title: 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.
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
authors.forename: Ron
authors.initials: R
authors.lastname: Ophir
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
authors.forename: Amir
authors.initials: A
authors.lastname: Sherman
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
authors.forename: Mor
authors.initials: M
authors.lastname: Rubinstein
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
authors.forename: Ravit
authors.initials: R
authors.lastname: Eshed
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Sharabi Schwager
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel.
authors.forename: Rotem
authors.initials: R
authors.lastname: Harel-Beja
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel.
authors.forename: Irit
authors.initials: I
authors.lastname: Bar-Ya'akov
authors.affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel.
authors.forename: Doron
authors.initials: D
authors.lastname: Holland
mesh_terms: D020869:Gene Expression Profiling; D005787:Gene Frequency; D014644:Genetic Variation; D029561:Lythraceae / Q000033:anatomy & histology / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*