Abstract
Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.
Highlights
Ginger (Zingiber officinale Rosc.) is a widely used spice, flavoring agent, herbal medicine and is employed in the perfume industry
The present study describes the first global analysis of ginger and mango ginger - R. solanacearum challenge inoculated regimes, which would serve as a blueprint of gene expression profile
In order to achieve a broad survey of genes associated with bacterial wilt resistance, we performed mRNA-Seq profiling of C. amada and Z. officinale leaves, following infection with R. solanacearum and the resulting sequencing data were subjected to bioinformatic analysis
Summary
Ginger (Zingiber officinale Rosc.) is a widely used spice, flavoring agent, herbal medicine and is employed in the perfume industry. In spite of extensive search, no resistance source to Pythium soft rot, Fusarium yellows and Ralstonia induced bacterial wilt could be located in Zingiber genus. This is due to lack of genetic variability among the accessions for disease resistance, which is one of the bottlenecks in ginger genetic improvement. The search for resistance has been extended to other closely related genera in the family, Zingiberaceae such as Curcuma amada, C. longa, C. zedoaria, C. aromatica, Kaempferia galanga, Elettaria cardamomum, Zingiber zerumbet and Z. officinale for their reaction to R. solanacearum biovar 3 (ginger specific strain) and Pythium species. The high level of resistance recorded in C. amada to Ralstonia wilt is providing an opportunity for developing bacterial wilt resistance in ginger. Lack of genetic variability in ginger coupled with available resistance in a closely related genus makes the use of functional genomics an ideal choice to impart R. solanacearum resistance in ginger
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