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DNA Fingerprinting of ‘Basmati’ Rice

The 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 in Indo-Gangetic plains, popularly known as Basmati, having exquisite quality grain characteristics, are prized commercial commodity. Efforts to improve the yield potential of Basmati have led to development of several crossbred Basmati-like cultivars.

This work was done at Center for Cellular and Molecular Biology, India as an additional work when I was involved in Coffee genomics. I am thankful to Dr. Ramesh Aggarwal, for his innovative ideas in analysing the data. Click on the publication section to view the detailed results..

Significance

In this study we have analysed the genetic diversity and interrelationship among 33 rice genotypes, comprising the traditional Basmati, improved Basmati-like genotypes developed in India and elsewhere, American long-grain rice and few non-aromatic rice, using DNA markers based approach of fluorescent-amplified fragment length polymorphism (f-AFLP). Using a set of nine primer pairs a total of 10,672 data points were scored over all the genotypes in the size range of 75 to 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, analysed using different clustering algorithms and principal component analysis suggest that: (a) there exists considerable genetic variability in the analysed genotypes; (b) the traditional Basmati could be distinctly separated from the crossbred Basmati-like genotypes as well as from the non-aromatic rice; (c) the crossbred Basmati-like cultivars from the subcontinent and elsewhere are genetically very distinct; and (d) the f-AFLP based clustering, in general, conforms to the putative pedigree of the improved genotypes. Moreover, the 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 the study. However, its utility to identify group specific DNA markers was discounted due to low frequency of observed group specific discrete markers.

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