Use of Three Different Marker Systems to Estimate Genetic Diversity of Indian Elite Rice Varieties

Abstract

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding
and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic
DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity
values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively.
The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the
genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of
153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity
coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis
revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients
of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift,
sampling of loci and unknown relationships among supposedly unrelated ancestors.