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Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity
Year:
2014
Source of publication :
PLoS ONE
Authors :
Bar-Ya'akov, Irit
;
.
Eshed, Ravit
;
.
Harel-Beja, Rotem
;
.
Holland, Doron
;
.
Ophir, Ron
;
.
Rubinstein, Mor
;
.
Schwager, Michal Sharabi
;
.
Sherman, Amir
;
.
Volume :
9
Co-Authors:
Ophir, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Sherman, A., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Rubinstein, M., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Eshed, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Schwager, M.S., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Harel-Beja, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Bar-Ya'akov, I., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Holland, D., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Facilitators :
From page:
To page:
(
Total pages:
1
)
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. © 2014 Ophir et al.
Note:
Related Files :
gene frequency
genetic analysis
India
Iran
Models, Genetic
phenotype
phenotypic variation
simple sequence repeat
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Related Content
More details
DOI :
10.1371/journal.pone.0088998
Article number:
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
25407
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 00:14
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Scientific Publication
Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity
9
Ophir, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Sherman, A., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Rubinstein, M., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Eshed, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Schwager, M.S., Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
Harel-Beja, R., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Bar-Ya'akov, I., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Holland, D., Department of Fruit Tree Sciences, Agricultural Research Organization, Newe Ya'ar Center, Ramat Yishai, Israel
Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity
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. © 2014 Ophir et al.
Scientific Publication
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