Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.)

Abstract

Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300-450 mg/100 g), medium calcium (200-300 mg/100 g) and low calcium (100-200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops.

Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

“…It was useful to analyze each of these components and their ramifications individually. Comparison of the diversity index calculated from the experimental data exhibited that EST-SSR was more polymorphic, which was in agreement with previous research in other plants (Milbourne et al, 1997;McGregor et al, 2000;Belaj et al, 2003;Panwar et al, 2010). However, TRAPs revealed high values of loci per assay unit, average number of polymorphic bands per assay unit, and high EMR, indicating that a large amount of genetic information could be detected using this marker, which was in keeping with the study by Alwala et al (2006) and Hu et al (2007).…”

Variation of Nutritional and Anti-Nutritional Contents in Finger Millet (Eleusine coracana (L.) Gaertn) Genotypes

“…( [19]) attributed the variation among genotypes in minerals contents to differences in ecological conditions from which the finger millet genotypes originated. The results of this study also differ with findings of other workers who reported differences in Ca content among 36 finger millet genotypes ( [20]). Lack of variability in mineral content among the genotypes of this study occurred possibly because few genotypes were used or they originated from related genetic pool.…”

Genetic diversity of bitter and sweet African bush mango trees (Irvingia spp., Irvingiaceae) in West and Central Africa

“…Therefore, they are widely used in genetic analysis (Berchowitz et al, 2001;Assogbadjo et al, 2010) as opposed to the RAPDs with low reproducibility (Powell et al, 1996). Microsatellites (or simple sequence repeats, SSRs) and especially chloroplast microsatellites (cpSSRs), have the power to reveal genetic diversity as well as phylogenetic relationships and hybridization between plant species (Wills et al, 2005;Panwar et al, 2010). Thus AFLPs and cpSSRs were used for these analyses.…”