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Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.

Ophir R, Sherman A, Rubinstein M, Eshed R, Sharabi Schwager M, Harel-Beja R, Bar-Ya'akov I, Holland D - PLoS ONE (2014)

Bottom Line: Pomegranate fruit has a variety of health-beneficial qualities.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.Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.

View Article: PubMed Central - PubMed

Affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.

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.

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Related in: MedlinePlus

Worldwide distribution of the pomegranate genetic groups.The genetic groups as clustered together by the genetic dendrogram were located on a world map by geographical regions. Genetic groups and subgroups are colored as in Figure 6.
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pone-0088998-g007: Worldwide distribution of the pomegranate genetic groups.The genetic groups as clustered together by the genetic dendrogram were located on a world map by geographical regions. Genetic groups and subgroups are colored as in Figure 6.

Mentions: The classification tree (i.e., dendrogram) revealed two major groups of accessions (G1 and G2); G2 was further divided into two subgroups (G2.1 and G2.2). Strictly speaking, the dendrogram implied altogether three statistically significant groups (bootstrap value >90%). Group G1 (P.G.160–61 to P.G.102–3) includes ornamental, inedible pomegranate accessions such as P. granatum var. Nana seedlings (e.g., P.G.149–50 and P.G.167–68), as well as accessions from India, China and Iran (ICI; e.g., P.G.145–46, P.G.202–213, P.G.102–3; brown bar, Figure 6). The G2 group (P.G.129–30 to P.G.117–18) includes accessions from the Mediterranean region, Central Asia and California. This group includes domesticated pomegranate cultivars and is further divided into two main subgroups: subgroup G2.1 (P.G.129–30 to P.G.105–6; yellow bar, Figure 6) consists mostly of the “Wonderful-like” (WL) accessions and seems to be genetically and phenotypically uniform. Most of the WL accessions were collected in Israel and contain divergent landraces and mutants [40]; subgroup G2.2 (P.G.211–222 to P.G.214–225) includes accessions originated from the Mediterranean basin, Central Asia and California and was split into two further subgroups: G2.2.1 (P.G.221–222 to P.G.165–66) and G2.2.2 (P.G.218–229 to P.G.117–18), although this separation was statistically insignificant. Nevertheless, G2.2.1 includes accessions introduced from Spain [“Mollar” (M); green bar, Figure 6] and accessions introduced from Central Asia and California (CAC; orange bar, Figure 6), both of which are more homogeneous than the rest of the G.2 members. In contrast, G2.2.2 includes slightly more of an admixture of accessions. In this subgroup, the exception is a few accessions that are genetically homogeneous and have similar phenotypic characteristics. For example, the “Early Red Sweet” (ERS) accessions (P.G.234–245 to P.G.154–55), which are characterized by dark red color of the arils and peel, sweet taste and soft seeds, clustered together with high statistical confidence. A world view of the geographical location representing the suggested origin of each of the subgroups described in the dendrogram of germplasm accessions is presented in Figure 7. The groups' location on the world map illustrates that the two major groups in the dendrogram are separated by their origin.


Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.

Ophir R, Sherman A, Rubinstein M, Eshed R, Sharabi Schwager M, Harel-Beja R, Bar-Ya'akov I, Holland D - PLoS ONE (2014)

Worldwide distribution of the pomegranate genetic groups.The genetic groups as clustered together by the genetic dendrogram were located on a world map by geographical regions. Genetic groups and subgroups are colored as in Figure 6.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928336&req=5

pone-0088998-g007: Worldwide distribution of the pomegranate genetic groups.The genetic groups as clustered together by the genetic dendrogram were located on a world map by geographical regions. Genetic groups and subgroups are colored as in Figure 6.
Mentions: The classification tree (i.e., dendrogram) revealed two major groups of accessions (G1 and G2); G2 was further divided into two subgroups (G2.1 and G2.2). Strictly speaking, the dendrogram implied altogether three statistically significant groups (bootstrap value >90%). Group G1 (P.G.160–61 to P.G.102–3) includes ornamental, inedible pomegranate accessions such as P. granatum var. Nana seedlings (e.g., P.G.149–50 and P.G.167–68), as well as accessions from India, China and Iran (ICI; e.g., P.G.145–46, P.G.202–213, P.G.102–3; brown bar, Figure 6). The G2 group (P.G.129–30 to P.G.117–18) includes accessions from the Mediterranean region, Central Asia and California. This group includes domesticated pomegranate cultivars and is further divided into two main subgroups: subgroup G2.1 (P.G.129–30 to P.G.105–6; yellow bar, Figure 6) consists mostly of the “Wonderful-like” (WL) accessions and seems to be genetically and phenotypically uniform. Most of the WL accessions were collected in Israel and contain divergent landraces and mutants [40]; subgroup G2.2 (P.G.211–222 to P.G.214–225) includes accessions originated from the Mediterranean basin, Central Asia and California and was split into two further subgroups: G2.2.1 (P.G.221–222 to P.G.165–66) and G2.2.2 (P.G.218–229 to P.G.117–18), although this separation was statistically insignificant. Nevertheless, G2.2.1 includes accessions introduced from Spain [“Mollar” (M); green bar, Figure 6] and accessions introduced from Central Asia and California (CAC; orange bar, Figure 6), both of which are more homogeneous than the rest of the G.2 members. In contrast, G2.2.2 includes slightly more of an admixture of accessions. In this subgroup, the exception is a few accessions that are genetically homogeneous and have similar phenotypic characteristics. For example, the “Early Red Sweet” (ERS) accessions (P.G.234–245 to P.G.154–55), which are characterized by dark red color of the arils and peel, sweet taste and soft seeds, clustered together with high statistical confidence. A world view of the geographical location representing the suggested origin of each of the subgroups described in the dendrogram of germplasm accessions is presented in Figure 7. The groups' location on the world map illustrates that the two major groups in the dendrogram are separated by their origin.

Bottom Line: Pomegranate fruit has a variety of health-beneficial qualities.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.Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.

View Article: PubMed Central - PubMed

Affiliation: Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.

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.

Show MeSH
Related in: MedlinePlus