Genetic relationships among a collection of Indica rice (Oryza sativa) genotypes of Kerala revealed by SSR markers

A study was conducted during 2005 to understand genetic relationship at molecular level among a collection of rice (Oryza sativa L.) varieties and land races of Kerala using SSR markers. Twenty eight SSR markers were used to screen the genotypes. The 28 SSR markers loci revealed 73 alleles in 76 cultivars with an average of 2.61 alleles/locus. The number of alleles/locus varied between 1 and 8. Out of 28 SSR markers, 4 were monomorphic hence percentage polymorphism was 85.7. The size of allele amplified among the 76 cultivars varied from 130 to 1 180 bp. Cluster analysis was done using pair-wise Jaccard’s similarity co-efficient which grouped 76 rice genotypes into 4 major clusters. Whereas 1 scented land race of Kerala, namely ‘Gandhakasala’ and the brown plant hopper resistant variety ‘Ptb 20’ were not grouped with any cluster. The genotypes ‘Vytilla 2’, ‘Ptb 20’, ‘Deepti’ and ‘Malakkaran’ were grouped in different clusters and observed to be genetically distant.