High-resolution DNA fingerprinting of Indian rice (Oryza sativa L) varieties by amplified fragment length polymorphism

To assess diversification of indica rice, fingerprinting of 42 Indian rice varieties (Oryza sativa L) and one accession of O. brachyantha Chev. et Roehr. was taken up using amplified fragment length polymorphism (AFLP). Six primer combinations of PstI and MseI were used for this purpose. On denaturing polyacrylamide sequencing gel, on average 41 scorable AFLP bands were obtained of which 81% were polymorphic. Each variety revealed a distinct fingerprint. Data were scored on the basis of presence and absence of bands and cluster analysis was performed using Dice similarity coefficients. The resultant dendrogram showed four major clusters and traits. Some varieties especially landraces revealed more polymorphism and unique loci. Such study will be a valuable tool for proper choice of parents in mapping populations or breeding programs to produce heterotic several inexplicable minor clusters. Some varieties were grouped according to parentages of the cross while some were grouped according to physiological combinations apart from providing a characteristic fingerprint.