Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways

Abstract

BackgroundIsoflavonoids are a class of specialized metabolites found predominantly in legumes. They play a role in signaling for symbiosis with nitrogen-fixing bacteria and inhibiting pathogen infection.ResultsA transcriptomic approach using soybean cultivars with high (Conrad and AC Colombe) and low (AC Glengarry and Pagoda) root isoflavonoid content was used to find elements that underlie this variation. Two genes, encoding the flavonoid-metabolizing enzymes, flavonoid 3′-hydroxylase (GmF3′H) and dihydroflavonol 4-reductase (GmDFR), had lower expression levels in high isoflavonoid cultivars. These enzymes compete with isoflavonoid biosynthetic enzymes for the important branch-point substrate naringenin and its derivatives. Differentially expressed genes, between the two sets of cultivars, encode transcription factors, transporters and enzymatic families of interest, such as oxidoreductases, hydrolases and transferases. In addition, genes annotated with stress and disease response were upregulated in high isoflavonoid cultivars.ConclusionsCoordinated regulation of genes involved in flavonoid metabolism could redirect flux into the isoflavonoid branch of the phenylpropanoid pathway, by reducing competition for the flavanone substrate. These candidate genes could help identify mechanisms to overcome the endogenous bottleneck to isoflavonoid production, facilitate biosynthesis in heterologous systems, and enhance crop resistance against pathogenic infections.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3463-y) contains supplementary material, which is available to authorized users.

Transcriptomics, Targeted Metabolomics and Gene Expression of Blackberry Leaves and Fruits Indicate Flavonoid Metabolic Flux from Leaf to Red Fruit

“…The overexpression of the isoform RuPAL1 over the RuPAL2 in fruits (Figure 8) is consistent with the complex role of this enzyme in directing the carbon flux to the flavonol pathway in key points of fruit ripening (Garcia-Seco et al, 2015; Dastmalchi et al, 2017) and further supports the initial activation of the flavonol synthesis in fruits, together with the presence of cholrogenic acid identified therein (Table 4). Interestingly, the almost two-fold expression of RuDFR and RuLAR in fruits suggests that accumulation of catechins (Table 3) is taking place in fruits, as these compounds are usually accumulated in seeds (Zhang et al, 2014) and is supported by the presence of catechins only in fruits (Tables 4, 5), probably synthetized from the quercetins originated in leaves.…”

“…Many studies have addressed flavonoid synthesis, identification and subcellular accumulation mechanisms in different plant species as in grapevine (Perez-Diaz et al, 2016), soybean (Dastmalchi et al, 2017), banana (Dong et al, 2016) among others (Zhao, 2015) resulting in characterization of many specific transporters in different organs and accurate flavonoid profiles. Long distance transport has been demonstrated in A. thaliana (Buer et al, 2007) And the possibility of long distance flavonoid translocation in grapevine has been suggested, based on the presence of a specific transporter on the vascular bundles, which expression increases from veraison to harvest (Petrussa et al, 2013).…”

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population

“…To gain further insight into the expression of genes underlying root trait QTLs we used the publicly available differential gene expression data of Williams 82, a parental line used in developing this inter-specific mapping population. Gene expressions across diverse soybean genetic backgrounds were obtained from Array express ( ) and RNA-sequencing datasets ( Ithal et al, 2007 ; Libault et al, 2010 ; Gong et al, 2014 ; Kour et al, 2014 ; Leisner et al, 2014 ; Lin et al, 2014 ; Shen et al, 2014 ; Valdés-López et al, 2014 ; Wu et al, 2014 ; Zabala and Vodkin, 2014 ; Aghamirzaie et al, 2015 ; Brown and Hudson, 2015 ; Devi et al, 2015 ; Huang and Schiefelbein, 2015 ; Jones et al, 2015 ; Lambirth et al, 2015 ; Lanubile et al, 2015 ; Okamoto et al, 2015 ; Shin et al, 2015 ; Whaley et al, 2015 ; Bellieny-Rabelo et al, 2016 ; Song et al, 2016 ; Cho et al, 2017 ; Dastmalchi et al, 2017 ; Huang et al, 2017 ; Waters et al, 2018 ; Adhikari et al, 2019 ; Li et al, 2019 ; Liu et al, 2019 ; Neupane et al, 2019 ; Wang et al, 2019 ) integrated into Genevestigator database, ( Zimmermann et al, 2014 ). The transcriptome data of the wild soybean parental line, PI 483460B used in this study is not available.…”

Effects of Phosphate-Solubilizing Bacteria and N2-fixing Bacteria on Nutrient Uptake, Plant Growth, and Bioactive Compound Accumulation in Cyclocarya paliurus (Batal.) Iljinskaja

“…However, we found only the concentration of isoquercetin was significantly correlated with N uptake, while other monomers indicated no significance (Table S1). Hence, different PGPR, such as PSB and NFB, may indirectly influence the biosynthesis of flavonoids through manipulating other factors, such as gene expression [41], enzyme activity [35,47], or phytohormone [48]. For all flavonoid monomers, they possess the common biosynthetic pathway with little difference.…”