Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicumstrain CPAC 15

Abstract

BackgroundBiological nitrogen fixation in root nodules is a process of great importance to crops of soybean [Glycine max (L.) Merr.], as it may provide the bulk of the plant’s needs for nitrogen. Legume nodulation involves several complex steps and, although studied for many decades, much remains to be understood.ResultsThis research aimed at analyzing the global expression of genes in soybean roots of a Brazilian cultivar (Conquista) inoculated with Bradyrhizobium japonicum CPAC 15, a strain broadly used in commercial inoculants in Brazil. To achieve this, we used the suppressive subtractive hybridization (SSH) technique combined with Illumina sequencing. The subtractive library (non-inoculated x inoculated) of soybean roots resulted in 3,210 differentially expressed transcripts at 10 days after inoculation were studied. The data were grouped according to the ontologies of the molecular functions and biological processes. Several classes of genes were confirmed as related to N2 fixation and others were reported for the first time.ConclusionsDuring nodule formation, a higher percentage of genes were related to primary metabolism, cell-wall modifications and the antioxidant defense system. Putative symbiotic functions were attributed to some of these genes for the first time.

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

“…For instance, the combination of SuperSAGE with NGS has already been applied to study the molecular aspects of resistance to ascochyta blight in several legumes Fondevilla et al, 2014a;García et al, 2013;Madrid et al, 2013). The combination of SSH with NGS has also started to be applied in soybean to study the genes involved during the symbiotic interaction (Barros de Carvalho et al, 2013) and in response to drought (Rodrigues et al, 2012;Oliveira-Vidal et al, 2012) to study disease and pest resistance. In addition, RNAseq technique that involves the sequencing of all transcripts expressed in a given situation is not only a powerful tool to develop de novo transcriptomes but also to compare the whole transcriptome expression profiling in two different situations.…”

Prediction of potential novel microRNAs in soybean when in symbiosis

“…In this study, we performed a computational prediction initially using transcripts expressed in the soybean roots inoculated with B. japonicum (Barros de Carvalho et al, 2013). Among the sequences of pre-miRNAs revealed by the ncRNA annotation pipeline (Table 1), we can see that the candidates gma-MIR-Cand04, gma-MIR-Cand05, and gma-MIR-Cand12 aligned with the precursor MIR1530, whereas gma-MIR-Cand10 aligned with MIR1520, and gma-MIR-Cand15 aligned with MIR1522.…”

“…This subtractive library has been integrated into the GENOSOJA project [see Barros de Carvalho et al (2013) for more details].…”

“…Computational strategies have proven to be successful, highly effective, and important in identifying new miRNAs, as shown by the studies of Qiu et al (2007), Xie et al (2007), and Lu and Yang (2010), among others, where new miRNAs and target genes were identified by in silico analysis based on expressed sequence tags of Gossypium hirsutum, Brassica napus, and Vigna unguiculata, respectively. Our study performed an in silico analysis of miRNAs and their target genes present in a subtractive library of soybean roots inoculated with the Bradyrhizobium japonicum strain CPAC 15 obtained in a previous study (Barros de Carvalho et al, 2013). We aimed to identify new miRNAs that could be involved in regulation of nodulation in the early developmental stages of soybean roots.…”

Molecular genetic and biochemical analysis of gibberellic acid involvement in the stages of soybean (Glycine max L.) nodule development

“…Three separate studies have reported using RNA-seq to identify differentially-expressed genes in the transcriptome of rhizobia-inoculated soybean roots (Libault et al, 2010a;Hayashi et al, 2012;Barros de Carvalho et al, 2013). The genes identified represent candidates required for nodule development.…”