Strategic Planning of Iranian Pomegranate Germplasm For Identification, Registration and Exploitation Using Integrated Omics Data

Although pomegranate is an ancient fruit plant it has gained commercial significance recently. nowadays there is increasing worldwide demand for this fruit owning to its superior pharmacological and economical properties. the cultivated species punica granatum is reported to contain 2n=16 chromosomes. a germplasm bank of several varieties and genotypes from different part of iran was collected in order to preserve crop`s wide diversity. once this collection was established, the next step was to characterize the phenotype of these genotypes to determine the phenotypic, metabolic and genomic variability that existed among all the different pomegranate genotypes. two hundred-fifty pomegranate accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes and to establish core collection. forty-seven morphometric characteristics were measured in trees, fruits, arils, seeds, leaves and flowers, as well as juice characteristics including anthocyanin and antioxidant content, total poly phenols, titratable acidity, total soluble solids and maturity index. principal component analysis, and cluster analysis using different software showed that there was a considerable phenotypic and metabolic diversity. the phenotypic cluster analysis produced a dendrogram with four main clusters. the dissimilarity level indicated that there were genotypes with high similar to completely different from each other, and genotypes from the same geographical areas are not necessarily the most closely related. within each genotypes group, different degrees of similarity were found, although there were no accessions that were identical. these results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from selection programs. the analyzed metabolite data showed high variation for a set of target metabolites within the pomegranate germplasm. in this study, we used the genotyping-by-sequencing of single nucleotide polymorphism (gbs-snp) to investigate the genetic diversity and population structure of pomegranate accessions. a filtered set of 14,553 snps was used to establish core collection and gene flow. in the current study, an attempt was made to define core collection using 47 morphological traits, 5 metabolites and snp data. information on additional acquired germplasm and presence of duplicates or mislabeled accessions in the entire collection was also used. three core collections based on morphological, metabolites and snp markers were generated. our data indicate that these markers have to be considered to obtain a core collection that represents the entire diversity. the defined core collection consisted of 121 accessions and represented about 48.4% of the entire collection. principal component analysis revealed the maximum diversity captured in the core from the base collection. these results show that the combination of morphological, metabolites and molecular markers is an efficient way to characterize the pomegranate core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases. this defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in pomegranate improvement programs. in addition, knowledge about the extent of pomegranate diversity is essential for gene pool management and these data may help in developing strategies for pomegranate germplasm selection and may allow for more efficient use of this germplasm in future breeding programs. finally, these results validate the efficiency of genomics-based tools to characterize and identify genetic diversity in pomegranate and provide a significant tool for genomics-assisted plant breeding in future.