TABLE 4.

Summary of key transcriptomics, proteomics, metabolomics, and ionomics studies under toxic metals/metalloids toxicity in different plant species.

Transcriptomics
Plant species	Stress conditions	Target tissues	Approach	Functional annotation methods	Key observations	References
Phytolacca americana	50 mg kg–1 CdCl2; 15 days	Roots, leaves, and stem	RNA-Seq	NR, SWISS-PROT, GO, KEGG	1,515 differentially expressed genes (DEGs) were identified. 12 DEGs validated using qRT-PCR. Genes related to toxic metal tolerance identified including nicotianamine synthases (8), ABC transporter (3), expansins (11), metallothionein (3), ZRT/IRT protein (4), and aquaporins (4)	Chen et al., 2017
Brassica juncea	25 μM CdSO4; 24 h	Roots	Microarray	Gene chip Arabidopsis ATH1 genome array	38 DEGs identified, and six DEGs validated by qRT-PCR. The DEGs were mainly involved in Cd metabolism.	Dalyan et al., 2017
Oryza sativa	100 μML–1 AlCl3; 24 h	Root tips	RNA-seq	KEGG, WEGO 2.0	14,550 DEGs identified, of which most were related to Al tolerance. Total of 92 genes were reported to be linked with different pathways that mediated Al-induced inhibition in plants.	Zhang et al., 2019c
Verbena bonariensis	100 mg kg–1 CdCl2; 20 days	Root	RNA-seq	GO and KEGG	23,424 DEGs identified. 10 DEGs validated by qRT-PCR. DEGs encoding lignin synthase, chalcone synthase, and anthocyanidin synthase identified under Cd stress.	Wang et al., 2019
Triticum aestivum	100 μM CdCl2; 24 h	Roots	RNA-seq	GO-GO network and pathway network analysis	1,269 and 399 DEGs identified in low and high Cd accumulation genotypes. Six genes validated using qRT-PCR. DEGs related to Cd uptake and transport include antioxidant defense, ATP binding, plant hormone signal transduction, and phenylpropanoid biosynthesis.	Zhou et al., 2019
Vicia faba	5, 10, 15, 20, 25 μM U; 72 h	Roots	RNA-seq	NR, KOG, GO, Swiss-Prot, eggNOG, KEGG, Pfam	4,974 DEGs identified. The uranium induction significantly up- and down-regulated 1,654 and 3,320 genes, respectively, involved in the regulation of cell metabolism and other processes, and processing of environmental and genetic information.	Lai et al., 2020
Fagopyrum tataricum	2,000, 10,000 bmgkg–1 Pb(NO3)2; 72 h	Leaves	RNA-seq	GO, KEGG	12,595 DEGs identified. Majority of DEGs were associated with phenylpropanoid synthesis pathway and up-regulated the expression of MAPKs and GSH metabolic genes along with the regulation of plant protecting metabolites and hormones.	Wang et al., 2020d
Medicago sativa	50, 150, 250, 500 mg kg–1 NiCl2; 60 days	Roots and shoots	RNA-seq	Fern Base, NCBI	Highly expressed prx1C, GST, and PC genes in roots and shoots actively mediated the negative impact of Ni on plant growth.	Helaoui et al., 2020
Oryza sativa	15 mM FeSO4; 2 days	Roots and leaves	RNA-seq	Top GO, Ensembl Plants, TAIR	1,147 and 1,038 DEGs identified under control and Fe treatment. The Fe stress affected “Hacha” genotype more abundantly by causing alterations in roots’ gene expression pattern. Total of 1,248 and 1,161 DEGs were less abundant in “Lachit” roots under control and Fe stress conditions.	Kar et al., 2020
Dendrobium officinale	2, 5, 9, 14 mg L–1 CdSO4; 30 days	Roots	RNA-seq	GO and KEGG	2,469 DEGs identified. DEGs helped identify complex metabolic pathways and regulated the transcription factors involved in regulating Cd stress.	Jiang et al., 2020
Proteomics
Plant species	Stress conditions	Target tissue	Extraction protocol	Analytical approach	Key observations	References
Artemisia annua	100 μM As + 100 μM Se; 3 days	Roots, shoots	TCA	2D- PAGE, MALDI-TOF-MS	20 differentially abundant proteins (DAPs) identified. The DAPs were involved in energy metabolism, secondary metabolism, photosynthesis, transcriptional regulators, transport proteins, and lipid metabolism.	Kumari and Pandey-Rai, 2018
Capsicum annuum	0 or 100 ppm Na2SeO4; 24 h	Shoots	EDTA	LC-MS/MS	4,693 DAPs identified. Identified DAPs were associated with protein processing, post-translational modification, chaperones, protein turnover, and metabolic process.	Zhang et al., 2019a
Proteomics
Plant species	Stress conditions	Target tissue	Extraction protocol	Analytical approach	Key observations	References
Eucalyptus camaldulensis	30, 50, 100 μM, CuSO4⋅5H2O; 6 weeks	Leaves, roots	TCA/acetone	MS	26 DAPs were identified. 11 DEPs were up-regulated, and 15 DAPs were down-regulated. Identified DEPs were involved in antioxidant enzymes, photosynthesis, metabolism, transcription, and translation.	Alotaibi et al., 2019
Arachis hypogaea	2 μM CdCl2; 7 days	Roots	TCA/Acetone	LC-ESI-MS/MS, RT-PCR	30 DAPs were found to be linked with heavy metal transport, while 86 DAPs were found to be associated with cell wall modification.	Yu R. et al., 2019
Stylosanthes guianensis	5 or 400 μM MnSO4; 10 days	Shoots, roots	Tris-HCl	LC-MS/MS	356 DAPs identified. 172 DAPs were strongly induced, while 96 DAPs were completely suppressed. Identified DAPs were involved in carbon fixation, defense response, signaling, metabolism, photosynthesis, and cell wall modulation.	Liu P. et al., 2019
Oryza sativa	25 μM AsIII, NaAsO2 + 25 μM SeIV, Na2SeO; 15 days	Roots, shoots	Acetone	MALDI-TOF/TOF, qRT-PCR	Significantly enhanced expression of 14,303 proteins for As + Se exposure, compared to As alone. In As stress, Se application effectively mitigated As toxicity, improving plant growth via regulation of 14-3-3 proteins. FBPase, AtpB, GLN1, and GLN2 proteins were found to be involved in defense, photosynthesis, and energy metabolism upon Se exposure.	Chauhan et al., 2020
Setaria italica	120 g hm–2 Na2SeO3; 72 h	Grains	HEPES-based buffer	LC-MS/MS	123 DAPs identified. The DAPs were mainly involved in amino acid and carbohydrate metabolism.	Liang et al., 2020
Nicotiana tabacum	5.36 mg kg–1 Zn+2; 10 days	Leaves	TCA/Acetone	LC-MS/MS	Zn stress resulted in the down-regulation of 8 proteins. Chl synthesis was not inhibited significantly, and only a few proteins involved in the electron transport chain showed down-regulation. Zn-stress did not significantly inhibit photosynthetic function in tobacco leaves.	Zhang et al., 2020b
Allium cepa	5–15 μM Pb(NO3)2; 6, 12, and 24 h	Roots	Tris-HCl	2-DE, AutoFlex TOF/TOF II-MS	17 DAPs identified. Lowered expression of Anx D1, SHMTI, and COMT2 resulted in decreased defensive response, respiration, and the response of other functions, respectively. Improved expression of NDPK, PR1, and CHI1 resulted in increased transcription, translation, and better pathogen invasion, respectively.	Lyu et al., 2020
Cichorium intybus	100, 200, and 300 μM Pb; 46 days	Leaves	Tris-HCl	SDS-PAGE	81 DAPs identified. Total of 16 proteins were up-regulated and 13 were down-regulated. Identified proteins were associated with plant-stress response and adaptation toward metal toxicity.	Malik and Pirzadah, 2020
Metabolomics
Plant species	Stress conditions	Target tissue	Analytical platform	Data analysis	Key observations	References
Cucumis sativus	10, 100, and 500 mg L–1 CuSO4; 7 days	Leaves	GC-TOF-MS, LC-MS/MS	PLS-DA	Total of 149 primary and 79 secondary metabolites were quantified. 1.4–2.4-folds of intermediates involved in TCA were found to be down-regulated upsetting carbohydrate metabolism.	Zhao L. et al., 2018
Glycine max	0.1–100 mg L–1 Mo; 48 h	Leaves, roots	UPLC, LC-MS	PCA, OPLS-DA, KEGG	Identified 42 and 19 significantly different metabolites (SDMs) in roots and leaves, respectively. Organic acids, gluconic acid, D-glucarate, and citric acid were amplified by 107. 63-, 4.42- and 2.87-folds after Mo exposure. Organic compounds such as 2-oxoarginine, L-nicotine, gluconic acid, D-glucarate, and citric acid played a significant role in chelating Mo and decreasing its toxicity.	Xu et al., 2018
Oryza sativa	400 ppm FeSO4.7H2O; 10 days	Roots, shoots	GC-MS	PCA, PLS-DA	Levels of elaidic acid increased, while linoleic- and linolenic acid decreased. In shoot and root, alteration of the fatty acid composition suggested metabolites alteration.	Turhadi et al., 2019
Metabolomics
Plant species	Stress conditions	Target tissue	Analytical platform	Data analysis	Key observations	References
Glycine max	25 μM Fe (III)−EDTA; 10 days	Roots, leaves	GC-MS	OPLS-DA	N assimilation was inhibited, which reduced proteins in roots and nodules. Sugars increased or maintained at a constant level in different tissues under Fe deficiency, which probably relates to oxidative stress, cell wall damage, and feedback regulation. Increased levels of ascorbate, nicotinate, raffinose, galactinol, and proline in different tissues possibly helped resist the oxidative stress induced by Fe deficiency.	Chu et al., 2019
Helianthus annuus	1, 5, and 25 mg L–1 Cr(VI); 7 days	Roots	capHPLC-ESI-QTOF-MS	PLS	70% of metabolites involved in LA metabolic pathway are affected by Cr(VI) stress. Detection of four EKODE isomers not included in LA metabolism and found only in the exposed roots. Oxidation of LA to HpODE isomers upon incubation with Cr(VI).	Ibarra et al., 2019
Brassica napus	100 μM CdCl2.2.5H2O; 8 days	Leaves	UPLC/MS	PCA, PLS-DA, KEGG	644 SDMs found in sensitive genotype ZD622, and 487 SDMs in tolerant genotype CB671. Most SDMs were involved in Cd-mediated stress tolerance pathways.	Mwamba et al., 2020
Elodea nuttallii	280 μg L–1 Cd as Cd(NO3)2; 24 h	Shoots	GC-MS, LC analysis	PCA, MetaboAnalyst KEGG	Cd stress caused significant variations in aminoacyl-tRNA biosynthesis and branched-chain amino acid pathways. In the shoot, Cd induces a concentration of 11 amino acids, 2 sugars, adonitol, and pipecolic acid in the cytosol, and Cd induces a concentration of glycine, ammonium, hydroxy.	Cosio and Renault, 2020
Cucumis melo L.	300 μmol L–1 CuSO4; 3 days	Roots	UPLC/MS	KEGG	70 DEGs identified; 42-downregulated and 28-upregulated. 318 SDMs identified, 150-downregulated and 168-upregulated. Identified SDMs and DEGs were involved in JA biosynthesis; comprising lipoxygenase related genes, and lecithin and linoleic acid metabolites.	Hu et al., 2020
Cucumis sativus L.	3 μM Se (Na2SeO3)–50 μM Cd (CdCl2); 7 days	Leaves, roots	GC-MS	OPLS-DA, PCA, HCA, KEGG	Intermediates of TCA, glycolysis, and some amino acids were upregulated. Differentially regulated metabolites have a significant role in developing Se-mediated Cd tolerance.	Sun et al., 2020
Vicia faba	25 μM U [UO2(NO3)2⋅6H2O, 238U]; 72 h	Roots	GC-MS	KEGG	53 SDMs identified to be related to carbohydrate metabolism; including 12-downregulated and 13-upregulated metabolites. U led to the imbalance of the expression of related metabolites in the energy metabolism pathway of plant cells.	Zhang et al., 2020d
Ipomoea batatas L.	1.68–5.16 mg kg–1 U, 0.78–2.02 mg kg–1 Cd; 150 days	Roots	UPLC-MS	PCA, OPLS-DA, KEGG	634 SDMs identified in U + Cd; including 428 up-regulated and 214 down-regulated metabolites. Induced expression of plant hormones and cyclic nucleotides in cells. Regulated primary and secondary root-metabolism to induce U and Cd toxicity resistance.	Zhang-Xuan et al., 2020
Ionomics
Plant species	Approach	Element		Tissue	Key observations	References
Zea mays	ICP−OES	Cd, Mo, Ca, Cu, Fe, K, Mg, Mn, P, S, and Zn		Shoot	Significant genotypic variation found among all minerals. ZmHMA2/3 and ZmMOT1 were found to be responsible for Cd and Mo contents in shoot.	Stich et al., 2020
Brassica napus	ICP−OES	B, Ca, Cu, Fe, K, Mg, Mn, Na, P, S, and Zn		Shoot and root	Total of 133 and 123 QTLs identified for the shoot and root ionome under OP and LP. Six QTL clusters were identified to be influencing mineral elements.	Wang et al., 2020e
Oryza sativa	Ex-3600 ED-XRF spectrometer	F, Co, Si, Ca, K, S, Zn, Cu, Ni, Fe, Mn, V, and Se		Seedling	Reduced fluoride toxicity and stimulated plant growth.	Banerjee et al., 2020
Solanum tuberosum	ICP-AES	Co, Zn, Cd, and Pb		Tubers	Reduced contamination of heavy metals in potato tubers	Muntean et al., 2019
Oryza sativa	ICP-MS	As, B, Ca, Cd, Cu, K, Mg, Mn, Mo, Na, Ni, P, Zn, and Ti		Straw and grain	Identified 70 novel ionomic QTLs and OsMOT1 as a causative gene underlying a QTL controlling Mo tolerance.	Wang et al., 2020a