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Pigeonpea (Cajanus cajan) is an important subsistence crop in India where traditional landraces and improved hybrids are grown along side each other. SSR primers used to determine varietal/hybrid specific informative molecular markers for precise identification of varieties and hybrid of pigeonpea. DNA isolation was carried out by CTAB method and quality as analysed on nanodrop, the absorbance ratio of DNA at A260/A280 and finally with electrophoresis. Eleven of the 12 SSR primers studied amplified 13 alleles. Primer CCttc001 was more useful on account of its ability to amplify maximum number of 2 alleles and were found to be the other promising SSR primers for detecting polymorphism among the different genotypes of pigeonpea. CCtta002, CCgtt001, CCtacccg001 and CCtc002 primers did not amplified genomic DNA of pigeonpea. SSR primers classified the eleven genotypes of pigeonpea into two different clusters with lot of variation in number and inclusion of genotypes in sub groups. Though these techniques indicated genotype GT-100 to be distantly apart from genotype GT 288 A, yet comparing other set of genotypes, GT-101 were distantly apart in SSR analysis. This indicated no uniformity in grouping of genotypes based on SSR primers.
Keywords: DNA, SSR primers, Genotypes, Molecular Markers