Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP

Cultivated rice is a high-volume, low-value cereal crop providing staple food to more than 50% of the world populace. A small group of rice cultivars, traditionally produced on the Indo-Gangetic plains and popularly known as Basmati, have exquisite quality grain characteristics and are a prized commercial commodity. Efforts to improve the yield potential of Basmati have led to the development of several crossbred Basmati-like cultivars. In this study we have analysed the genetic diversity and interrelationships among 33 rice genotypes consisting of the traditional Basmati, improved Basmati-like genotypes developed in India and elsewhere, American long-grain rice and a few non-aromatic rice using a DNA marker-based approach - fluorescent-amplified fragment length polymorphism (f-AFLP). Using a set of nine primer-pairs we scored a total of 10,672 data points over all of the genotypes in the size range of 75-500 bp. The scored data points corresponded to a total of 501 AFLP markers (putative loci/genome landmarks) of which 327 markers (65%) were polymorphic. The f-AFLP marker data, which were analysed using different clustering algorithms and principal component analysis, indicate that: (1) considerable genetic variability exists in the analysed genotypes; (2) traditional Basmati cultivars could be distinctly separated from the crossbred Basmati-like genotypes as well as from the non-aromatic rice; (3) the crossbred Basmati-like cultivars from the subcontinent and elsewhere are genetically very distinct; (4) f-AFLP-based clustering, in general, conforms to the putative pedigree of the improved genotypes. Moreover, analysis to ascertain the scope of AFLP as a technique suggests that the polymorphism revealed by three selective primer-pair combinations is sufficient to obtain reliable estimates of genetic diversity for the type of material used in this study. However, its utility to identify group-specific DNA markers was discounted due to a low frequency of observed group-specific discrete markers.