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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.

Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers

“…Similarity coefficients among cultivars ranged from 0.64 to 0.94 with an average of 0.82 which were highly similar to the values obtained among 42 Indian elite rice varieties (0.59 to 0.95, average 0.80; Davierwala et al 2000), 40 varieties of Pakistan rice (0.5 to 0.96, average 0.82; Rabbani et al 2008) and 45 accessions of the AA-genome Oryza species (0.59 to 0.92). The relatively high level of similarity was detected between closely related genotypes derived from common ancestors such as KDML105 and RD15 (0.94), FL496 and MATATAG2 (0.92) and IR28 and IR29 (0.90).…”

“…The low Pearson's correlation (r = 0.329) between the two similarity matrices indicated that clusters produced based on the two marker systems were not conserved. Similar correlation (r = 0.39) was obtained from a study involving 42 Indian elite rice varieties using 8 RAPD and 9 SSR primers (Davierwala et al 2000). The higher correlation between RAPD and SSR markers had been obtained by Ravi et al (2003) who observed a correlation of 0.582 from a genetic diversity analysis among 40 cultivated rice varieties and five wild relatives using 36 RAPD and 38 SSR primers.…”

“…However, other authors reported higher level of polymorphism for rice i.e. 80% among 42 Indian elite varieties estimated by using 40 RAPD primers (Davierwala et al 2000), 72.9% among 7 Egyptian genotypes using 8 RAPD primers (Saker et al 2005) and 89.4% among 40 cultivars of Pakistani rice using 25 RAPD primers (Rabbani et al 2008). Nevertheless, it is evident that RAPD can efficiently distinguish all of the rice cultivars in this study.…”

“…aromatic and non-aromatic coarse grain rice (Pervaiz et al 2009). Analysis based on SSR markers (Davierwala et al 2000) was able to divide Indian elite rice cultivars into clusters according to complex physiological characters namely early duration maturity, medium duration maturity and semi-deepwater and deep-water rice. Analysis of microsatellite markers at 25 loci among 33 rice genotypes differing in salinity tolerance (tolerant, moderately tolerant and susceptible) could divide rice into two major groups i.e.…”

Assessing genetic diversity in 23 early Polish oat cultivars based on molecular and morphological studies

“…The average AFLP MI was comparable with values obtained in previous studies, for example on barley (Varshney et al 2007), durum wheat (Martos et al 2005) and soybean (Powell et al 1996). In the case of ISSR, the MI value was twofold higher than those described earlier for rice (Davierwala et al 2000), cashew (Archak et al 2003) and bitter gourd (Behera et al 2008). In numerous studies, where the AFLP and ISSR markers were compared, higher value of MI was typical for AFLP.…”