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פותח על ידי קלירמאש פתרונות בע"מ -
Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
Year:
2015
Source of publication :
BMC Genomics
Authors :
אשל, דני
;
.
בן מיכאל, תומר
;
.
גרשברג, חן
;
.
דורון-פייגנבאום, עדי
;
.
קמחי, שגיא
;
.
קמנצקי, רינה
;
.
רוחקין שלום, שרית
;
.
שמש, עינת
;
.
שרמן, עמיר
;
.
Volume :
16
Co-Authors:
Kamenetsky, R., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Faigenboim, A., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Shemesh Mayer, E., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Ben Michael, T., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Gershberg, C., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Kimhi, S., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Esquira, I., Classeed Ltd., Gibraltar
Rohkin Shalom, S., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Eshel, D., Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Rabinowitch, H.D., The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Sherman, A., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Facilitators :
From page:
0
To page:
0
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Total pages:
1
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Abstract:
Background: Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic. Results: A transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1-4% of the reads were found in the foliage leaves. Conclusions: The de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics. © 2015 Kamenetsky et al.
Note:
Related Files :
Allium sativum
bioinformatics
breeding
enzymes
flowering
Genetics
metabolism
photosynthesis
Plant Breeding
seeds
עוד תגיות
תוכן קשור
More details
DOI :
10.1186/s12864-015-1212-2
Article number:
12
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
21351
Last updated date:
02/03/2022 17:27
Creation date:
16/04/2018 23:43
You may also be interested in
Scientific Publication
Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
16
Kamenetsky, R., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Faigenboim, A., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Shemesh Mayer, E., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Ben Michael, T., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Gershberg, C., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Kimhi, S., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Esquira, I., Classeed Ltd., Gibraltar
Rohkin Shalom, S., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel, Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Eshel, D., Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Rabinowitch, H.D., The Hebrew University of Jerusalem, Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, Jerusalem, Israel
Sherman, A., Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
Background: Garlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic. Results: A transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1-4% of the reads were found in the foliage leaves. Conclusions: The de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics. © 2015 Kamenetsky et al.
Scientific Publication
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