{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T10:01:47Z","timestamp":1790157707553,"version":"4.1.0"},"reference-count":89,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Cereal crops increasingly encounter drought, salinity and alkalinity, heat, waterlogging, potentially toxic elements, and compound stresses that constrain productivity and grain quality. Secondary metabolites, also referred to as specialized metabolites in the recent literature, represent a dynamic component of cereal stress adaptation rather than a passive catalogue of stress markers. This review aims to synthesize current evidence on how specialized-metabolite pathways contribute to abiotic stress responses in cereals, with particular emphasis on regulatory mechanisms, evidence strength, chemical form, subcellular localization, recovery, and translational relevance. We critically assess evidence from transcriptomics, metabolomics, genetic perturbation, biochemical assays, multi-omics integration, and physiological studies across major cereal crops and evaluate evidence according to causal, associative, and in vitro categories. The evidence reveals that perturbations at the plasma membrane, cell wall, chloroplast, mitochondrion, and endomembrane system levels generate reactive oxygen species, Ca2+ signatures, phospholipid signals, and hormone changes that are decoded by CDPK\/CPK, CBL\u2013CIPK, SnRK2, and MAPK cascades. These signaling networks converge on MYB\u2013bHLH\u2013WD40, WRKY, NAC, ERF\/AP2, HSF, and bZIP regulators and redirect carbon and reducing power through phenylpropanoid, flavonoid, lignin, carotenoid, terpenoid, benzoxazinoid, cyanogenic, and related pathways. Comparative analysis across rice (Oryza sativa L.), wheat (Triticum aestivum L.), maize (Zea mays L.), barley (Hordeum vulgare L.), oat (Avena sativa L.), sorghum (Sorghum bicolor L.), and millets shows conserved regulatory features but substantial crop-, genotype-, tissue-, developmental-stage-, and dose-dependent variation. Functional evidence further indicates that enzyme activity, chemical modification, transport, and subcellular compartmentation can determine whether metabolites contribute to ROS buffering, photosynthetic and membrane protection, cell-wall reinforcement, osmotic or ionic homeostasis, toxic-ion sequestration, or signaling. The review also identifies important limitations in current research, including overreliance on associative omics evidence, insufficient consideration of combined stresses and rehydration, growth\u2013defence trade-offs, and limited field and reproductive-stage validation. To distinguish growth dilution from genuine biosynthetic increases, absolute metabolite content per grain or organ should be measured alongside concentration per unit dry weight. We conclude that improving cereal resilience requires context-dependent and experimentally validated coordination of regulators, biosynthetic enzymes, chemical modification, transport, and compartmentation rather than indiscriminate elevation of total specialized-metabolite concentration.<\/jats:p>","DOI":"10.3390\/plants15192905","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T08:14:39Z","timestamp":1790151279000},"page":"2905","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Specialized Metabolites in Cereal Crops Under Abiotic Stress: Regulatory Mechanisms, Functional Validation, and Breeding Implications"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3388-1839","authenticated-orcid":false,"given":"Muhammad Ali","family":"Shah","sequence":"first","affiliation":[{"name":"School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8386-7560","authenticated-orcid":false,"given":"Imran","family":"Azeem","sequence":"additional","affiliation":[{"name":"School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2417-6153","authenticated-orcid":false,"given":"Rehmat","family":"Ullah","sequence":"additional","affiliation":[{"name":"Key Laboratory of Crop Genetic Breeding and Germplasm Innovation, Guangxi Key Laboratory of Agro-Environment and Agri-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3155-5204","authenticated-orcid":false,"given":"Haseeb","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waqas","family":"Liaqat","sequence":"additional","affiliation":[{"name":"Department of Field Crops, Faculty of Agriculture, Recep Tayyip Erdo\u011fan University, Rize 53300, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1915-4010","authenticated-orcid":false,"given":"Muhammad Faheem","family":"Jan","sequence":"additional","affiliation":[{"name":"Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"ref_1","unstructured":"Food and Agriculture Organization of the United Nations (FAO) (2025). The Impact of Disasters on Agriculture and Food Security 2025, FAO."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41558-021-01000-1","article-title":"Anthropogenic climate change has slowed global agricultural productivity growth","volume":"11","author":"Ault","year":"2021","journal-title":"Nat. Clim. Change"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/s43016-021-00400-y","article-title":"Climate impacts on global agriculture emerge earlier in new generation of climate and crop models","volume":"2","author":"Ruane","year":"2021","journal-title":"Nat. Food"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/s41586-025-09085-w","article-title":"Impacts of climate change on global agriculture accounting for adaptation","volume":"642","author":"Hultgren","year":"2025","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/s41576-021-00413-0","article-title":"Abiotic stress responses in plants","volume":"23","author":"Zhang","year":"2022","journal-title":"Nat. Rev. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1104\/pp.20.00433","article-title":"Plant secondary metabolites as defenses, regulators, and primary metabolites: The blurred functional trichotomy","volume":"184","author":"Erb","year":"2020","journal-title":"Plant Physiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1038\/s41589-021-00822-6","article-title":"Adaptive mechanisms of plant specialized metabolism connecting chemistry to function","volume":"17","author":"Weng","year":"2021","journal-title":"Nat. Chem. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.2307\/3870059","article-title":"Stress-induced phenylpropanoid metabolism","volume":"7","author":"Dixon","year":"1995","journal-title":"Plant Cell"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Di, X., Hu, R., Gao, Y., Schaller, H., Madhujith, T., Hao, G., Hemmerlin, A., and Liao, P. (2026). Bridging metabolic pathways: Coordinated regulation of isoprenoid and phenylpropanoid metabolism in plants. J. Exp. Bot., erag199. Epub ahead of print.","DOI":"10.1093\/jxb\/erag199"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.devcel.2020.10.012","article-title":"Thriving under stress: How plants balance growth and the stress response","volume":"55","author":"Zhang","year":"2020","journal-title":"Dev. Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.plantsci.2012.07.014","article-title":"Flavonoids as antioxidants in plants: Location and functional significance","volume":"196","author":"Agati","year":"2012","journal-title":"Plant Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1111\/tpj.12388","article-title":"Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids","volume":"77","author":"Nakabayashi","year":"2014","journal-title":"Plant J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41592-021-01197-1","article-title":"Mass spectrometry-based metabolomics: A guide for annotation, quantification and best reporting practices","volume":"18","author":"Alseekh","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1111\/j.1365-313X.2005.02593.x","article-title":"Methods and concepts in quantifying resistance to drought, salt, and freezing, abiotic stresses that affect plant water status","volume":"45","author":"Verslues","year":"2006","journal-title":"Plant J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1146\/annurev.arplant.59.032607.092752","article-title":"Flooding stress: Acclimations and genetic diversity","volume":"59","author":"Voesenek","year":"2008","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/nrg3901","article-title":"Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability","volume":"16","author":"Mickelbart","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41586-019-1679-0","article-title":"Genetic strategies for improving crop yields","volume":"575","author":"Parker","year":"2019","journal-title":"Nature"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1146\/annurev-arplant-060223-013842","article-title":"Using synthetic biology to understand the function of plant specialized metabolites","volume":"75","author":"Bai","year":"2024","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s11306-007-0082-2","article-title":"Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group, Metabolomics Standards Initiative","volume":"3","author":"Sumner","year":"2007","journal-title":"Metabolomics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41580-022-00499-2","article-title":"Reactive oxygen species signalling in plant stress responses","volume":"23","author":"Mittler","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nature13593","article-title":"OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis","volume":"514","author":"Yuan","year":"2014","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/s41477-020-0667-6","article-title":"Calcium spikes, waves, and oscillations in plant development and biotic interactions","volume":"6","author":"Tian","year":"2020","journal-title":"Nat. Plants"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1038\/s41580-022-00479-6","article-title":"Plant hormone regulation of abiotic stress responses","volume":"23","author":"Waadt","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev-cellbio-011620-031429","article-title":"Combinatorial control of plant specialized metabolism: Mechanisms, functions, and consequences","volume":"36","author":"Lacchini","year":"2020","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1093\/jxb\/erq442","article-title":"Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway","volume":"62","author":"Hichri","year":"2011","journal-title":"J. Exp. Bot."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1126\/science.aag2347","article-title":"Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum","volume":"354","author":"Laursen","year":"2016","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.molp.2014.12.007","article-title":"Carotenoid metabolism in plants","volume":"8","author":"Nisar","year":"2015","journal-title":"Mol. Plant"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.tplants.2009.11.006","article-title":"The \u201cins\u201d and \u201couts\u201d of flavonoid transport","volume":"15","author":"Zhao","year":"2010","journal-title":"Trends Plant Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ygeno.2014.11.006","article-title":"Genomic characterization, phylogenetic comparison and differential expression of the cyclic nucleotide-gated channels gene family in pear (Pyrus bretschneideri Rehd.)","volume":"105","author":"Chen","year":"2015","journal-title":"Genomics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/nature22009","article-title":"Plant signalling in symbiosis and immunity","volume":"543","author":"Zipfel","year":"2017","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1146\/annurev-arplant-042817-040322","article-title":"Reactive oxygen species in plant signaling","volume":"69","author":"Waszczak","year":"2018","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Cramer, G.R., Urano, K., Delrot, S., Pezzotti, M., and Shinozaki, K. (2011). Effects of abiotic stress on plants: A systems biology perspective. BMC Plant Biol., 11.","DOI":"10.1186\/1471-2229-11-163"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.tplants.2016.08.002","article-title":"ROS Are Good","volume":"22","author":"Mittler","year":"2017","journal-title":"Trends Plant Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.plantsci.2005.05.004","article-title":"Role of ABA, salicylic acid, calcium and hydrogen peroxide on antioxidant enzymes induction in wheat seedlings","volume":"169","author":"Agarwal","year":"2005","journal-title":"Plant Sci."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Chen, H., Bullock, D.A., Alonso, J.M., and Stepanova, A.N. (2022). To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses. Plants, 11.","DOI":"10.3390\/plants11010033"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1104\/pp.126.2.485","article-title":"Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology","volume":"126","year":"2001","journal-title":"Plant Physiol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Dong, G., Zhao, S., Ding, Y., Ma, Y., Ma, X., Liu, C., and Hou, B. (2025). Rice glycosyltransferase OsDUGT1 is involved in heat stress tolerance by glycosylating flavonoids and regulating flavonoid metabolism. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1516990"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Liu, J., Zhang, L., Huang, L., Yang, T., Ma, J., Yu, T., Zhu, W., Zhang, Z., and Tang, J. (2022). Uncovering the gene regulatory network of maize hybrid ZD309 under heat stress by transcriptomic and metabolomic analysis. Plants, 11.","DOI":"10.3390\/plants11050677"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Wang, F., Zhou, Z., Liu, X., Zhu, L., Guo, B., Lv, C., Zhu, J., Chen, Z.-H., and Xu, R. (2024). Transcriptome and metabolome analyses reveal molecular insights into waterlogging tolerance in barley. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-05091-8"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/mp\/ssp106","article-title":"Phenylpropanoid biosynthesis","volume":"3","author":"Vogt","year":"2010","journal-title":"Mol. Plant"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Chali, B.A., Li, Y., Ahanger, M.A., Thin, P.P., Wan, J., and Xu, P. (2026). Induction of glutathione and flavonoid biosynthesis activates antioxidant enzymes to enhance drought tolerance in rice. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-08448-3"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Fu, C., Li, H., Wu, X., Tang, M., Xiao, B., Lv, R., Zhang, Z., Gao, X., Liu, B., and Yang, C. (2022). Salinity tolerance in a synthetic allotetraploid wheat (S1S1AA) is similar to its higher tolerant parent Aegilops longissima (S1\u02e1S1) and linked to flavonoids metabolism. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.835498"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Shen, W., Ren, Q., Dai, Y., Zhang, Y., and Xiong, F. (2026). Integrated transcriptomics and metabolomics with machine learning identify flavonoids as key effectors in wheat root thermotolerance. Plants, 15.","DOI":"10.3390\/plants15060965"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Huang, M., Du, J., Zhao, Y., Cui, J., Zhang, M., Cao, F., Wang, J., Chu, C., Li, S., and Xia, X. (2026). Integrated transcriptome and metabolome analysis reveals the molecular mechanisms of drought response in Setaria italica during the booting stage. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-08353-9"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Sun, Y., Jing, H., Li, Z., Wan, K., Ma, J., Zhang, H., Xue, J., and Li, R. (2025). Integrated transcriptomic, metabolomic and lipidomic analyses uncover the crucial roles of lipid metabolism pathways in oat (Avena sativa) responses to heat stress. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11972-5"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.cj.2025.01.019","article-title":"Chalcone isomerase gene (OsCHI3) increases rice drought tolerance by scavenging ROS via flavonoid and ABA metabolic pathways","volume":"13","author":"Liu","year":"2025","journal-title":"Crop J."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Mohagheghian, B., Saeidi, G., and Arzani, A. (2025). Phenolic compounds, antioxidant enzymes, and oxidative stress in barley (Hordeum vulgare L.) genotypes under field drought-stress conditions. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06750-0"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Huo, Y., Wang, M., Wan, X., Zhao, Y., Han, H., Zhang, B., Hou, S., Ren, X., Song, J., and Han, Y. (2026). SiLRL1, a bHLH transcription factor from foxtail millet, promotes carotenoid accumulation and improves drought tolerance. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-025-07825-8"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Liu, X., Yin, B., Shang, C., Bao, X., Wang, L., Wang, T., and Zhen, W. (2026). Flavonoid metabolism is involved in regulating the growth of winter wheat upon rehydration. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1693576"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Radwan, N.S., Lamlom, S.F., Emwas, A.H., Jaremko, M., and Abdelsalam, N.R. (2026). Cultivar-specific metabolomic and morpho-physiological responses reveal distinct salt tolerance mechanisms in rice (Oryza sativa L.). BMC Plant Biol., 26.","DOI":"10.1186\/s12870-025-08086-1"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Yang, S., Tao, Y., Liu, M., Zhou, H., Chen, G., Xu, J., Zhang, H., and Mo, J. (2026). Transcriptome and metabolome analysis demonstrate critical contribution of flavonoid biosynthesis and galactose metabolism to salt resistance of rice roots. Sci. Rep., Epub ahead of print.","DOI":"10.1038\/s41598-026-60030-x"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e1335845","DOI":"10.1080\/15592324.2017.1335845","article-title":"Metabolomics analysis of rice responses to salinity stress revealed elevation of serotonin and gentisic acid levels in leaves of tolerant varieties","volume":"12","author":"Gupta","year":"2017","journal-title":"Plant Signal. Behav."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Xiong, W., Zhang, L., Wang, Y., Wei, G., Zhu, K., Zhao, K., and Wu, Z. (2025). Correlative transcriptome and metabolome analysis of the maize shoot response to salt stress. Plants, 14.","DOI":"10.3390\/plants14233554"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Han, M., Tan, Q., Yang, Y., Zhang, H., Wang, X., and Li, X. (2025). Integrative transcriptomic and metabolomic insights into saline\u2013alkali stress tolerance in foxtail millet. Plants, 14.","DOI":"10.3390\/plants14111602"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"e70895","DOI":"10.1111\/tpj.70895","article-title":"Overexpression of barley heat stress transcription factor HvHsfA6a provides thermotolerance by modulating transcriptome and metabolome","volume":"126","author":"Chaudhary","year":"2026","journal-title":"Plant J."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e17252","DOI":"10.1111\/tpj.17252","article-title":"Rice glycosyltransferase UGT706F1 functions in heat tolerance through glycosylating flavonoids under the regulation of transcription factor MYB61","volume":"121","author":"Zhao","year":"2025","journal-title":"Plant J."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"5841","DOI":"10.1093\/jxb\/eraa591","article-title":"The hypoxia\u2013reoxygenation stress in plants","volume":"72","author":"Castillo","year":"2021","journal-title":"J. Exp. Bot."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev-arplant-043015-112301","article-title":"Toxic heavy metal and metalloid accumulation in crop plants and foods","volume":"67","author":"Clemens","year":"2016","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Jiao, Z., Shi, Y., Wang, J., Wang, Z., Zhang, X., Jia, X., Du, Q., Niu, J., Liu, B., and Du, R. (2023). Integration of transcriptome and metabolome analyses reveals sorghum roots responding to cadmium stress through regulation of the flavonoid biosynthesis pathway. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1144265"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"131931","DOI":"10.1016\/j.jhazmat.2023.131931","article-title":"Multiple insights into lignin-mediated cadmium detoxification in rice (Oryza sativa)","volume":"458","author":"Dong","year":"2023","journal-title":"J. Hazard. Mater."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"9931","DOI":"10.1073\/pnas.0802361105","article-title":"Transporters of arsenite in rice and their role in arsenic accumulation in rice grain","volume":"105","author":"Ma","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"15699","DOI":"10.1073\/pnas.1414968111","article-title":"A rice ABC transporter, OsABCC1, reduces arsenic accumulation in the grain","volume":"111","author":"Song","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s42003-025-08077-w","article-title":"Mechanisms of plant acclimation to multiple abiotic stresses","volume":"8","author":"Jiang","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Yue, Z., Liu, Y., Zheng, L., Zhang, Q., Wang, Y., Hao, Y., Zhang, M., Chen, Y., Wang, Z., and He, L. (2024). Integrated transcriptomics, metabolomics, and physiological analyses reveal differential response mechanisms of wheat to cadmium and\/or salinity stress. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1378226"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"109357","DOI":"10.1016\/j.soilbio.2024.109357","article-title":"Dynamic interplay among soil nutrients, rhizosphere metabolites, and microbes shape drought and heat stress responses in summer maize","volume":"191","author":"Yuan","year":"2024","journal-title":"Soil Biol. Biochem."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Zhang, F., Yang, L., Zhao, Z., Wang, J., Zhang, K., Chen, B., Duan, Y., Wu, H., Wang, Y., and Zhu, K. (2026). Comparative investigation into metabolic pathways and corresponding gene expression profiles of sorghum under drought stress. Agronomy, 16.","DOI":"10.3390\/agronomy16090849"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Chmielewska, K., Rodziewicz, P., Swarcewicz, B., Sawikowska, A., Krajewski, P., Marczak, \u0141., Ciesio\u0142ka, D., Kuczy\u0144ska, A., Miko\u0142ajczak, K., and Ogrodowicz, P. (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.","DOI":"10.3389\/fpls.2016.01108"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1007\/s44372-025-00431-w","article-title":"Integrative multi-omics approaches for crop abiotic stress tolerance","volume":"2","author":"Dakal","year":"2025","journal-title":"Discov. Plants"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41477-021-00887-0","article-title":"Stress-induced reactive oxygen species compartmentalization, perception and signalling","volume":"7","author":"Castro","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1351\/PAC-REP-12-07-15","article-title":"Methods of measurement and evaluation of natural antioxidant capacity\/activity: IUPAC Technical Report","volume":"85","author":"Apak","year":"2013","journal-title":"Pure Appl. Chem."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"a034744","DOI":"10.1101\/cshperspect.a034744","article-title":"The sweet side of plant-specialized metabolism","volume":"11","author":"Louveau","year":"2019","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1093\/mp\/sst080","article-title":"A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: Application in the study of rice metabolomics","volume":"6","author":"Chen","year":"2013","journal-title":"Mol. Plant"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s41576-021-00434-9","article-title":"Navigating the pitfalls of applying machine learning in genomics","volume":"23","author":"Whalen","year":"2022","journal-title":"Nat. Rev. Genet."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1038\/s41592-024-02362-y","article-title":"Guiding questions to avoid data leakage in biological machine learning applications","volume":"21","author":"Bernett","year":"2024","journal-title":"Nat. Methods"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"3438","DOI":"10.1038\/ncomms4438","article-title":"Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights","volume":"5","author":"Wen","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"12767","DOI":"10.1038\/ncomms12767","article-title":"Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals","volume":"7","author":"Chen","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/s41477-021-00858-5","article-title":"Enhancing grain-yield-related traits by CRISPR\u2013Cas9 promoter editing of maize CLE genes","volume":"7","author":"Liu","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41587-022-01281-7","article-title":"Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size","volume":"40","author":"Song","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1146\/annurev-arplant-050213-040027","article-title":"Cyanogenic glycosides: Synthesis, physiology, and phenotypic plasticity","volume":"65","author":"Gleadow","year":"2014","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Zhang, Z., Wang, Y., and Li, R. (2025). Genome-wide analysis of Zm4CL genes identifies Zm4CL8 regulating drought and salt tolerance in maize. Agronomy, 15.","DOI":"10.3390\/agronomy15051100"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1016\/j.tibtech.2025.01.006","article-title":"CRISPR\/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing","volume":"43","author":"Oliveira","year":"2025","journal-title":"Trends Biotechnol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"112246","DOI":"10.1016\/j.plantsci.2024.112246","article-title":"A coiled-coil domain mutation in the NLR receptor SbYR1 coordinates plant growth and stress tolerance in sorghum","volume":"350","author":"Li","year":"2025","journal-title":"Plant Sci."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"kiaf071","DOI":"10.1093\/plphys\/kiaf071","article-title":"Caffeic acid O-methyltransferase-dependent flavonoid defenses promote sorghum resistance to fall armyworm infestation","volume":"197","author":"Kundu","year":"2025","journal-title":"Plant Physiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2564","DOI":"10.1093\/plphys\/kiad675","article-title":"Primary, seminal and lateral roots of maize show type-specific growth and hydraulic responses to water deficit","volume":"194","author":"Protto","year":"2024","journal-title":"Plant Physiol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/jxb\/erad423","article-title":"Imaging plant metabolism in situ","volume":"75","author":"Horn","year":"2024","journal-title":"J. Exp. Bot."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1146\/annurev-arplant-050718-100221","article-title":"Modeling plant metabolism: From network reconstruction to mechanistic models","volume":"71","author":"Clark","year":"2020","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_87","first-page":"338","article-title":"Functional diversifications of cyanogenic glucosides","volume":"13","year":"2010","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1104\/pp.111.180224","article-title":"Benzoxazinoid metabolites regulate innate immunity against aphids and fungi in maize","volume":"157","author":"Ahmad","year":"2011","journal-title":"Plant Physiol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1111\/tpj.13430","article-title":"Drought-related secondary metabolites of barley (Hordeum vulgare L.) leaves and their metabolomic quantitative trait loci","volume":"89","author":"Piasecka","year":"2017","journal-title":"Plant J."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/19\/2905\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T09:04:46Z","timestamp":1790154286000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/19\/2905"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,23]]},"references-count":89,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["plants15192905"],"URL":"https:\/\/doi.org\/10.3390\/plants15192905","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,23]]}}}