Analysis of genetic diversity among Ixora cultivars (Rubiaceae) using random amplified polymorphic DNA

Abstract

We have optimized the genomic DNA extraction method from fresh and dry laminas, as well as fresh and dry corolla lobes of Ixora cultivars. Some woody tropical species such as these contain excessive amounts of phenolic compounds that co-precipitate with DNA resulting in poor or no amplification during the polymerase chain reaction (PCR). Repeated precipitation with CsCl coupled with phenol chloroform extraction yielded high quality DNA suitable for consistent PCR amplification. The DNA from fresh laminas of 22 cultivars of Ixora was subjected to random amplified polymorphic DNA (RAPD) analysis. Individual taxa could be identified using specific DNA markers from the RAPD profiles. Cluster analysis of data from six primers grouped all 22 cultivars distinctly under two cultivar groups, viz, Ixora Coccinea and I. Javanica. The percentage genetic similarity was calculated for all the cultivars based on the RAPE) data. The two cultivar groups and the outgroup plants were also clearly distinguishable with polar ordination using a matrix of genetic dissimilarities (one minus similarity). Our data indicate that besides the use of RAPD markers for identification of particular Ixora cultivars within a germplasm collection, the phylogenetic relationships generated by RAPD analysis may be useful for future breeding programmes.