期刊论文详细信息
BMC Genomics
Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.)
Amir Sherman4  Haim D Rabinowitch3  Dani Eshel2  Sarit Rohkin Shalom2  Itzhak Esquira1  Sagie Kimhi4  Chen Gershberg4  Tomer Ben Michael3  Einat Shemesh Mayer3  Adi Faigenboim4  Rina Kamenetsky4 
[1] Classeed Ltd., Gibraltar, British;Institute of Postharvest and The Food Sciences, ARO, The Volcani Center, Bet Dagan, Israel;Robert H. Smith Faculty of Agricultural, Food, and Environmental Quality Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel;Institute of Plant Sciences, ARO, The Volcani Center, Bet Dagan, Israel
关键词: Garlic virus;    Sulfur metabolism;    Breeding;    Flowering;    Assembly;   
Others  :  1109872
DOI  :  10.1186/s12864-015-1212-2
 received in 2014-06-24, accepted in 2014-12-31,  发布年份 2015
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【 摘 要 】

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.

【 授权许可】

   
2015 Kamenetsky et al.; licensee Biomed Central.

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