Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules

Abstract

Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, only fragmentary information is available in regard to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis in soybean nodules grown under P-sufficient (500 μM KH2PO4) and P-deficient (25 μM KH2PO4) conditions to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of (differentially expressed genes) DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including eight Pi transporters (PTs), eight genes coding proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway, are involved in maintaining Pi homeostasis in nodules.

Transcriptomic Analysis Reveals the Molecular Adaptation of Three Major Secondary Metabolic Pathways to Multiple Macronutrient Starvation in Tea (Camellia sinensis)

“…Function enrichment of DEG using GO and KEGG analysis showed the majority of DEGs were common to all nutrient deprivation conditions, indicating the close connection among nutrient starvation induced responses. GO term analysis displayed that DEGs under N starvation stress were mainly overrepresented in metabolic process, biological regulation, cell part, catalytic activity, binding, and transporter activity categories, which were also observed in P and K deficiency treatment, and similar results have been described previously for Arabidopsis and rice [39][40][41]. KEGG enrichment further detected many common changed pathways when treated with N, P, and K starvation, including phenylpropanoid biosynthesis, starch and sucrose metabolism, sugar metabolism, and plant hormone signal transduction pathways, suggesting that these pathways are crucial as mediators of responses to N, P, and K starvation in tea, supporting the idea that these pathways are relatively conserved in plants [40,42,43].…”

GmPAP12 Is Required for Nodule Development and Nitrogen Fixation Under Phosphorus Starvation in Soybean

“…In soybean, in low P stress growing in hydroponic conditions, P content in both leaves and roots are 10 times higher in high P than in low P treatment, whereas in nodules, only 1.75 times are increased (Sulieman et al, 2010;Qin et al, 2012). In this study, with regard to P content, it was much less affected in nodules than in shoot and root in P deficiency, suggesting that nodules represent a P sink to maintain Pi homeostasis and the ability of N 2 fixation during nodule development; it is hypothesized that nodules try to regulate N 2 fixation process to adaptation to low P stress by allocating P from other organs to nodules (Cabeza et al, 2014;Xue et al, 2018).…”

“…Additionally, the secretion of PAPs in plants is a widely known as an adaptation strategy in response to P deficiency. Under low P conditions, in nodules of M. truncatula, chickpea, and soybean, they were found to be differentially upregulated by RNA-seq transcriptome analysis, which indicates that nodules acclimated to P deficiency by increasing P turnover (Cabeza et al, 2014;Nasr Esfahani et al, 2017;Xue et al, 2018).…”

“…These strategies include alteration of root morphology and architecture, increased activity of high affinity of Pi transporters and acid phosphatases (APases), and accumulation of anthocyanins (Franco-Zorrilla et al, 2004;Jain et al, 2012;Liang et al, 2014). At the molecular level, in order to elucidate the mechanism of plant response to P deficiency, several transcription factors were identified, including MYB, bHLH, GRAS, ERF, and WRKY families (Zhang et al, 2016;Diedhiou and Diouf, 2018;Xue et al, 2018). MYB is one of the largest transcription factor families in the plant kingdom, among which PHR1 (phosphate starvation response regulator (1) functions as a central regular in P starvation signaling, first identified in Arabidopsis thaliana.…”

Response of Soybean Root to Phosphorus Deficiency under Sucrose Feeding: Insight from Morphological and Metabolome Characterizations

“…Once the soybean seedlings reached VE stage, the distilled water was replaced with a nutrient solution containing 4. 24 , and 9 μmol•L -1 Fe-EDTA. Two Suc levels were maintained, i.e., 0% Suc (-S) and 1% Suc (+S, 0.0292 mM (with purity > 99:9%)).…”