananthapuram during 2004-2006. The major objectives of the study were to characterize indigenous rice collection of Kerala on the basis of two molecular markers viz. ISSR and RAPD and to assess the genetic diversity using molecular marker technique.
The study using RAPD markers produced 222 amplicons of which 182 were polymorphic thus giving a polymorphism of 81.98 per cent. Twenty primers were used for the study. Of these the primer 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). The amplification products had size ranging from 2.0 kb to less than 0.5 kb. The analysis produced nine unique positive products and seven unique negative products.
Clustering based on Jaccard’s similarity coefficient revealed the highest similarity between the accessions Chettivirippu and Pokkali 3 (0.825). The least similarity index of 0.451 was between the accessions Cheeravithu and Vellakkoli. The Njavara group of accessions, 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.
ISSR analysis was carried out using two primers. The amplification using the two primers produced 19 amplicons of which 16 were polymorphic giving 84.21 per cent polymorphism. The amplification products had size ranging from 0.2 kb to more than 1.0 kb. A unique negative marker was amplified by the primer (GA) 8T in the accession Karuthacheera with a size of nearly 0.6 kb. The UPGMA clustering was done using Jaccard’s similarity coefficient values. The highest similarity of 1.00 was shown by the accessions, Athikiramundakan and Veluthakattamodan and by Vellamundakan and Chettivirippu. The least similarity was between the accessions Karuthacheera and Pandivella (0.230). The accession Karuthacheera was unique and formed a single cluster at similarity value of 0.420.
The pattern of clustering for the individual marker systems did not show any congruence with each other. However the cluster analysis of combination of the two marker systems produced a better picture of the genetic relationship. The present study using the two dominant DNA markers, RAPD and ISSR, showed that both the DNA markers are effective and promising for detecting genetic variation. It has been observed that ISSR is superior to RAPD in terms of polymorphism detected.
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