RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2

Abstract

Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages.

Drought‐induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels

“…It was also reported in M. truncatula and Glycine max that nodules affected by drought stress succumb to early senescence and as such influence nutrient remobilisation (Van de Velde et al ., ; Ladrera et al ., ). Thus, senescence of protein‐rich nodules may extend the useful lifespan of nodules during times where reduced water and carbon supply (Atkins et al ., ; Marquez‐Garcia et al ., ; Yuan et al ., ) limit the nodules’ ability to fix gaseous nitrogen.…”

Nodule‐specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation

“…Cystatins are thought to regulate proteolysis during nodule senescence by balancing protein turnover processes (van Wyk et al, 2014). Cysteine protease silencing in Astragalus sinicus (Li et al, 2008) and cystatin overexpression in Lotus japonicus (Yuan et al, 2017) hairy roots inhibited nodule senescence and produced better aboveground growth. These studies suggest that an increased number of nodule-specific cystatin genes in the Arachis lineage could confer a positive effect on nodulation.…”

Transcriptomic analysis with the progress of symbiosis in ‘crack-entry’ legumeArachis hypogaeahighlights its contrast with ‘infection thread’ adapted legumes

“…This analysis shows that within 1dpi-4dpi the number of downregulated DEGs were ~18-fold higher than the number of upregulated DEGs whereas in other stages the difference was ~3-5fold. Previous reports on symbiosis associated transcriptome of other legumes also indicated the prevalence of higher number of downregulated transcripts (Boscari et al, 2012;Yuan et al, 2017b). But the significantly high number of downregulated transcripts in early stages of nodule inception could be a unique feature for A.…”

“…Transcriptome analyses during symbiosis in several legumes like M. truncatula, L. japonicus, Glycine max and Cicer arietinum provided molecular insights into symbiosis that uses the 'root hair' mode entry (Takanashi et al, 2012;Limpens et al, 2014;Parida et al, 2016;Yuan et al, 2017a). These resources have been useful in determining gene expression associated with different stages of RNS, for example symbiont recognition, onset of infection, meristem activity for nodule organogenesis and functional differentiation of infected cells (Breakspear et al, 2014;Roux et al, 2014).…”