Aug 2026· Plant Biotechnology Journal· 0 citations· 51 references
Medicine
TL;DR
Findings reveal that FA9 interacts with VAP to promote lipid droplet biogenesis and lipid transport, thereby driving fatty acid accumulation in soybean seeds.
Abstract
ABSTRACT As a major commercial legume crop, soybean ranks among the world's most significant sources of edible oil and plant protein. We previously identified a SEIPIN homologue (FA9) at the fatty acid 9 locus that promotes fatty acid accumulation in soybean. To examine the detailed molecular mechanisms by which FA9 regulates lipid metabolism, we performed single‐cell RNA sequencing (scRNA‐seq) and spatial transcriptomics (stRNA‐seq) of wild‐type and FA9‐knockout soybean seeds at the late maturity stage. scRNA‐seq analysis identified 26 transcriptional clusters and revealed the spatial distribution of FA9 in seeds, in which the deletion of FA9 altered lipid and storage‐related transcriptional programmes. On the basis of single‐cell sequencing and immunoprecipitation–mass spectrometry (IP–MS), the vesicle‐associated membrane protein (VAMP)‐associated protein (VAP) was identified, and subsequent experiments demonstrated that FA9 interacts specifically with VAP via its N‐terminal FFAT motif at the endoplasmic reticulum. Seeds of vap knockout (vap‐KO1 and vap‐KO2) and fa9 vap double knockout (fa9 vap‐KO) lines, created by CRISPR–Cas9 gene editing, had higher protein contents and lower total fatty acid contents than wild‐type soybean, whereas overexpression of FA9 and VAP enhanced lipid droplet formation in Nicotiana benthamiana. These findings reveal that FA9 interacts with VAP to promote lipid droplet biogenesis and lipid transport, thereby driving fatty acid accumulation in soybean seeds. This research provides new insight into the molecular mechanisms that regulate seed oil synthesis and identifies potential target genes for improvement of soybean oil quality through molecular breeding.
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.
Yannan Shi, Yongchao Guo, Jinping Wang et al.· Plants· 0 citations
Abstract Plant seeds accumulate triacylglycerol (TAG) as a major storage reserve that supports postgermination growth and seedling establishment. Vegetable oils are also essential for human nutrition and provide renewable feedstocks for industrial and biotechnological applications. In 1998, Focks and Benning published a landmark study in Plant Physiology describing the Arabidopsis WRINKLED1 mutants (wri1), which display a distinctive wrinkled seed phenotype and a dramatic reduction in seed oil accumulation. The conceptual importance of this discovery was not simply the identification of a low-oil mutant, but the demonstration that seed oil accumulation depends on developmental control of carbon flux from carbohydrates into fatty acid precursors. Cloning of the Arabidopsis WRI1 (AtWRI1) gene in 2004 transformed this physiological phenotype into a molecular framework by identifying WRI1 as a member of the APETALA2 (AP2) family of transcription factors that activates late glycolytic and fatty acid biosynthetic genes. Subsequent work uncovered the AW-box cis-element, upstream seed-maturation regulators, WRI1-interacting partners, post-transcriptional and post-translational modification mechanisms controlling WRI1 stability and activity, and the structural basis of WRI1-DNA recognition. These discoveries established WRI1 as a central regulatory node linking seed development, carbohydrate metabolism, and seed oil accumulation. More recent studies have broadened WRI1 biology beyond canonical seed oil biosynthesis to include non-seed oil-storing tissues, hormone and nutrient-associated processes, environmental responses, and structure-guided crop engineering. Here, we revisit the original Plant Physiology classic and trace how one mutant phenotype reshaped modern understanding of plant carbon partitioning, transcriptional regulation, and metabolic engineering
Que Kong, Sitakanta Pattanaik, Fantao Kong et al.· Plant Physiology· 0 citations
BACKGROUND
Soybean is a crucial global source of protein and oil. The CBP/p300 histone acetyltransferases (HACs) are key transcriptional regulators, yet their diversity and functions in soybean remain unexplored at a pan-genomic level.
RESULTS
Here, we constructed a pan-genomic resource for the HAC gene family across 29 wild, landrace, and cultivated soybean accessions, identifying 142 HAC genes. These genes are confined to chromosomes 7, 8, 15, and 19, indicating strong evolutionary constraints. Phylogenetic analysis divided HACs into five subgroups with distinct domain architectures: Group 4-5 retain full CBP/p300 domains, whereas Group 1-3 show progressive domain loss. Pan-transcriptomic analyses revealed an expression dichotomy: Group 3-5 are broadly expressed, while Group 1-2 exhibit endosperm-specific expression during early seed development, suggesting specialized roles in nutrient transfer and embryogenesis. Notably, elite cultivars (e.g., Wm82, ZH13) have lost Group 2 homologs preserved in wild soybeans, highlighting domestication-driven erosion of epigenetic diversity. Co-expression network analysis prioritized Wm82-HAC1 (Group 1) as a candidate gene coordinating nutrient metabolism and seed maturation pathways.
CONCLUSION
Our study provides the first comprehensive panorama of epigenetic regulators in the soybean pan-genome. Our findings reveal how subfunctionalization and domestication help shape the HAC regulatory network in soybean, highlighting wild germplasm as a valuable reservoir for recovering lost alleles (Group2 homologs) and identifying Wm82-HAC1 (Group 1) as a prime target for precision breeding of seed traits.
Chaojun Wang, Dan Huang, Zhicheng Dong et al.· BMC Plant Biology· 0 citations
Nitrogen is the most yield‐limiting macronutrient in wheat (
Triticum aestivum
L.), yet no prior review has integrated nitrogen deficiency symptomology, physiology, and multi‐omics approaches encompassing transcriptomics, proteomics, metabolomics, and epigenomics into a single mechanistic framework for wheat specifically. Wheat's hexaploid genome, distinctive nitrogen remobilisation architecture, and unique grain protein composition generate responses that cannot be extrapolated from diploid cereals. Two stress modes must be distinguished: acute nitrogen withdrawal induces rapid NLP7‐mediated
NRT2
transporter activation within minutes, whereas chronic low‐nitrogen supply drives sustained epigenetic and root architectural adaptations over weeks. Post‐translational modifications, including NRT2 phosphorylation and thioredoxin‐regulated starch biosynthetic enzyme activity, govern nitrogen remobilisation dynamics independently of transcript abundance. The novel synthesis offered here repositions epigenetic regulation, specifically H3K27ac and H3K27me3 dynamics at
NRT2
, GS, and storage protein loci, as a principal determinant of cultivar‐specific nitrogen use efficiency operating independently of DNA sequence variation. Sub‐genome homologue epigenetic asymmetry in hexaploid wheat provides phenotypic buffering capacity unavailable to diploid cereals. The rhizosphere microbiome is identified as an integral co‐regulator of nitrogen acquisition whose molecular interactions with plant signalling networks remain uncharacterised. Three wheat‐specific dimensions absent from rice and maize are identified: sub‐genome epigenetic asymmetry, an unusually high nitrogen harvest index amplifying remobilisation failure costs, and a gliadin‐glutenin quality trade‐off driven by differential chromatin accessibility. Five knowledge gaps define the immediate research agenda: single‐cell omics under nitrogen deficiency, developmental time‐series multi‐omics, CRISPR validation of NUE quantitative trait locus candidates, molecular characterisation of organic versus mineral nitrogen responses, and climate‐nitrogen epigenomics under elevated carbon dioxide. Wheat‐specific multi‐omics investment is required as a primary research objective rather than an agronomic supplement.
Baber Ali, Zeeshan Khan, N. Imin· Journal of Sustainable Agric...· 0 citations
BACKGROUND
Lipids represent the major storage reserve in Brassica napus seeds. During germination, lipid mobilization delivers indispensable energy to support seedling establishment, thereby profoundly influencing germination vigor and subsequent seedling growth capacity. Although lipid mobilization is fundamentally required for successful rapeseed germination, the temporal coordination between transcriptional reprogramming and lipid metabolic conversion remains largely elusive, and the underlying molecular regulatory network remains to be systematically deciphered.
RESULTS
We conducted an integrated transcriptomic and lipidomic analysis on dry B. napus seeds and germinating seeds at 6, 12, 24, and 48 h after imbibition. The results revealed distinct stage-specific characteristics of gene expression and lipid metabolism during germination. In the early imbibition stage, differentially expressed genes (DEGs) were primarily enriched in biological processes related to water transport, stress response, and signal transduction, whereas significant changes in lipid metabolism were observed to be relatively delayed. During the initiation of germination, triacylglycerols (TGs) underwent rapid degradation, accompanied by a significant up-regulation of genes involved in the β-oxidation and gluconeogenesis pathways. In the late germination stage, genes responsible for membrane lipid synthesis were sharply up-regulated, which induced extensive membrane lipid remodeling.
CONCLUSION
This work represents the first systematic integration of transcriptomic and lipidomic data focusing on dynamic changes during the germination stage in B. napus, systematically illustrating the global molecular and lipid metabolic features of rapeseed seeds across sequential imbibition stages. It further delineates stage-specific expression patterns of key functional genes and lipid metabolites throughout germination. Collectively, these results advance our comprehensive understanding of the regulatory networks controlling rapeseed seed germination, and offer reliable theoretical references and candidate gene resources for breeding high-yield and high-quality B. napus varieties.
Bo Zhang, Jun-yan Wu, Li Ma et al.· BMC Genomics· 0 citations
3‐Ketoacyl‐CoA synthase (
KCS
) genes are essential for the biosynthesis of cuticular wax and very‐long‐chain fatty acids, which are key adaptation mechanisms for drought tolerance in plants. Nitric oxide (NO) is a well‐established signaling molecule implicated in plant abiotic stress responses, although its involvement in regulating KCS‐mediated wax biosynthesis during drought remains poorly understood. In this study, 21
SlKCS
genes were identified in the tomato (
Solanum lycopersicum
) genome through genome‐wide analysis. These genes were unevenly distributed across 12 chromosomes, with six duplicated gene pairs evolving under strong purifying selection. Synteny analysis revealed greater collinearity with
Glycine
max
than with the monocot
Oryza sativa
, consistent with the evolutionary divergence between dicot and monocot lineages. Promoter analysis identified 81
cis
‐regulatory elements, including 19 stress‐responsive motifs such as MYC, MYB, STRE, and ABRE, suggesting the involvement of
SlKCS
genes in abiotic stress responses. Based on these findings, the expression of four representative genes (
SlKCS5
,
SlKCS7
,
SlKCS12
, and
SlKCS20
) was examined under nitric oxide donor sodium nitroprusside (SNP), drought stress, and combined SNP + drought treatments, using qRT‐PCR. All four genes exhibited treatment‐dependent expression patterns, with
SlKCS20
showing the strongest response, reaching approximately 58‐fold higher expression under drought stress. Drought stress also significantly increased cuticular wax accumulation in both leaves and stems, while combined SNP and drought treatment resulted in the greatest wax deposition, particularly in stems. These changes were accompanied by reduced leaf water loss, increased chlorophyll content, and partial recovery of the net photosynthetic rate under drought stress. Together, these findings suggest that exogenous SNP enhances drought tolerance by promoting cuticular wax accumulation and improving physiological performance, providing new insights into the role of
SlKCS
genes in drought adaptation.
Anam Munsif, Syeda Amina Usman, Aqsa Rubab et al.· New Zealand journal of crop...· 0 citations
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
