Introduction
Plants face a multitude of biotic and abiotic stresses that threaten their growth, development, and productivity. Biotic stresses, such as fungal infections, and abiotic stresses, including drought, salinity, and temperature extremes, activate complex molecular networks involving transcriptional reprogramming, metabolic adjustments, and signaling cascades. Recent advancements in omics technologies have enabled comprehensive exploration of these mechanisms across diverse plant species. This review synthesizes findings from six studies on lily (Lilium spp.), licorice (Glycyrrhiza uralensis), potato (Solanum tuberosum), rice (Oryza sativa), soybean (Glycine max), and pigeonpea (Cajanus cajan), focusing on their molecular strategies to combat stress. By integrating transcriptomic, metabolomic, and gene family analyses, we highlight conserved pathways, species-specific adaptations, and future directions for crop improvement.
Transcriptional and metabolic reprogramming in lily bulb rot resistance
In this Research Topic Chang et al. showed that Fusarium oxysporum-induced lily bulb rot triggers dynamic transcriptomic shifts, with 3,922, 7,595, and 6,590 DEGs at early (LYBH2), mid- (LYBH3), and late-stage (LYBH4) infection, respectively. In this study, key upregulated TFs—WRKY (regulating lignin via SA/JA signaling; Rushton et al., 1996; Deng et al., 2023) and AP2/ERF (modulating SA/ET/JA pathways; Ma et al., 2017b) were found to drive phenylpropanoid-derived antimicrobials.
The metabolomic analysis identified stage-specific flavonoids: Kaempferol-3-O-rutinoside-7-O-rhamnoside (LYBH2, antibacterial; Ma et al., 2017b), quercetin-3-O-glucoside (LYBH3, antiviral; Wei et al., 2021), and lignification enhancers (LYBH4; Ninfali et al., 2020). Despite upregulated lignin genes (PAL, CCoAOMT; Sun et al., 2024), minimal metabolite shifts suggest post-transcriptional regulation.
Soybean drought response: physiology, transcriptome and metabolome
In the study of Wang et al., drought stress was found to reduce photosynthesis and water use efficiency (WUE), with non-stomatal limitations dominating under severe drought (SD). Rehydration restored WUE in moderate drought (MD) but not severe drought (SD), indicating irreversible damage (Qi et al., 2021). Moreover, the chlorophyll fluorescence parameters (Fv/Fm, ΦPSII) mirrored photosynthetic recovery under drought stress.
The transcriptome analysis in this study, revealed that drought stress induced the expression of the PAO1, 4, 5 and P5CS genes to promote the accumulation of spermidine and proline, enhancing soybean drought tolerance. Moreover, the metabolome analysis also identified proline, DL-tryptophan, and phenylalanine as key osmolytes under drought stress. Proline accumulation in MD plants aligned with barley and wheat studies (Chmielewska et al., 2016), while tryptophan derivatives may correlate with antioxidant responses (Rabara et al., 2017). Integrated transcript-metabolite networks highlighted phenylpropanoid and amino acid pathways as critical hubs.
MAPK signaling in licorice salt stress adaptation
Gao et al., revealed that the MAPK cascade, conserved across eukaryotes, transduces stress signals via phosphorylation (Jagodzik et al., 2018). In G. uralensis, 21 GuMAPKs were classified into four subgroups (A–D) based on TEY/TDY activation motifs (López-Bucio et al., 2014). Subgroups A (GuMAPK3/6) and D (GuMAPK16) exhibited colinearity with Arabidopsis and tomato homologs, underscoring evolutionary conservation. Within GuMAPKs, gene duplication, particularly segmental duplication, drove functional diversification, as seen in three homologous pairs (Wang et al., 2021).
Under 200 mM NaCl, GuMAPK5, 7, 9, and 16 were upregulated, while Bacillus subtilis inoculation further enhanced their expression, indicating microbial priming of salt tolerance. Protein interaction networks linked GuMAPKs to PR1 (pathogenesis-related protein) and RBOHD (ROS-generating NADPH oxidase), bridging biotic and abiotic stress responses (Yamada et al., 2016). At 300 mM NaCl, GuMAPK16-2 downregulation post-inoculation suggested stress threshold modulation.
COLs gene family in potato tuberization and cold stress
Yin et al., discovered that potato tuberization is regulated by photoperiod-sensitive StCOL genes (Abelenda et al., 2016). Phylogenetic analysis classified StCOLs into three subfamilies with conserved motifs/structures (2–4 exons) and 10 motifs/6 PTMs affecting protein function. Synteny revealed 13 StCOLs share a common ancestor, highlighting evolutionary conservation. Cold-responsive StCOL2, 3, 9, and 15 contained low-temperature cis-elements. StCOL9 downregulation post-chilling suggests its role as a negative regulator, akin to AtCOL1 in Arabidopsis (Mikkelsen and Thomashow, 2009). These genes likely integrate photoperiod and temperature cues to optimize tuberization under stress.
ALOGs gene family in rice development and abiotic stress
Liu et al., explained that the ALOG domain, derived from retroposon recombinases, governs rice reproductive development (Turchetto et al., 2023). Phylogenetic analysis divided 14 OsG1L genes into six clades, with OsG1L1/2/5/6 regulating panicle architecture (Beretta et al., 2023). Collinearity between OsG1L3/4/5 and OsG1L7/8 suggested subfunctionalization. Rice ALOG promoters are enriched with ABA-responsive ABRE motifs (half with ≥5 ABREs; up to 12 in one member) and drought-linked MBS elements. Most ALOG genes are downregulated under ABA/drought, consistent with ABA-insensitive root/seed phenotypes in LSH8 mutants (promoter ABREs, nuclear localization; Zou et al., 2021). Similarly, OsG1L7 (9 ABREs, nuclear) is suppressed by ABA/drought, suggesting shared roles in ABA signaling. These findings highlight ALOG family involvement in ABA-mediated stress responses via promoter cis-elements and transcriptional regulation.
BAGs gene family in pigeonpea and their response in thermotolerance
The study by Alekhya et al. conducted a comprehensive genomic and functional characterization of the BAG gene family in pigeonpea (C. cajan), revealing critical insights into their role in heat stress response. Alekhya et al., demonstrated that Pigeonpea’s nine BAGs genes (five chromosomes) show lineage-specific evolution via Whole Genome Duplication (WGD). UBL domains in BAG1/2/4 suggest ubiquitin roles, while BAG6’s IQ motif links to calcium signaling. Phylogenetically, five clades (shared with tomato/soybean) reflect exon/intron divergence, with non-conserved structures (as in Arabidopsis, rice, wheat (Doukhanina et al., 2006; Rana et al., 2012; Ge et al., 2016) driving functional diversification.
In heat-tolerant genotype TS3R, CcBAG4 (interacting with HSP70) was upregulated, suppressing cell death (Doukhanina et al., 2006). Conversely, CcBAG5/6 showed upregulation in susceptible lines, mirroring tomato SlBAG9 (homolog of AtBAG5) overexpression-induced heat sensitivity (Ding et al., 2022). MiRNA targeting of CcBAG6 in TS3R suggested post-transcriptional silencing, enhancing thermotolerance.
Convergent mechanisms and future perspectives
Conserved stress-response mechanisms across species involve transcriptional hubs (WRKY, AP2/ERF, NAC TFs) coordinating stress-specific gene regulation, metabolic pathways (phenylpropanoid/amino acid biosynthesis) producing chemical defenses, and signaling networks (MAPK cascades, BAG-HSP chaperones) linking stress perception to protection. Translational innovations include CRISPR editing (e.g., StCOL9, OsG1L7) for climate resilience, microbiome engineering (B. subtilis) priming MAPK pathways, and metabolic engineering (proline/lignin) enhancing drought/fungal resistance. These strategies integrate molecular insights with biotechnology, offering scalable solutions for sustainable crop improvement amid climate challenges.
Statements
Author contributions
XL: Writing – original draft, Writing – review and editing. GN: Conceptualization, Supervision, Writing – review and editing. RZ: Conceptualization, Supervision, Writing – review and editing. MS: Conceptualization, Supervision, Writing – original draft, Writing – review and editing.
Funding
The author(s) declare that financial support was received for the research and/or publication of this article. We are grateful for support from the financially supported by the National Natural Science Foundation of China (Nos 32102462 and 32072652); The Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS); The Natural Science Foundation of Jiangsu Province (BK2022148); The earmarked fund for CARS, CARS-23-B05. This research acknowledged the supports of The Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, the Ministry of Agriculture, China. Finally, we gratefully acknowledge the authors, editors, and reviewers for their contributions to this Research Topic.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Generative AI statement
The author(s) declare that no Generative AI was used in the creation of this manuscript.
Correction note
This article has been corrected with minor changes. These changes do not impact the scientific content of the article.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
1
AbelendaJ. A.Cruz-OróE.Franco-ZorrillaJ. M.PratS. (2016). Potato StCONSTANS-like1 suppresses storage organ formation by directly activating the FT-like StSP5G repressor. Curr. Biol.26, 872–881. 10.1016/j.cub.2016.01.066
2
BerettaV. M.FranchiniE.DinI. U.LacchiniE.BroeckL. V. D.SozzaniR.et al (2023). The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice. Plant J.115 (2), 351–368. 10.1111/tpj.16229
3
ChmielewskaK.RodziewiczP.SwarcewiczB.SawikowskaA.KrajewskiP.MarczakŁ.et al (2016). Analysis of drought-induced proteomic and metabolomic changes in barley (Hordeum vulgare L.) leaves and roots unravels some aspects of biochemical mechanisms involved in drought tolerance. Front. Plant Sci.7, 1108. 10.3389/fpls.2016.01108
4
DengJ.WangZ.LiW.ChenX.LiuD. (2023). WRKY11 upregulated dirigent expression to enhance lignin/lignans accumulation in Lilium regale wilson during response to fusarium wilt. J. Integr. Agric.23, 2703–2722. 10.1016/j.jia.2023.07.032
5
DingH.QianL.JiangH.JiY.FangY.ShengJ.et al (2022). Overexpression of a Bcl-2-associated athanogene SlBAG9 negatively regulates high-temperature response in tomato. Int. J. Biol. Macromol.194, 695–705. 10.1016/j.ijbiomac.2021.11.114
6
DoukhaninaE. V.ChenS.van der ZalmE.GodzikA.ReedJ.DickmanM. B. (2006). Identification and functional characterization of the BAG protein family in Arabidopsis thaliana. J. Biol. Chem.281 (27), 18793–18801. 10.1074/jbc.M511794200
7
GeS.KangZ.LiY.ZhangF.ShenY.GeR.et al (2016). Cloning and function analysis of BAG family genes in wheat. Funct. Plant Biol.43 (5), 393–402. 10.1071/FP15317
8
JagodzikP.Tajdel-ZielinskaM.CieslaA.MarczakM.LudwikowA. (2018). Mitogen-activated protein kinase cascades in plant hormone signaling. Front. Plant Sci.9, 1387. 10.3389/fpls.2018.01387
9
López-BucioJ. S.DubrovskyJ. G.Raya-GonzálezJ.Ugartechea-ChirinoY.López-BucioJ.de Luna-ValdezL. A.et al (2014). Arabidopsis thaliana mitogen-activated protein kinase 6 is involved in seed formation and modulation of primary and lateral root development. J. Exp. Bot.65, 169–183. 10.1093/jxb/ert368
10
MaY.LiuY.SunA.DuY.YeM.PuX.et al (2017b). Intestinal absorption and neuroprotective effects of kaempferol-3-O-rutinoside. RSC Adv.7, 31408–31416. 10.1039/C7RA05415G
11
MikkelsenM. D.ThomashowM. F. (2009). A role for circadian evening elements in cold-regulated gene expression in arabidopsis. Plant J.60, 328–339. 10.1111/j.1365-313X.2009.03957.x
12
NinfaliP.AntonelliA.MagnaniM.ScarpaE. S. (2020). Antiviral properties of flavonoids and delivery strategies. Nutrients12 (9), 2534. 10.3390/nu12092534
13
QiM.LiuX.LiY.SongH.YinZ.ZhangF.et al (2021). Photosynthetic resistance and resilience under drought, flooding and rewatering in maize plants. Photosynth. Res.148 (1-2), 1–15. 10.1007/s11120-021-00825-3
14
RabaraR. C.TripathiP.RushtonP. J. (2017). Comparative metabolome profile between tobacco and soybean grown under water-stressed conditions. Biomed. Res. Int.2017, 3065251. 10.1155/2017/3065251
15
RanaR. M.DongS.AliZ.KhanA. I.ZhangH. S. (2012). Identification and characterization of the Bcl-2-associated athanogene (BAG) protein family in rice. Afr. J. Biotechnol.11 (1), 88–98. 10.5897/AJB11.3474
16
RushtonP. J.TorresJ. T.ParniskeM.WernertP.HahlbrockK.SomssichI. E. (1996). Interaction of elicitor-induced DNA-Binding proteins with elicitor response elements in the promoters of parsley PR1 genes. Embo J.15 (20), 5690–5700. 10.1002/j.1460-2075.1996.tb00953.x
17
SunJ.WangY.ZhangX.ChengZ.SongY.LiH.et al (2024). Transcriptomic and metabolomic analyses reveal the role of phenylalanine metabolism in the maize response to stalk rot caused by Fusarium proliferatum. Int. J. Mol. Sci.25 (3), 1492. 10.3390/ijms25031492
18
TurchettoC.SilvérioA. D. C.WaschburgerE. L.LacerdaM. E. G.QuintanaI. V.Turchetto-ZoletA. C. (2023). Genome-wide identification and evolutionary view of ALOG gene family in solanaceae. Genet. Mol. Biol.46 (3), e20230142. 10.1590/1415-4757-GMB-2023-0142
19
WangZ.WanY.MengX.ZhangX.YaoM.MiuW.et al (2021). Genome-wide identification and analysis of mkk and mapk gene families in brassica species and response to stress in Brassica napus. Int. J. Mol. Sci.22, 544. 10.3390/ijms22020544
20
WeiY.ZhangY.MengJ.WangY.ZhongC.MaH. (2021). Transcriptome and metabolome profiling in naturally infested Casuarina equisetifolia clones by Ralstonia solanacearum. Genomics113 (4), 1906–1918. 10.1016/j.ygeno.2021.03.022
21
YamadaK.YamaguchiK.ShirakawaT.NakagamiH.MineA.IshikawaK.et al (2016). The arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation. EMBO J.35 (22), 2468–2483. 10.15252/embj.201694248
22
ZouJ. P.LiZ. F.TangH. H.ZhangL.LiJ. D.LiY. H.et al (2021). Arabidopsis LSH8 positively regulates ABA signaling by changing the expression pattern of ABA-Responsive proteins. Int. J. Mo.l Sci.22 (19), 10314. 10.3390/ijms221910314
Summary
Keywords
transcriptomics, metabolomics, gene family abundance, plant stress, molecular mechanisms
Citation
Luo X, Ntatsi G, Zhou R and Sun M (2025) Editorial: Multi-omics and molecular biology studies on abiotic stress in crops. Front. Genet. 16:1607710. doi: 10.3389/fgene.2025.1607710
Received
08 April 2025
Accepted
26 June 2025
Published
03 July 2025
Corrected
04 July 2025
Volume
16 - 2025
Edited and reviewed by
Andrew H. Paterson, University of Georgia, United States
Updates
Copyright
© 2025 Luo, Ntatsi, Zhou and Sun.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Georgia Ntatsi, ntatsi@aua.gr; Rong Zhou, zhour@njau.edu.cn; Mintao Sun, sunmintao@caas.cn
Disclaimer
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.