Transcriptomic Characterization of Soybean Roots in Response toBradyrhizobiumInfection by RNA Sequencing

Abstract

Legumes interact with rhizobium convert N 2 into ammonia for plant use. To investigate the plant basal nitrogen fixation mechanisms induced in response to Bradyrhizobium, differential gene expression in root of inoculated and mock-inoculated soybean was analysed by RNA-Seq. A total of 55787 transcripts were aligned to soybean genome reference sequences, 280 and 316 transcripts were found to be up-and down-regulated, respectively, in inoculated relative to mock-inoculated soybean's root at V1 stage. Gene ontology (GO) analyses detected 104, 182 and 178 genes associated with cell component category, molecular function category and biological process category, respectively. Pathway analysis revealed that 98 differentiallly expressed genes (115 transcripts) involved in 169 biological pathways. We selected 19 differentially expressed genes and analyzed their expressions in mock-inoculated, inoculated USDA110 and CCBAU45436 using qRT-PCR. The results were consistent with those obtained from rhizobia infected RNA-Seq data. These showed that the results of RNA-Seq have reliability and universality. Additionally, this study showed some novel genes associated with nitrogen fixation process comparison with the previously identified QTLs.KEYWORDS Symbiotic nitrogen fixation; Soybean; Transcriptomic; RNA-Seq analysis; Rhizobium . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/024224 doi: bioRxiv preprint first posted online Aug. 19, 2015; Nitrogen is the most limiting element for crop growth and usually supplied by application of fertilizer, which brings on substantial costs to farmers and with potentially adverse effects on the environment. The leguminous plants establish a symbiotic relationship with rhizobia (symbiotic nitrogen fixation, SNF) to directly capture N 2 to support plant growth. Nitrogen conversion takes place in a unique organ (root nodule). The development of root nodules commences with a molecular dialogue between the host plant and a compatible strain of rhizobium, involving a succession of complex process that lead to profound changes in both symbionts (Oldroyd et al., 2011).The plant excretes molecular signals, flavonoids, phenolic compounds which induce the synthesis of specific rhizobia-produced lipo-chito-oligosaccharides, called Nod factors (NFs). NFs directly stimulate their putative receptor protein (NFRs), such as LjNFR1/5 (Nod factor through receptor-like kinase) in Lotus japonicus and MtLYK3 (LysM-receptor like kinas 3)/ NFP (Nod factor perception) in Medicago Trucatula (Arrighi et al., 2006; Limpens et al., 2003;Madsen et al., 2003;Radutoiu et al., 2003), which are LysM (peptidoglycanbinding lysine motif) receptor-like of the legumes (Kochi et al., 2010; Subramanian et al., 2006). Many molecular events are triggered in a coordinate manner, leading to morphological and physiological changes in the host plant, necessary for a successful symbiosis (...