Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2009
Publication Date: 11/20/2009
Publication URL: hdl.handle.net/10113/49205
Citation: Libault, M., Farmer, A., Brechenmacher, L., Franck, W.L., Drnevich, J., Langley, R.J., Bilgin, D.D., Radwan, O., Neece, D.J., Clough, S.J., May, G., Stacey, G. 2009. Complete Transcriptome of the Soybean Root Hair Cell, a Single Cell Model, and its Alteration in Response to Bradyrhizobium japonicum Infection. Plant Physiology. 152: 541-552. Interpretive Summary: Nitrogen is a limiting factor in the growth of many plants. The ability of legumes like soybean to establish a symbiotic relationship with rhizobia bacteria to fix atmospheric nitrogen to usable ammonia means that nitrogen is not a limiting factor for these plants. The establishment of this nitrogen fixation is complex, not fully understood, and involves specific regulation of hundreds of genes. Knowing the identity of these genes and their expression behavior, will help plant scientists ensure healthy legume plants, plus it increases the possibiltiy of one day establishing nitrogen fixation in non-legumes and potentially eliminating agriculture's need for petrolium-based nitrogen amendments. In this study, we utilized genomic technologies to identify over 1900 soybean genes as being candidates as genes needed to establish the initial interaction between the nitrogen-fixing bacteria and the root hair cells that they infect. The results will be of interest to plant biotechnologists, biologists, and breeders.
Technical Abstract: Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean and Bradyrhizobium japonicum). Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity of the symbiosis, a significantly larger number of genes are likely involved. To identify genes involved in root hair cell infection, we performed a large scale transcriptomic analysis of B. japonicum inoculated and mock-inoculated soybean using 3 different technologies: microarray hybridization, Illumina-Solexa ultra-high-throughput sequencing and quantitative RT-PCR. Together, these analyses establish a complete transcriptomic map of the soybean root hair cell and its response to B. japonicum infection. A total of 1973 soybean genes were differentially expressed with high significance during root hair infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN. The regulation of 60 genes was confirmed by qRT-PCR. Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes supporting their rapid specialization. Finally, we identified a large number of polyadenylated B. japonicum transcripts, a modification described in bacteria as a signal for mRNA degradation.