A bioinformatic insight into the genetic diversity within pomegranate cultivars: from nuclear to chloroplast genes

The pomegranate (Punica granatum L.) is an ancient fruit plant which has been consumed for its nutritional value and medicinal properties by mankind. Several studies have been carried out on the genetic variability and cultivar genetic finger printing of this plant species. Some of these studies claimed presence of very low degree of genetic variability in these cultivars, while some others reported a good level of genetic diversity in them. The similar controversy exists about the suitability of different molecular markers for genetic variability studies as well as cultivar discrimination. We therefore carried out the print study to compare the level of genetic variability as revealed by both nuclear (SSRs), and chloroplast genetic regions (trnH-psbA spacer, and matk gene) to reveal the discriminating power of these markers and provide some data on barcoding and mini-barcodes of pomegranate cultivars. We used both experimental data produced in our lab also utilized some published sequencing data from NCBI database. We used different bioinformatic approaches. DAPC analysis revealed that SSR markers are suitable for genetic variability analysis of pomegranate cultivars, but revealed some degree of genetic admixture among pomegranates. Therefore, these markers are suitable for gene flow studies but may not portray exact cultivar assignment. Both trnH-psbA and matK sequences could produce a better cultivar assignment. Barcoding and mini-barcode analyses revealed that pomegranates may be divided in two major genetic groups with some degree of divergence within these two major groups. Data indicates that, pomegranate plants possibly migrated or were introduced from Iran to the other parts of the world and it was accompanied with genetic divergence as discussed in this report.