PubMed

Rev Esp Cardiol (Engl Ed). 2025 Mar 15:S1885-5857(25)00087-8. doi: 10.1016/j.rec.2025.02.011. Online ahead of print.NO ABSTRACTPMID:40097004 | DOI:10.1016/j.rec.2025.02.011

New Phytol. 2025 Mar 17. doi: 10.1111/nph.70051. Online ahead of print.ABSTRACTArbuscular mycorrhiza (AM) improves mineral nutrient supply, stress tolerance, and growth of host plants through re-programing of plant physiology. We investigated the effect of AM on the root secondary metabolome of the model legume Lotus japonicus using untargeted metabolomics. Acetonitrile extracts of AM and control roots were analysed using ultra-high-performance liquid chromatography-electrospray ionization-ion mobility-time-of-flight-mass spectrometry (UPLC-ESI-IM-ToF-MS). We characterized AM-regulated metabolites using co-chromatography with authentic standards or isolation and structure identification from L. japonicus roots using preparative high-performance liquid chromatography and nuclear magnetic resonance spectroscopy. Arbuscular mycorrhiza triggered major changes in the root metabolome, with most features representing unknown compounds. We identified three novel polyphenols: 5,7-dihydroxy-4'-methoxycoumaronochromone (lotuschromone), 4-hydroxy-2-(2'-hydroxy-4'-methoxyphenyl)-6-methoxybenzofuran-3-carbaldehyde (lotusaldehyde), and 7-hydroxy-3,9-dimethoxypterocarp-6a-ene (lotuscarpene). Further AM-enhanced secondary metabolites included the previously known lupinalbin A and B, ayamenin D, biochanin A, vestitol, acacetin, coumestrol, and betulinic acid. Lupinalbin A, biochanin A, ayamenin D, liquiritigenin, isoliquiritigenin, lotuscarpene, medicarpin, daidzein, genistein, and 2'-hydroxygenistein inhibited Rhizophagus irregularis spore germination upon direct application. Our results show that AM enhances the production of polyphenols in L. japonicus roots and highlights a treasure trove of numerous unknown plant secondary metabolites awaiting structural identification and functional characterization.PMID:40095637 | DOI:10.1111/nph.70051

Plant Biol (Stuttg). 2025 Mar 17. doi: 10.1111/plb.70001. Online ahead of print.ABSTRACTJasmonates regulate plant development and defence. In angiosperms, the canonical bioactive jasmonate is jasmonoyl-isoleucine (JA-Ile), which is formed in Arabidopsis thaliana by JAR1 and GH3.10. In contrast to other jasmonate biosynthesis or perception mutants, however, gh3.10 jar1 knockout lines are still fertile. Therefore we investigated whether further jasmonates and GH3 enzymes contribute to regulation of fertility. Jasmonate levels were analysed by liquid chromatography-mass spectrometry. The substrate range of recombinant GH3.10 and related GH3 enzymes was studied using non-targeted ex vivo metabolomics with flower and leaf extracts of A. thaliana and in vitro enzyme assays. Jasmonate application experiments were performed to study their potential bioactivity. In flowers and wounded leaves of gh3.10 jar1 knockout lines JA-Ile was below the detection limit. While 12-hydroxy-JA was identified as the preferred substrate of GH3.10, no other recombinant GH3 enzymes tested were capable of JA-Ile formation. Additional JA conjugates found in wounded leaves (JA-Gln) or formed in flowers upon MeJA treatment in the absence of JA-Ile (JA-Gln, JA-Asn, JA-Glu) were identified. The aos gh3.10 jar1 was introduced as a novel tool to test for the bioactivity of JA-Gln to regulate fertility. This study found JAR1 and GH3.10 are the only contributors to JA-Ile biosynthesis in Arabidopsis and identified a number of JA conjugates as potential bioactive jasmonates acting in the absence of JA-Ile. However, their contribution in regulating fertility is yet to be conclusively determined.PMID:40095511 | DOI:10.1111/plb.70001

Exp Dermatol. 2025 Mar;34(3):e70077. doi: 10.1111/exd.70077.ABSTRACTKeloid is characterised by the reprogramming of cellular metabolism, wherein keloid cells adapt their metabolic pathways to meet the demands for energy and biosynthetic precursors. Investigating the intricate relationship between cellular metabolism and the biological behaviour of keloid holds the potential to yield novel therapeutic strategies for keloid. To elucidate the molecular alterations and potential underlying regulatory mechanisms in keloids, we created comprehensive metabolic profiling at the pathway level by analysing metabolomic, transcriptomic and single-cell RNA-sequencing data from keloids and adjacent skin. Viability assay and clonogenic assay were performed to validate the function of the metabolic pathway(s) in primary keloid fibroblast cells. Integrated analysis revealed an upregulation of arginine and proline metabolism in keloids. According to single-cell RNA-seq data, elevated expression of genes related to arginine and proline metabolism, such as P4HA3, P4HA2, P4HA1, PYCR1, OAT and ASS1, was predominately highly expressed in fibroblast-2. Fibroblast-2 displayed more obvious phenotypes of mesenchymal fibroblast. Critical genes from integrated analysis including P4HA3, P4HA2, P4HA1, PYCR1 and AZIN2, and metabolites including fumaric acid and 2-oxo-5-amino-pentanoic acid showed prognostic relevance with disease-free survival of keloid. Additionally, an In vitro study showed that arginine deprivation therapy (ADT) inhibited and radiosensitised the proliferation of keloid-derived fibroblasts. In conclusion, our thorough multiomics study deepens our understanding of the link between arginine and proline metabolism and keloid proliferation and radiosensitivity. Elevated activity of arginine and proline metabolism in mesenchymal fibroblasts may be a potential therapeutic pathway for keloid.PMID:40095415 | DOI:10.1111/exd.70077

Curr Atheroscler Rep. 2025 Mar 17;27(1):37. doi: 10.1007/s11883-025-01284-0.ABSTRACTPURPOSE OF REVIEW: This paper reviews the existing literature on lipidomics as a tool for improved cardiovascular risk estimation in both primary and secondary prevention populations.RECENT FINDINGS: Detailed lipidomic signatures identified by mass spectrometry have been shown to enhance risk estimation for clinical CAD and the presence of subclinical CAD on CTCA in multiple large cohort populations. In patients with established atherosclerotic disease, ceramide and phospholipid-based risk scores improve prediction for recurrent cardiovascular events and cardiovascular death. Lipidomic profiles and lipidomic-enhanced risk scores have been shown to improve prediction of incident cardiovascular disease, recurrent cardiovascular events and cardiovascular death independent of traditional risk factors. Simplified risk scores utilizing the ratios of several ceramide species improve clinical utility, however resources and infrastructure limit widespread implementation. There are currently no therapeutics to address lipidomic risk aside from traditional risk factor modification.PMID:40095146 | DOI:10.1007/s11883-025-01284-0

Anal Bioanal Chem. 2025 Mar 17. doi: 10.1007/s00216-025-05828-w. Online ahead of print.ABSTRACTCongenital hypothyroidism (CH) can be detected early during thyroid-stimulating hormone (TSH) screening based on dried blood spot (DBS) samples. However, it falls short in differentiating between neonates with elevated TSH levels and those with CH, which leads to many neonates undergoing secondary diagnosis through venous blood sampling. Metabolomics was used to analyze metabolic alterations in neonates with CH, and identify DBS-based metabolite biomarkers for CH screening to reduce secondary diagnosis. Based on non-targeted metabolomics, the metabolic alterations in neonates with CH were analyzed in a discovery set and novel biomarkers were identified. The results of the discovery set revealed that the metabolic alterations in neonates with CH were primarily in amino acid and lipid metabolism, and identified novel metabolite biomarkers were thyroxine, 2-piperidinone, and PC (14:0/20:4). Then, these biomarkers were validated in a validation set, and the screening performance was still satisfactory. A rapid 3.5-min targeted method for three potential biomarkers was further developed and used to analyze a confirmation set. Analysis of the confirmation set re-validated the reliability of the biomarkers, and a biomarker combinational model equation and an appropriate cutoff value were defined. Each set of DBS samples included neonates with health, hyperthyrotropinemia, and CH. The novel metabolite biomarkers from DBS samples demonstrate significant potential for CH screening in neonates, effectively reducing the requirement associated with secondary diagnosis of mis-screened neonates.PMID:40094997 | DOI:10.1007/s00216-025-05828-w

Clin J Am Soc Nephrol. 2025 Mar 17. doi: 10.2215/CJN.0000000682. Online ahead of print.ABSTRACTBACKGROUND: Research suggests that eating a plant-dominant dietary pattern is beneficial to people with chronic kidney disease (CKD). The aim was to investigate how increasing the diversity of plant food intake would impact metabolomic, microbiome and clinical parameters in people with CKD.METHODS: This study was a cross-over, randomized controlled trial involving 25 Australian adults diagnosed with stage 3-4 CKD. Participants were randomly allocated to follow two diets for 6 weeks each, separated by a minimum 4-week washout period: a high-diversity plant-based diet (HDPD, ≥30 unique plant foods weekly) and a low-diversity plant-based diet (LDPD, ≤15 unique plant foods weekly), alongside a usual kidney diet prescription. Data collection was completed at four timepoints (beginning and end of each intervention period). Primary outcome included a change in uremic toxins (indoxyl sulfate and p-Cresyl sulfate) concentrations. Secondary and exploratory outcomes included diet quality and nutritional status, fecal microbiome composition and diversity, plasma metabolome, symptom burden, quality of life scores, blood pressure, biochemical and anthropometric measures.RESULTS: Plasma and urinary uremic toxin levels did not consistently decrease across the cohort; however, significant reductions were observed in responders to the HDPD, particularly those with poorer kidney function and higher baseline uremic toxin levels. Neither diet caused electrolyte imbalances. The HDPD significantly improved diet quality, reduced potential renal acid load by an average of 47% from baseline, with an estimated marginal mean reduction of 9.96 (95% CI: -16.28 to -3.64), and compared to the LDPD, decreased total symptom burden, including constipation (95% CI: -4.11 to -0.54 and -0.91 to -0.22, respectively). It also shifted the gut microbiome toward increased production of beneficial metabolites like butyrate/isobutyrate. In contrast, the LDPD reduced microbial diversity and decreased the abundance of 27 species and 33 functional genes.CONCLUSIONS: This study demonstrated the safety and clinically relevant therapeutic benefits of aiming to incorporate 30 or more unique plant foods weekly in the diet of individuals with moderate CKD. It was observed that individuals with more advanced kidney disease and higher levels of uremic toxins may derive the greatest benefit from adopting a HDPD.TRIAL REGISTRATION: ACTRN12619000442101.PMID:40094861 | DOI:10.2215/CJN.0000000682

Plants (Basel). 2025 Mar 5;14(5):819. doi: 10.3390/plants14050819.ABSTRACTMaize (Zea mays L.) is the world's most productive cereal crop, yet it is threatened by several diseases. Among them, Fusarium stalk rot (FSR) causes an average global yield loss of 4.5%. The mycotoxins deoxynivalenol, zearalenone, fumonisins, and moniliformin persist in grain and silage after harvest and pose a risk to human and animal health. This review describes the lifestyle of the fungal pathogens that cause FSR, studies how to optimize resistance evaluation, identifies quantitative trait loci (QTLs) and candidate genes (CGs), and, finally, considers the methods for selecting FSR resistance, especially through genomic selection. To screen maize genotypes for FSR resistance, several artificial inoculation methods have been employed in most studies, including toothpick insertion, ball-bearing pellets, root infection, and the oat kernel method. However, these methods have several limitations in effectively inducing FSR disease infection. Needle injection of inoculum into the stem is recommended, especially when combined with a quantitative or percentage scale because it effectively phenotypes maize populations for FSR resistance. Nine studies with larger populations (≥150 progenies) investigated the genetic architecture of FSR resistance. The inheritance is clearly quantitative. Four major QTLs and several minor QTLs are reported to confer resistance to FSR pathogens, and a few CGs have been identified. Genomic selection is recommended as an effective method for developing routinely FSR-resistant maize, but only two studies have explored this area. An omics analysis (proteomics, transcriptomics, and metabolomics) of the expression of candidate genes should validate their role in FSR resistance, and their use might accelerate selection.PMID:40094830 | DOI:10.3390/plants14050819

Plants (Basel). 2025 Feb 28;14(5):742. doi: 10.3390/plants14050742.ABSTRACTHydrangea (Hydrangea macrophylla) is distinguished by having sepals instead of real petals, a trait that facilitates color diversity. Floral color is largely predetermined by structural genes linked to anthocyanin production, but the genetic factors determining floral hue in this non-model plant remain unclear. Anthocyanin metabolites, transcriptome, and the CIEL*a*b* hue system were employed to elucidate the biochemical and molecular mechanisms of floral color formation in three hydrangea cultivars: 'DB' (deep blue), 'LB' (light blue), and 'GB' (green blue). UPLC-MS/MS identified 47 metabolites, with delphinidin, cyanidin, malvidin, petunidin, pelargonidin, and peonidin being prominent. Delphinidins were 90% of the primary component in 'DB'. The dataset identifies 51 and 31 DEGs associated with anthocyanin, flavonoid, and chlorophyll biosynthesis, with CHS, CHI, F3H, F3'5'H, DFR, ANS, BZ1, and 3AT displaying the highest expression in 'DB'. Notably, DFR (cluster-46471.3) exhibits high expression in 'DB' while being down-regulated in 'LB' and 'GB', correlating with higher anthocyanin levels in floral pigmentation. Comparative analyses of 'LB' vs. 'DB', 'DB' vs. 'GB', and 'LB' vs. 'GB' revealed 460, 490, and 444 differentially expressed TFs, respectively. WRKY, ERF, bHLH, NAC, and AP2/ERF showed the highest expression in 'DB', aligning with the color formation and key anthocyanin biosynthesis-related gene expression. The findings reveal the molecular mechanisms behind floral pigmentation variations and lay the groundwork for future hydrangea breeding programs.PMID:40094733 | DOI:10.3390/plants14050742

Phytopathology. 2025 Mar 17. doi: 10.1094/PHYTO-01-25-0022-R. Online ahead of print.ABSTRACTPhytophthora cinnamomi is a destructive phytopathogen responsible for crown rot, trunk canker, and root rot in over 5,000 plant species worldwide. Despite its significant impact, the molecular interactions between this oomycete and host plants are not well understood. This study aimed to investigate the physiological and molecular responses of Solanum lycopersicum (tomato) to Phytophthora cinnamomi infection. The initial defense response in tomato seeds included producing reactive oxygen species (ROS) and callose deposition. Screening of commercial tomato varieties revealed varying levels of susceptibility, with the variety Marmande exhibiting heightened vulnerability. Three days post-inoculation, Marmande showed increased expression of genes associated with ROS generation, and biosynthesis pathways for phenylpropanoids and flavonoids. Additionally, 850 genes related to cell wall remodeling, including those involved in lignin biosynthesis and pectin methyl esterase inhibitors (PMEIs), were significantly upregulated. Seven days post-inoculation, a stronger transcriptional response was observed, with activation of ethylene (ET) and jasmonic acid (JA) signaling pathways, while salicylic acid (SA) showed minimal activity. Metabolomic analysis of infected roots revealed elevated levels of metabolites linked to lycopene, flavonoids, and phenylpropanoids. Furthermore, infected roots exhibited a significant reduction in pectin levels, which was corroborated by in vitro assays showing zoospore-mediated pectin degradation. These results suggest that the degradation of root pectin is a key mechanism facilitating zoospore invasion in susceptible tomato hosts. This study provides new insights into the molecular mechanisms underlying host-pathogen interactions and identifies potential targets for managing Phytophthora cinnamomi-induced crop diseases.PMID:40094725 | DOI:10.1094/PHYTO-01-25-0022-R

Plants (Basel). 2025 Mar 1;14(5):753. doi: 10.3390/plants14050753.ABSTRACTRapeseed (Brassica napus) is an important oilseed crop and yellow-seeded and black-seeded varieties have different metabolite profiles, which determines the quality and edibility of their oil. In this study, we performed a non-targeted metabolomics analysis of seeds from four rapeseed varieties at eight developmental stages. This analysis identified 4540 features, of which 366 were annotated as known metabolites. The content of these metabolites was closely related to seed developmental stage, with the critical period for seed metabolite accumulation being between 10 and 20 days after pollination. Through a comparative analysis, we identified 18 differentially abundant flavonoid features between yellow-seeded and black-seeded rapeseed varieties. By combining the flavonoid data with transcriptome data, we constructed a gene regulatory network that may reflect the accumulation of differentially abundant flavonoid features. Finally, we predicted 38 unknown features as being flavonoid features through molecular networking. These results provide valuable metabolomics information for the breeding of yellow-seeded rapeseed varieties.PMID:40094714 | DOI:10.3390/plants14050753

Plants (Basel). 2025 Feb 27;14(5):725. doi: 10.3390/plants14050725.ABSTRACTGlobal climate change minimizes fresh water resources used in agriculture worldwide. It causes drought stress, which has adverse effects on plants. To ensure food security, crops and vegetables capable of tolerating shortages of water over the growth period are needed. This study aimed to elucidate the morphological and biochemical responses of three colored cauliflower (Brassica oleracea var. botrytis) cultivars (Clapton, Trevi, and Di Sicilia Violetto) and one broccoli cultivar (Brassica oleracea var. italica var. Magic) to different irrigation treatments (85-100%, 65-80%, 45-60%, and 25-40% field capacity). Assessment of growth parameters revealed no significant difference among all the treatments for root fresh weight, leaf area, and floret size. Major water shortages reduced the floret and stem fresh weight of the Clapton cultivar. Additionally, under severe drought stress, only the Di Sicilia Violetto cultivar had a decrease in plant height, but no impact on the number of leaves was observed. The measurement of pigment contents in the leaves showed no significant difference in carotenoids in all the cultivars; just the chlorophyll contents decreased with moderate stress in the Di Sicilia Violetto cultivar. This research demonstrates that cauliflower and broccoli are likely drought-tolerant vegetables and common irrigation regimes may be reviewed.PMID:40094680 | DOI:10.3390/plants14050725

Plants (Basel). 2025 Feb 26;14(5):721. doi: 10.3390/plants14050721.ABSTRACTPistacia palaestina hosts several Fordini gall-forming aphid species, which manipulate its anatomy and metabolism, creating galls that provide nutrients and protection. This study compared the extended metabolic profiles of P. palaestina leaves and galls induced by Baizongia pistaciae, Paracletus cimiciformis, and Geoica spp. GC-MS analysis of ethyl acetate (EtOAc) and methanol (MeOH) extracts revealed a high abundance of shikimic acid and quinic acid isomers, along with diverse hydrocarbons, lipids, terpenoids, phenolics, and carbohydrates, each showing distinct distributions across gall types. Paracletus cimiciformis galls closely resembled intact leaves, exhibiting limited metabolic disruption. In contrast, the larger, more complex galls of Baizongia and Geoica underwent profound metabolic modifications. These aphids manipulate host metabolism, leading to triterpenoid and phenolics accumulation, which likely fortifies gall structure and enhances chemical defense. The considerable variation among individual trees suggests that specific host plant templates significantly influence the metabolic profile of the galls.PMID:40094633 | DOI:10.3390/plants14050721

Plants (Basel). 2025 Feb 23;14(5):684. doi: 10.3390/plants14050684.ABSTRACTEpigallocatechin-3-O-gallate (EGCG) is an important ingredient that indicates tea quality and has healthcare functions. Magnesium nutrition can improve the quality and yield of tea plants, but its regulatory role in the biosynthesis of EGCG in tea plants has not been clarified. Herein, we performed a comprehensive analysis of the metabolomics and transcriptomics of the shoots of 'Huangdan' at five magnesium concentrations: L1-L5 (0, 0.15, 0.45, 0.6, and 0.9 mmol/L mg2+, respectively). The results showed that the EGCG content of tea shoots treated with low magnesium concentrations was higher compared to those treated with high magnesium concentrations. The contents of related metabolites such as p-coumaric acid and cyanide in the EGCG synthesis pathway increased in the L4 and L5 treatment groups, while those of dihydroquercetin, dinnamic acid, and epicatechin increased significantly in the L2 and L3 treatment groups. Under the influence of magnesium treatment, the biosynthesis of EGCG was affected by a series of structural genes: CsPAL (HD.01G0005520), HD.02G0024350), Cs4CL (HD.15G0008250, HD.13G0010220), CsDFR (HD.04G0026220), CsANS(HD.12G0016700) with CsaroDE (HD.03G0002480)-positive regulation, and CsPAL (HD.13G0009900, HD.06G0008610), CsC4H (HD.06G0017130), Cs4CL (HD.02G0027390, HD.04G0003270), CsCHS (HD.10G0022640), CsCHI (HD.01G0011100), CsF3'H (HD.15G0015490), CsF3'5'H (HD.13G0004300), CsANS (HD.07G0023630), and Csaro B (HD.01G0028400) with CsSCPL (HD.01G0041070)-negative regulation. Transcription factors MYB 44 and WRKY 17 may play a key role in EGCG biosynthesis, which is significantly induced by magnesium nutrition in tea tree shoots. This study elucidates the effect of magnesium nutrition on EGCG biosynthesis in tea plants and provides key candidate transcription factors to provide a reference for further research on high-EGCG tea varieties to improve tea quality.PMID:40094619 | DOI:10.3390/plants14050684

Plants (Basel). 2025 Feb 24;14(5):692. doi: 10.3390/plants14050692.ABSTRACTLanthanum (La) is often used in industry and agriculture, leading to its accumulation in natural environments and potential ecological risks. The objective of this study was to examine the effects on the growth, metabolism, and nutrient composition of Brassica rapa exposed to at low (1 µM), medium (1 mM), and high (10 mM) La concentrations. We used chemical analytical, molecular, and metabolomic methods and found that high La exposure induced a hormetic effect, triggering both stimulatory and inhibitory responses. La reduced aluminum (Al), cobalt (Co), nickel (Ni), and chromium (Cr) levels at all concentrations, while medium and high doses also decreased phosphorus (P) and iron (Fe). La accumulation in B. rapa increased with La levels, affecting metabolic processes by modulating reactive oxygen species (ROS), increasing proline, and reducing total polyphenol content. Flavonoid levels were altered, chlorophyll and carotenoids declined, and non-photochemical quenching increased. Gene expressions related to flavonoid, carotenoid, and chlorophyll metabolism, as well as ion transport, exhibited a dose-dependent modulation. On the contrary, fatty acid composition remained unaffected. Our results indicate that La accumulates in in B. rapa and disrupts the plant metabolism. Despite an evident effect on plant productivity, our results also raise concerns about the potential health risks of consuming La-enriched B. rapa plants.PMID:40094588 | DOI:10.3390/plants14050692

Plants (Basel). 2025 Feb 24;14(5):688. doi: 10.3390/plants14050688.ABSTRACTAs the main active ingredient in Anoectochilus roxburghii, kinsenoside has important health and medical effects including hepatoprotective, anti-oxidant, and bacteriostasis, among others. In recent years, with the limited application of high-throughput technology to A. roxburghii, there has been no research on the key regulatory genes involved in the synthesis of kinsenoside. Therefore, we examined three species of A. roxburghii that are widely planted in mainland China and Taiwan Province, A. roxburghii cultivar 'Jian ye', Anoectochilus formosanus, and Anoectochilus burmannicus, determining the content of kinsenoside, performing transcriptomic and metabolomic sequencing, identifying UDP glycosyltransferases, and screening for UDP glycosyltransferases that may be involved in kinsenoside synthesis. The results showed that among the three species of A. roxburghii, the content of kinsenoside in A. roxburghii cv. 'Jian ye' was the highest. Transcriptome and metabolome data showed that A. roxburghii cv. 'Jian ye' and the two other species of A. roxburghii have 3702 and 5369 differentially expressed genes and 69 and 120 differentially accumulated metabolites, respectively. Meanwhile, differentially expressed genes and differentially accumulated metabolites are enriched in the glucose metabolism and hormone pathways. We also treated the A. roxburghii samples with exogenous auxin and characterized the related genes. In A. roxburghii, we identified 73 members of the UDP glycosyltransferase family. Through phylogenetic tree, transcriptome data expression profile, and qPCR analyses, we screened for members that may be involved in the synthesis of kinsenoside. In summary, the results of this study provide insights for breeding high-kinsenoside-content and high-intron varieties of A. roxburghii.PMID:40094578 | DOI:10.3390/plants14050688

Plants (Basel). 2025 Feb 21;14(5):671. doi: 10.3390/plants14050671.ABSTRACTSoybean is a vital crop globally and a key source of food, feed, and biofuel. With advancements in high-throughput technologies, soybeans have become a key target for genetic improvement. This comprehensive review explores advances in multi-omics, artificial intelligence, and economic sustainability to enhance soybean resilience and productivity. Genomics revolution, including marker-assisted selection (MAS), genomic selection (GS), genome-wide association studies (GWAS), QTL mapping, GBS, and CRISPR-Cas9, metagenomics, and metabolomics have boosted the growth and development by creating stress-resilient soybean varieties. The artificial intelligence (AI) and machine learning approaches are improving genetic trait discovery associated with nutritional quality, stresses, and adaptation of soybeans. Additionally, AI-driven technologies like IoT-based disease detection and deep learning are revolutionizing soybean monitoring, early disease identification, yield prediction, disease prevention, and precision farming. Additionally, the economic viability and environmental sustainability of soybean-derived biofuels are critically evaluated, focusing on trade-offs and policy implications. Finally, the potential impact of climate change on soybean growth and productivity is explored through predictive modeling and adaptive strategies. Thus, this study highlights the transformative potential of multidisciplinary approaches in advancing soybean resilience and global utility.PMID:40094561 | DOI:10.3390/plants14050671

Plants (Basel). 2025 Feb 20;14(5):633. doi: 10.3390/plants14050633.ABSTRACTPotato (Solanum tuberosum L.) has high nutritional value and strong adaptability and plays an extremely important role in global food security. Excessive use of nitrogen (N) fertilizer in potato production has increased costs and environmental pollution. In this study, the N use efficiency (NUE) of two potato varieties (DXY and DN310) was determined under high nitrogen conditions. The N use efficiency of DXY was relatively high. The differences between the rhizosphere microbial population groups of the two varieties were determined using the metagenomic sequencing method. The genes related to N efficiency were jointly identified using transcriptome and metabolome analyses. Significant difference was observed between the two varieties of microorganisms, leading to different rhizosphere microorganisms. Compared with DN310, the roots of DXY retained more available N and generated less NO. Additionally, DXY exhibited relatively low disease susceptibility. Combined transcriptome and metabolome analyses indicated that the differentially expressed metabolites in the two different varieties under high N conditions were mainly enriched in amino acid metabolism and sugar metabolism pathways. Using weighted gene co-expression network analysis, two genes associated with N fertilizer response were identified: PGSC0003DMG400025888 and PGSC0003DMG400017276. This study provided valuable insights into breeding potato varieties with high N efficiency.PMID:40094559 | DOI:10.3390/plants14050633

Plants (Basel). 2025 Feb 21;14(5):665. doi: 10.3390/plants14050665.ABSTRACTLesion mimic mutants provide unique tools to investigate plant-pathogen interactions, often exhibiting hypersensitive responses in the absence of biotic or abiotic stresses. The overexpression of the S-domain receptor-like kinase gene, SPL11 cell-death suppressor 2 (SDS2), in rice leads to constitutive programmed cell death and enhanced resistance to fungal and bacterial pathogens. However, the mechanisms underlying this broad-spectrum resistance remain unclear. This study integrates transcriptomic and metabolomic analyses of the SDS2-ACT mutant to uncover gene expression and metabolic shifts associated with disease resistance. To identify SDS2-specific physiological changes related to pathogen resistance, leaf tissues from the SDS2-ACT mutant and the Kitkaake WT line were subjected to both transcriptomic and non-targeted metabolic profiling. Transcriptomic analyses identified 1497 differentially expressed genes (DEGs), including up-regulated genes involved in terpenoid and flavonoid biosynthesis, phytohormone signaling, and defense-related pathways (including pathogenesis-related [PR] genes). Metabolomic profiling revealed significant alterations in the accumulation of several compound classes, including putative: terpenoids, phenylpropanoids, phytohormones, fatty acids, and sugars. These changes are likely correlated with the observed cell death and resistance phenotypes in the SDS2-ACT mutant. This study provides an overall landscape of the transcriptomic and metabolomic alterations in a lesion mimic mutant, identifying candidate defense-related genes and metabolites for functional analysis in rice.PMID:40094528 | DOI:10.3390/plants14050665

Plants (Basel). 2025 Feb 20;14(5):652. doi: 10.3390/plants14050652.ABSTRACTPomegranate (Punica granatum L.) is an important economic tree, possessing both edible and ornamental value. Flower color is an important ornamental trait of pomegranate, but the color formation pattern and related molecular mechanisms of pomegranate petals are still unclear. In this study, we conducted physiological, transcriptomic, and metabolomic studies on the petals of Tunisia and White pomegranate varieties during the blooming stage. The results showed that compared to White petals, the contents of anthocyanin, carotenoid, and sucrose in Tunisia petals were significantly increased, while the flavonoid content was significantly decreased. Through RNA-seq, 23 DEGs were identified in the anthocyanin synthesis, and 3 DEGs were identified in the carotenoid synthesis. Transcription factor genes such as MYB, bHLH, WRKY, and MADS were identified as key candidates for regulating anthocyanin metabolism. Metabolomic analysis revealed that eight DEMs are associated with anthocyanin synthesis and three DEMs are associated with carotenoid synthesis. In addition, caffeic acid and its derivatives were significantly upregulated in Tunisia petals. In summary, we propose the following hypothesis: the accumulation of anthocyanins and carotenoids is the reason for the red color of Tunisian petals, and the upregulation of structural genes, including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, PSY, and LCYB, leads to an increase in their content. Transcription factor genes such as MYB, bHLH, bZIP, MADS, and WRKY may also play a positive role in anthocyanin accumulation. The research results provide a basis for the theory of pomegranate petal color formation.PMID:40094520 | DOI:10.3390/plants14050652