Physiological and iTRAQ-Based Quantitative Proteomics Analysis of Methyl Jasmonate-Induced Tolerance in Brassica napus Under Arsenic Stress

How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications

MAIN CONCLUSION

Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.

Allene oxide synthase 1 contributes to limiting grain arsenic accumulation and seedling detoxification in rice

Arsenic (As) is a cancerogenic metalloid ubiquitously distributed in the environment, which can be easily accumulated in food crops like rice. Jasmonic acid (JA) and its derivatives play critical roles in plant growth and stress response. However, the role of endogenous JA in As accumulation and detoxification is still poorly understood. In this study, we found that JA biosynthesis enzymes Allene Oxide Synthases, OsAOS1 and OsAOS2, regulate As accumulation and As tolerance in rice. Evolutionary bioinformatic analysis indicated that AOS1 and AOS2 have evolved from streptophyte algae (e.g. the basal lineage Klebsormidium flaccidum) - sister clade of land plants. Compared to other two AOSs, OsAOS1 and OsAOS2 were highly expressed in all examined rice tissues and their transcripts were highly induced by As in root and shoot. Loss-of-function of OsAOS1 (osaos1-1) showed elevated As concentration in grains, which was likely attributed to the increased As translocation from root to shoot when the plants were subjected to arsenate [As(V)] but not arsenite [As (III)]. However, the mutation of OsAOS2 (osaos2-1) showed no such effect. Moreover, osaos1-1 and osaos2-1 increased the sensitivity of rice plants to both As(V) and As(III). Disrupted expression of genes involved in As accumulation and detoxification, such as OsPT4, OsNIP3;2, and OsOASTL-A1, was observed in both osaos1-1 and osaos2-1 mutant lines. In addition, a As(V)-induced significant decrease in Reactive Oxygen Species (ROS) production was observed in the root of osaos1-1 but not in osaos2-1. Taken together, our results indicate OsAOS1 modulates both As allocation and detoxification, which could be partially attributed to the altered gene expression profiling and ROS homeostasis in rice while OsAOS2 is important for As tolerance.

Hormonal regulation of anthocyanin biosynthesis for improved stress tolerance in plants

Due to unprecedented climate change, rapid industrialization and increasing use of agrochemicals, abiotic stress, such as drought, low temperature, high salinity and heavy metal pollution, has become an increasingly serious problem in global agriculture. Anthocyanins, an important plant pigment, are synthesized through the phenylpropanoid pathway and have a variety of physiological and ecological functions, providing multifunctional and effective protection for plants under stress. Foliar anthocyanin accumulation often occurs under abiotic stress including high light, cold, drought, salinity, nutrient deficiency and heavy metal stress, causing leaf reddening or purpling in many plant species. Anthocyanins are used as sunscreens and antioxidants to scavenge reactive oxygen species (ROS), as metal(loid) chelators to mitigate heavy metal stress, and as crucial molecules with a role in delaying leaf senescence. In addition to environmental factors, anthocyanin synthesis is affected by various endogenous factors. Plant hormones such as abscisic acid, jasmonic acid, ethylene and gibberellin have been shown to be involved in regulating anthocyanin synthesis either positively or negatively. Particularly when plants are under abiotic stress, several plant hormones can induce foliar anthocyanin synthesis to enhance plant stress resistance. In this review, we revisit the role of plant hormones in anthocyanin biosynthesis and the mechanism of plant hormone-mediated anthocyanin accumulation and abiotic stress tolerance. We conclude that enhancing anthocyanin content with plant hormones could be a prospective management strategy for improving plant stress resistance, but extensive further research is essentially needed to provide future guidance for practical crop production.

Genetic variation and molecular characterization of Zygophyllum coccineum L. ecotypes of the iron mining area of El-Wahat El-Bahariya in Egypt

Remediation and mitigation processes can recover the ecosystems affected by mining operations. Zygophyllum coccineum L. is a native indigenous xerophyte that grows in Egypt's Western Desert, particularly around the iron mining ore deposits, and accumulates high rates of potentially toxic elements (PTEs) in its succulent leaves. The present study evaluated the genetic variation and molecular responses of Z. coccineum to heavy metal stressful conditions in three sites. Results revealed that Z. coccineum bioaccumulation capacity was greater than unity and varied amongst the three locations. In response to heavy metal toxicity, Z. coccineum plants boosted their antioxidative enzymes activity and glutathione levels as a tolerance strategy. Anatomically, a compact epidermis, a thick spongy mesophyll with water storage cells, and a thicker vascular system were observed. Protein electrophoretic analysis yielded 20 fragments with a polymorphism rate of 85%. The antioxidant genes (CAT: catalase, POD: peroxidase and GST: polyphenol oxidase) showed greater levels of expression. In addition, DNA-based molecular genetic diversity analyses using Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers yielded 54 amplified fragments (i.e. 24 monomorphic and 30 polymorphic), with 12 unique fragments and a polymorphism rate of 55.5%. The greatest PIC values were recorded for SCoT-6 (0.36) and for both of the 14 A and 44 B ISSR primers (0.25). Diversity index (DI) of all SCoT and ISSR amplified primers was 0.23. The present findings reveal the distinct heavy metal's adaption attributes of Z. coccineum, indicating its improved survival in severely arid mining environments.

Arsenic-Induced Oxidative Stress and Antioxidant Defense in Plants

The non-essential metalloid arsenic (As) is widely distributed in soil and underground water of many countries. Arsenic contamination is a concern because it creates threat to food security in terms of crop productivity and food safety. Plants exposed to As show morpho-physiological, growth and developmental disorder which altogether result in loss of productivity. At physiological level, As-induced altered biochemistry in chloroplast, mitochondria, peroxisome, endoplasmic reticulum, cell wall, plasma membrane causes reactive oxygen species (ROS) overgeneration which damage cell through disintegrating the structure of lipids, proteins, and DNA. Therefore, plants tolerance to ROS-induced oxidative stress is a vital strategy for enhancing As tolerance in plants. Plants having enhanced antioxidant defense system show greater tolerance to As toxicity. Depending upon plant diversity (As hyperaccumulator/non-hyperaccumulator or As tolerant/susceptible) the mechanisms of As accumulation, absorption or toxicity response may differ. There can be various crop management practices such as exogenous application of nutrients, hormones, antioxidants, osmolytes, signaling molecules, different chelating agents, microbial inoculants, organic amendments etc. can be effective against As toxicity in plants. There is information gap in understanding the mechanism of As-induced response (damage or tolerance response) in plants. This review presents the mechanism of As uptake and accumulation in plants, physiological responses under As stress, As-induced ROS generation and antioxidant defense system response, various approaches for enhancing As tolerance in plants from the available literatures which will make understanding the to date knowledge, knowledge gap and future guideline to be worked out for the development of As tolerant plant cultivars.

Methyl Jasmonate Alleviated the Adverse Effects of Cadmium Stress in Pea (Pisum sativum L.): A Nexus of Photosystem II Activity and Dynamics of Redox Balance

The accumulation of cadmium (Cd) in leaves reduces photosynthetic capacity by degrading photosynthetic pigments, reducing photosystem II activity, and producing reactive oxygen species (ROS). Though it was demonstrated that the application of Methyl Jasmonate (MeJA) induces heavy metal (HM) stress tolerance in plants, its role in adjusting redox balance and photosynthetic machinery is unclear. In this study, the role of MeJA in modulating photosystem II (PSII) activity and antioxidant defense system was investigated to reduce the toxic effects of Cd on the growth of pea (Pisum sativum L.) cultivars. One-week-old seedlings of three pea varieties were subjected to Cd stress (0, 50, 100 μm), and MeJA (0, 1, 5, 10 μm) was applied as a foliar spray for 2 weeks. Cadmium stress reduced the growth of all three pea varieties. Cadmium stress decreased photosynthetic pigments [Chl a (58.15%), Chl b (48.97%), total Chl (51.9%) and carotenoids (44.01%)] and efficiency of photosystem II [Fv/Fm (19.52%) and Y(II; 67.67%)], while it substantially increased Cd accumulation along with an increase in ROS (79.09%) and lipid peroxidation (129.28%). However, such adverse effects of Cd stress varied in different pea varieties. Exogenous application of MeJA increased the activity of a battery of antioxidant enzymes [superoxide dismutase (33.68%), peroxidase (29.75%), and catalase (38.86%)], improved photosynthetic pigments and PSII efficiency. This led to improved growth of pea varieties under Cd stress, such as increased fresh and dry weights of shoots and roots. In addition, improvement in root biomass by MeJA was more significant than that of shoot biomass. Thus, the mitigating effect of MeJA was attributed to its role in cellular redox balance and photosynthetic machinery of pea plants when exposed to Cd stress.

Histological and proteome analyses of Microbacterium foliorum-mediated decrease in arsenic toxicity in Melastoma malabathricum

Arsenic (As) is an increasing threat across the globe, widely known as a non-threshold carcinogen, and it is reaching harmful values in several areas of the world. In this study, the effect of plant growth promoting bacteria (Microbacterium foliorum) on inorganic arsenic (Arsenate) phytoremediation by Melastoma malabathricum plants was investigated through histological analysis and proteome profiling of the M. malabathricum plants. Two-dimensional gel electrophoresis and transmission electron microscopy were used to conduct the proteome and histological analysis. When arsenic-treated cells were compared to untreated cells, substantial changes were found (1) severely altered the morphology of the cells, intensely disturbed; (2) the cell wall was thicker; (3) drastically changed the cytoplasm, the cells were polygonal in shape, different in size (scattered), and relatively dense. Compared to the control group, the ultra-structure of the root cells of the control group revealed intact cytoplasm, vacuole, and cell wall under exposure to As + bacteria that had a minor effect on the cell form. To further understand As + bacteria interaction, proteome profiling of the root cell was analyzed. The As-induced oxidative stress enrichment was confirmed by the up-regulation of tubulin, nucleoside diphosphate kinase, and major allergen during As + bacteria exposure It was observed that the profusion of proteins involved in defence, protein biogenesis, signaling, photosynthesis, nucleoside and energy metabolism was greater in As + bacteria as compared to the rooting out of As only. Overall, it can be obviously seen that the current study demonstrates the effectiveness of phytoremediation by M. foliorum on proteins involved and responsive pathways in dealing with As toxicity in M. malabathricum plant.

Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L

Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.

Emerging Trends in Metalloid-Dependent Signaling in Plants

Metalloids are semiconducting elements that constitute a small group in the periodic table of elements. Their occurrence in nature either poses an environmental threat or benefit to plants. The precise mechanisms or manner of crosstalk of metalloid interference and sensing remain open questions. Standard plant nutrient solutions contain the metalloid boron (B) as a micronutrient, while silicon (Si) is considered a beneficial element routinely supplied only to some plants such as grasses. By contrast, arsenic (As) is a severe environmental hazard to most organisms, including plants, while the less abundant metalloids germanium (Ge), antimony (Sb), and tellurium (Te) display variable degrees of toxicity. Here we review the molecular events and mechanisms that could explain the contrasting (or overlapping) action of metalloids on the cell and cell signaling.

Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China

Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality.

Melatonin induced changes in photosynthetic efficiency as probed by OJIP associated with improved chromium stress tolerance in canola (Brassica napus L.)

Chromium toxicity is considered as a major problem for agricultural soil that reduced crop productivity by affecting photosynthetic tissues. Exogenous application of melatonin can alleviate the adverse effects of chromium toxicity on plant growth. However, little is known about its effect on thylakoidal protein complexes responsible for conversion of solar energy to biochemical energy. Chlorophyll fluorescence a transients considered one of the best non-invasive and rapid method for the evaluation of photosynthetic (Photosystem II) efficiency of plants and plant health under environmental stress conditions. In the present study, three-week old plants of two canola cultivars AC-Excel and DGL were applied to melatonin (0, 1, 5, 10 μM) when grown under chromium stress (0, 50 and 100 μM) for further two weeks. Chromium stress reduced the growth (fresh and dry weights of shoots and roots) of both canola cultivars and exogenous application of 5 and 10 μM melatonin improved the growth of canola at 50 or 100 μM chromium stress. This improvement was greater in cv DGL than in AC-Excel. Increasing chromium decreased the photosynthetic pigments (chlorophyll a and chlorophyll b). However, 5 and 10 μM melatonin application improved chlorophyll a at 50 μM chromium stress. Structural stability and efficiency of photosystem II (PSII) measured as performance index (PI_ABS) and ratios of fluorescence (Fv/Fm, Fv/Fo) Fv decreased due to chromium stress. JIP-test parameters showed that chromium stress increased the absorption and trapping fluxes with decrease in electron transport fluxes which caused the damage to reaction centers (RC), detachment of oxygen evolving complex (OEC) from RC or inefficiency of electron transfer from OEC to RC. Such adverse effects were greater in cv AC-Excel. However exogenous application of melatonin improved PI_ABS, electron transport per reaction center (ET/RC), reduced variable fluorescence at J step (V_J) reflecting melatonin protected PSII from chromium stress induced damage by protecting OEC. Thus, OJIP fluorescence transients are quite helpful for understanding the intersystem electron transport beyond photosystem II in canola cultivars due to melatonin application under chromium stress.

Findings

Exogenous application of melatonin alleviated toxic effects of chromium on plant growth of canola by modulating photosynthesis, enhanced photosystem II efficiency and regulation of electron transport flux to protect photo-inhibition of PSII from oxidative damage.

CRISPR/Cas9-Mediated SlMYC2 Mutagenesis Adverse to Tomato Plant Growth and MeJA-Induced Fruit Resistance to Botrytis cinerea

Methyl jasmonate (MeJA), a natural phytohormone, played a critical role not only in plant growth but also in plant defense response to biotic and abiotic stresses. MYC2, a basic helix-loop-helix transcription factor, is a master regulator in MeJA signaling pathway. In the present work, slmyc2 mutants were generated by the clustered regularly interspaced short palindromic repeats and associated Cas9 protein (CRISPR/Cas9) system to investigate the role of SlMYC2 in tomato plant growth and fruit disease resistance induced by exogenous MeJA. The results showed that slmyc2 mutants possessed a higher number of flowers and a lower fruit setting rate in comparison with wild-type plants. In addition, the fruit shape of slmyc2 mutant was prolate, while the control fruits were oblate. Knockout of SlMYC2 significantly decreased the activities of disease defensive and antioxidant enzymes, as well as the expression levels of pathogen-related (PR) genes (SlPR-1 and SlPR-STH2) and the key genes related to jasmonic acid (JA) biosynthesis and signaling pathway including allene oxide cyclase (SlAOC), lipoxygenase D (SlLOXD), SlMYC2, and coronatine insensitive 1 (SlCOI1), and consequently aggravated the disease symptoms. By contrast, the disease symptoms were largely reduced in MeJA-treated fruit that possessed higher activities of these enzymes and expression levels of genes. However, the induction effects of MeJA on fruit disease resistance and these enzymes' activities and genes' expressions were significantly attenuated by knockout of SlMYC2. Therefore, the results indicated that SlMYC2 played positive regulatory roles not only in the growth of tomato plants but also in MeJA-induced disease resistance and the antioxidant process in tomato fruits.

iTRAQ-Based Quantitative Proteomic Analysis of the Arabidopsis Mutant opr3-1 in Response to Exogenous MeJA

Jasmonates (JAs) regulate the defense of biotic and abiotic stresses, growth, development, and many other important biological processes in plants. The comprehensive proteomic profiling of plants under JAs treatment provides insights into the regulation mechanism of JAs. Isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic analysis was performed on the Arabidopsis wild type (Ws) and JA synthesis deficiency mutant opr3-1. The effects of exogenous MeJA treatment on the proteome of opr3-1, which lacks endogenous JAs, were investigated. A total of 3683 proteins were identified and 126 proteins were differentially regulated between different genotypes and treatment groups. The functional classification of these differentially regulated proteins showed that they were involved in metabolic processes, responses to abiotic stress or biotic stress, the defense against pathogens and wounds, photosynthesis, protein synthesis, and developmental processes. Exogenous MeJA treatment induced the up-regulation of a large number of defense-related proteins and photosynthesis-related proteins, it also induced the down-regulation of many ribosomal proteins in opr3-1. These results were further verified by a quantitative real-time PCR (qRT-PCR) analysis of 15 selected genes. Our research provides the basis for further understanding the molecular mechanism of JAs’ regulation of plant defense, photosynthesis, protein synthesis, and development.

Jasmonic acid application triggers detoxification of lead (Pb) toxicity in tomato through the modifications of secondary metabolites and gene expression

Jasmonic acid (JA) is an important phytohormone associated in defense responses against stress. Crop plants experience heavy metal toxicity and needs to be explored to enhance the crop production. Lead (Pb) is one of the dangerous heavy metal that pollutes soil and water bodies and is released from various sources like discharge from batteries, automobile exhaust, and paints. The present study was designed to evaluate the role of JA (100 nM) on photosynthetic pigments, secondary metabolites, organic acids, and metal ligation compounds in tomato seedlings under different concentrations of Pb (0.25, 0.50, and 0.75 mM). It was observed that Pb treatment declined pigment content, relative water content, and heavy metal tolerance index. Expression of chlorophyllase was also enhanced in Pb-treated seedlings. Seeds primed with JA lowered the expression of chlorophyllase under Pb stress. JA application enhanced the contents of secondary metabolites (total phenols, polyphenols, flavonoids, and anthocyanin) which were confirmed with enhanced expression of chalcone synthase and phenylalanine ammonia lyase in Pb-exposed seedlings. Treatment of JA further elevated the levels of organic acids and metal chelating compounds under Pb toxicity. JA up-regulated the expression of succinate dehydrogenase and fumarate hydratase in Pb-exposed seedlings. Results revealed that seeds primed with JA reduced Pb toxicity by elevating, the levels of photosynthetic pigments, secondary metabolites, osmolytes, metal ligation compounds, organic acids, and polyamine accumulation in tomato seedlings.

Jasmonic acid induced changes in physio-biochemical attributes and ascorbate-glutathione pathway in Lycopersicon esculentum under lead stress at different growth stages

Lead (Pb) is one of most toxic heavy metals that adversely affect growth and developmental in plants. It becomes necessary to explore environment safe strategies to ameliorate its toxic effects. Phytohormones play an imperative role in regulating stress protection in plants. Jasmonic acid (JA) is recognized as a potential phytohormone which mediates immune and growth responses to enhance plant survival under stressful environment. The present study was undertaken to evaluate the effect of JA on the growth, metal uptake, gaseous exchange parameters, and on the contents of pigments, osmolytes, and metal chelating compounds in tomato plants under Pb stress during different stages of growth (in 30-, 45-, and 60-day-old plants). We observed a decrease in shoot and root lengths under Pb stress. Treatment of JA improved the shoot and root lengths in the Pb-treated plants. The Pb uptake was increased with the increasing concentrations of Pb, however, seeds pretreated with JA reduced the Pb uptake by the plants. The chlorophyll and carotenoid contents increased by JA treatment in plants under Pb stress. Pre-soaking of seeds in JA, improved gaseous exchange parameters, such as internal CO₂ concentration, net photosynthetic rate, stomatal conductance, and transpiration rate under Pb stress. JA enhanced the enzyme activity of ascorbate-glutathione cycle and reduced H₂O₂ concentration in Pb-treated plants. The contents of osmolyte and metal chelating compounds (total thiols, and non-protein and protein-bound thiols) were increased with the increase in Pb stress. In seeds primed with JA, the contents of osmolytes and metal chelating compounds were further increased in the Pb-treated plants. Our results suggested that treatment of JA ameliorated the toxic effects of Pb stress by reducing the Pb uptake and improving the growth, photosynthetic attributes, activity of ascorbate-glutathione cycle and increasing the contents of osmolytes and metal chelating compounds in the tomato plants.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.