Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

Abstract

Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.

Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

“…Ten pomegranate accessions from the varietal groups Mollar de Elche, Mollar de Albatera, Mollar de Orihuela, Valencianas and Bordes were evaluated, resulting in different genetic profiles for the different groups as well as for the accessions within a single group. Other studies on pomegranate have shown the large genetic variability of this crop by using molecular techniques such as simple sequence repeats markers (SSR, Ferrara et al, 2014; Pirseyedi et al, 2010; Hasnaoui et al, 2012), random amplified polymorphic DNA (RAPD, Hasnaoui et al, 2010; Narzary et al, 2009), microsatellite markers (Singh et al, 2015), or single-nucleotide polymorphism (SNP) markers Ophir et al (2014). …”

“…The study measured the structure of the population among the wild and domesticated accessions. Ophir et al (2014), in a study using Single Nucleotide Polymorphism (SNP) Markers on 105 worldwide pomegranate accessions, located in the pomegranate germplasm collection at the Newe Ya’ar Research Center in northern Israel, observed that genetic diversity was primarily due to the geographic location of origin.…”

Mining and characterization of SSRs from pomegranate (Punica granatum L.) by pyrosequencing

“…Although some effort has been made for the development of superior cultivars by conventional breeding of this crop, the genomic resources like expressed sequence tags (ESTs), sequenced genes or high‐density genetic maps are lacking (Ophir et al. ). Evaluations of genetic diversity of pomegranate have been conducted in the past using dominant markers like randomly amplified polymorphic DNA (RAPD) by Dorgac et al.…”

Evaluation of the genetic diversity of pomegranate accessions from Turkey using new microsatellite markers

“…Thus, it is very important to use sensitive and accurate molecular techniques such as SSR, AFLP, or SNP to detect DNA variation and to identify pomegranate germplasm, which would be most helpful to breeders and nursery workers for selection and propagation of a cultivar (Hasnoui et al, 2012;Nemati et al, 2012;Ophir et al, 2014). In the present study, we report for the first time the application Table 2.…”