Integrated Transcriptomic and Metabolomic Profiling Reveals the Involvement of the miR397-5p–SbLAC14 Module in Condensed Tannin Accumulation in Developing Sorghum Seeds
Results provide a genetic entry point for metabolic engineering and breeding efforts aimed at modulating grain phenolic profiles and indicate that SbmiR397-5p negatively regulates the expression of SbLAC14 in relation to CT biosynthesis, identifying it as a potential target for manipulating CT metabolism in sorghum.
Abstract
Sorghum seeds accumulate substantial amounts of condensed tannins (CTs), which are also referred to as proanthocyanidins (PAs), contributing to their characteristic astringent taste. Flavan-3-ol polymers, known as PAs, are sequestered within plant vacuoles and become catalytically activated via laccase enzymes. However, the biological roles and regulatory pathways of laccases in sorghum are still largely unclear. Here, integrated transcriptomic and metabolomic profiling of developing sorghum seeds identified 7942 differentially expressed genes between low- and high-CT lines, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealing flavonoid biosynthesis as a key pathway; weighted gene co-expression network analysis (WGCNA) further pinpointed SbLAC14 as a hub gene within the module most strongly correlated with CT content. We then examined its regulation by microRNA397 (SbmiR397-5p). Dual-luciferase assays confirmed the binding of SbmiR397-5p to SbLAC14 in co-transformed tobacco leaves. Overexpressing SbLAC14 in transgenic Arabidopsis significantly increased CT accumulation while decreasing catechin and epicatechin levels. Furthermore, transgenic plants overexpressing miR397 (OEmiR397-5p) exhibited reduced CT content, accompanied by a lightening of seed color. Conversely, transgenic lines overexpressing a miR397-insensitive laccase transcript exhibited a reversed phenotypic outcome. Our findings indicate that SbmiR397-5p negatively regulates the expression of SbLAC14 in relation to CT biosynthesis, identifying it as a potential target for manipulating CT metabolism in sorghum. Those results provide a genetic entry point for metabolic engineering and breeding efforts aimed at modulating grain phenolic profiles.
BACKGROUND
C-glycosyl flavones rarely accumulate at high levels in rice seeds, and the genetic basis underlying their biosynthesis and regulation remains poorly understood. The rice yel-sdj mutant, carrying a mutation in DE-ETIOLATED 1 (OsDET1), shows elevated accumulation of C-glycosyl flavones in the embryo and pericarp, providing a useful system for dissecting the molecular mechanisms controlling these metabolites. Here, we performed comparative transcriptomic and metabolomic analyses, together with genome-editing-based functional validation, to identify key genes involved in C-glycosyl flavone biosynthesis in rice seeds.
RESULTS
Transcriptomic profiling of developing seeds revealed that differentially expressed genes (DEGs) between wild-type and yel-sdj were significantly enriched in secondary metabolite and flavonoid biosynthetic pathways. Several genes associated with C-glycosyl flavone biosynthesis, including the rice C-glycosyltransferase (OsCGT), were upregulated in developing yel-sdj grains. To validate its function, we generated OsCGT knockout lines in the yel-sdj background. Loss of OsCGT markedly reduced the accumulation of C-glycosyl flavones, particularly isoorientin, in the embryo and restored embryo coloration to a wild-type-like phenotype. In contrast, despite the significant reduction in C-glycosyl flavone accumulation, pericarp pigmentation was not obviously altered, and embryo lethality was not rescued.
CONCLUSIONS
These findings demonstrate that OsCGT is essential for C-glycosyl flavone biosynthesis in yel-sdj seeds, particularly for isoorientin accumulation in the embryo, and indicate that embryo lethality is a fundamental consequence of the OsDET1 mutation rather than OsCGT-dependent flavone accumulation. This study expands current understanding of flavonoid regulation in rice seeds and identifies OsCGT as a potential target for metabolic engineering to improve the nutraceutical and functional value of rice grains.
Backki Kim, Hee-Jin Choi, Sangrae Shim et al.· BMC Plant Biology· 0 citations
: Mint is notably rich in phenolic acids, flavonoids, antioxidants and other bioactive components, and is widely used as food, medicine, spices, and flavoring agents. Thus, metabolite composition serves as a critical indicator for assessing mint quality. In this study, two mint genotypes of Mentha canadensis L., were sampled, namely purple mint and green mint. The two genotypes are distinguished by stem color: the purple mint exhibits purple stems, whereas the green mint has green stems. The purple mint exhibited significantly higher anthocyanin and total flavone contents than green mint. Integrated transcriptomic and metabolomic analyses were performed to elucidate the regulatory mechanisms underlying pigment and flavonoid accumulation in mint stems. High-throughput RNA-Seq yielded 167,901 unigenes, of which 34,608 genes were differentially expressed. These differentially expressed genes (DEGs) were mainly involved in the lignin metabolic process and flavonoid biosynthetic process. A total of 143 differentially expressed metabolites (DEMs) were enriched in isoflavonoid, flavonoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesis pathways. Co-analysis of DEGs and DEMs revealed that the flavone and flavonol biosynthesis pathway (ko00944) contained the most DEMs, followed by the flavonoid biosynthesis pathway (ko00941) and the anthocyanin biosynthesis pathway (ko00942). Furthermore, nine key genes and metabolites were identified using the O2PLS model. These findings provide a theoretical basis for understanding the key pathways and genes involved in pigment and flavonoid regulation in mint stems.
Xiang-Dong Wang, Hai-Long An, Yan-Zhi Ma et al.· Phyton· 0 citations
The seeds of Polygonatum sibiricum exhibit dormancy, which poses a major challenge for its cultivation. To elucidate the regulatory mechanisms underlying dormancy release, we performed integrated transcriptomic and metabolomic analyses on seeds at 0, 5, 10, and 15 d after seed imbibition. Physiological assays revealed progressive declines in abscisic acid (ABA) and starch levels, alongside increases in gibberellin (GA) and soluble sugar contents, reflecting the metabolic changes accompanying the transition from dormancy to germination. Transcriptomic analysis identified 11,520 expressed genes, with 6753, 7775 and 9387 differentially expressed genes (DEGs) at T5, T10, and T15, respectively. KEGG enrichment highlighted starch and sucrose metabolism and plant hormone signal transduction as key pathways. Notably, the GA biosynthesis gene GA3ox was markedly upregulated, while the DELLA repressor (Isoform0012761) showed sustained downregulation, suggesting relieved GA signaling. In the ABA pathway, CYP707A catabolic genes exhibited biphasic expression, and ABA signaling components (PYL, PP2C, SnRK2) showed stage-specific remodeling. A total of 316, 412, and 479 differentially expressed transcription factors were identified across stages, with the GRAS family being the largest. Co-expression network analysis revealed 19 transcription factors integrating starch/sucrose metabolism with ABA and GA signaling, most of which were downregulated, except one C2H2 member showing sustained upregulation. These findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant.
Xiaoyu Su, Chunming Li, Lei Li et al.· International Journal of Mol...· 0 citations
This study investigated the regulatory effects of sowing date on seed quality formation in the brewing sorghum cultivar Hongyingzi using integrated transcriptomic and metabolomic approaches. Three sowing dates (early, normal, and late) were applied, and seeds were collected at 19, 26, and 33 days after pollination. Sowing date interacted with seed development to significantly affect morphological characteristics, pericarp structure, and metabolite accumulation. Transcriptomic analysis identified 3651 shared differentially expressed genes (DEGs) mainly enriched in photosynthesis, starch and sucrose metabolism, and flavonoid biosynthesis. Metabolomic profiling detected 1105 differentially expressed metabolites (DEMs), which were involved in flavonoid and starch–sucrose metabolism. Integrated analysis confirmed these two pathways as key responses to sowing date. Weighted gene co-expression network analysis (WGCNA) identified 17 hub genes, five of which were upregulated and contained light-responsive elements. These findings reveal the molecular mechanism underlying sowing date-mediated seed quality formation and provide a theoretical basis for high-quality sorghum production.
These findings collectively support flavanone 3-hydroxylase (F3H) as a candidate regulatory node governing organ-specific flavonoid partitioning in Rhododendron yedoense var.
R. Fei, Si-Yu Duan, Xiu-Ting Zhao et al.· Plants· 0 citations
Magnoliae Flos (MF)
, the dried flower buds of
Magnolia denudata
Desr.,
Magnolia biondii
Pamp., and
Magnolia sprengeri
Pamp., is a crucial East Asian medicinal herb used to treat allergic rhinitis and other ailments. However, the molecular basis for its quality differences remains unclear.
This study integrates GC-MS-based volatile metabolomics, high-throughput RNA sequencing, and RT-qPCR validation to elucidate the terpenoid metabolic differences and their regulatory mechanisms among the three
MF
varieties.
The metabolomic analysis screened 55 differential terpenoids (15 key markers) that distinguish the
MF
varieties, with terpenoids being the primary metabolic category and the
M. sprengeri
vs.
M. biondii
group exhibiting the most differential metabolites. The transcriptomic analysis revealed
TPS26
as key candidate genes involved in monoterpene synthesis, while IMPMBI2G0000034954 and IMPMBI2G0000034957 were identified as candidate genes for sesquiterpene synthesis. The expression abundances of these genes exhibited significant linear correlations with the accumulation levels of differential terpenoids, though such coordinated variation does not confirm direct causal regulation.
Collectively, this work reveals the molecular basis of terpenoid diversity in
MF
, and provides theoretical references for germplasm discrimination, quality evaluation and genetic improvement of medicinal magnolia resources.
Rui Ma, Hong-Dan Liu, Weimeng Feng et al.· Frontiers in Plant Science· 0 citations