Assessment of genetic diversity and relationships among species using gene targeted CAAT box-derived polymorphism markers.

To detect the genetic variation and relationships among different ecotypes/species, the gene targeted CAAT box derived polymorphism (CBDP) markers were employed in terms of their efficiency. In this study, 25 CBDP primers amplified a total of 323 different polymorphic fragments that discriminate all 26 ecotypes/species and produced an informative and differentiated dendrogram and population structure. The CBDP markers were found to be effective in genetic diversity estimation with regard to the averages polymorphism (100%), polymorphism information content (PIC = 0.89), marker index (MI = 4.5) and the effective multiplex ratio (EMR = 5.01) which were higher than other reported markers on . The extent of heterozygosity (0.034≤≤0.223) and Shannon index (0.042≤≤0.278) indicated a high level of genetic variation among species. The species containing the highest basic chromosome number (X = 12) revealed the highest values for the number of different () and effective ( ) alleles, Shannon index (), and heterozygosity (). Additionally, the tetraploid species showed high values of , , and compared to the diploid species. Mean of gene differentiation () among species was 0.792, and the estimation of gene flow () was 0.13, indicating high genetic differentiation. Remarkably, similar results were obtained from the principal co-ordinate analysis (PCoA) as compared with the cluster analysis, in which all different species formed individual groups. In conclusion, because the CBDP markers are derived from the gene containing regions of the genome, consequently, the high genetic diversity among studied species would be more useful for crop improvement programmes, such as hybridization between species and QTL mapping. The potential of CBDPs for analysing the phylogeny and genetic diversity of species is another key result with practical implications.