Proteomics and Metabolomics in Plant Science: Multi-Omics Innovations in Agriculture

Modern agriculture and plant science face complex challenges, from crop resilience under drought, salinity, and pathogens to improving nutritional quality and flavor. Plants respond to environmental stress through intricate changes at genetic, protein, metabolite, and phenotypic levels. Traits like flavor and development are governed by tightly regulated metabolic networks. In this context, proteomics (large-scale protein profiling) and metabolomics (comprehensive metabolite analysis) offer an integrated perspective linking regulatory mechanisms to functional outcomes. By examining both protein regulators and metabolic products, multi-omics approaches help decipher how crops orchestrate stress tolerance, growth, and quality. This holistic view is proving invaluable for crop improvement – from pinpointing stress-response pathways to identifying bioactive compounds – ultimately guiding molecular breeding, functional gene discovery, and metabolic engineering. In short, proteomics and metabolomics enable scientists to see the full picture of plant biology, bridging the gap between genotype and phenotype in order to develop hardier, healthier, and more productive crops.

Proteomics in Plant Research

Proteomics provides critical insights into how plants sense and respond to their environment at the protein level. Under stresses such as drought or high salinity, plants reprogram their proteome to activate defense proteins, antioxidants, and other protective enzymes. For example, proteomic analyses have identified stress-responsive proteins including transcription factors, kinase signaling proteins, heat shock proteins, and redox enzymes that help mitigate damage. In rice, drought-stressed leaves showed increased levels of defense-related proteins and ROS-scavenging enzymes (superoxide dismutase, peroxidase, etc.), indicating an active antioxidant response even as photosynthetic proteins were impaired. Advanced mass spectrometry techniques such as Tandem Mass Tag (TMT) labeling and Data-Independent Acquisition (DIA) allow high-throughput protein quantification in plant tissues. Using these tools, researchers can profile thousands of proteins in leaves, roots, or seeds in a single experiment and monitor how protein networks (e.g. hormone signaling pathways or photosynthetic complexes) adjust under different conditions. Targeted proteomics methods like Parallel Reaction Monitoring (PRM) further enable precise measurement of key proteins (for instance, specific enzymes or transcription factors). Altogether, proteomics is illuminating the molecular mechanisms of plant immunity, stress tolerance, growth and development – from uncovering pathogen resistance factors to mapping the proteome shifts during fruit ripening. These protein-level insights provide targets for genetic improvement and markers for selecting resilient or high-quality crop varieties.

Metabolomics in Plant Research

Metabolomics captures the chemical phenotype of plants by profiling a broad array of metabolites – from primary metabolites (sugars, amino acids, organic acids) essential to growth, to secondary metabolites (flavonoids, alkaloids, terpenoids, etc.) involved in defense, flavor, and other specialized functions. Plant metabolomics has become a powerful tool to understand flavor and nutritional quality, as well as the plant’s adaptive responses. For example, the taste of tomato fruits is determined by the balance of sugars (glucose, fructose) and organic acids (citrate, malate, ascorbate, glutamate), alongside volatile aroma compounds. Metabolomic analyses can differentiate cultivars with sweeter versus more acidic fruits based on their sugar/acid profiles, guiding flavor improvement efforts. Likewise, metabolomics helps identify health-promoting phytochemicals: e.g. high-throughput profiling can reveal which varieties of berries or vegetables accumulate unique antioxidants or vitamins. In crop stress research, metabolomics provides key “output” data on what protective compounds accumulate – for instance, osmoprotectants like proline or polyols under drought, or flavonoids that quench excess ROS under UV stress. Both untargeted metabolomics (global screening for hundreds of metabolites via LC-MS or NMR) and targeted metabolomics (quantification of specific metabolite classes such as phytohormones, amino acids, or carotenoid) are employed. Untargeted studies enable discovery of novel or unexpected metabolite changes, while targeted assays precisely measure known signaling molecules like abscisic acid (ABA) or secondary metabolites of interest. Importantly, advances in high-resolution MS and expanded plant metabolite libraries now allow detection of thousands of metabolites in a single run, offering an unprecedented view of the plant’s chemical state. By linking these metabolic readouts to genotypes or treatments, researchers can uncover pathways of nutrient accumulation, flavor biosynthesis, and stress mitigation – information that can be harnessed to breed crops with better nutritional and sensory qualities or greater environmental resilience.

Why Multi-Omics in Agriculture?

Single-omics offers fragments; integrating proteomics + metabolomics connects molecular causes to biochemical effects. Proteomics pinpoints regulators—enzymes, transporters, signaling hubs—while metabolomics reads out phenotype-defining metabolites (energy status, osmotic balance, defense compounds). Joint analysis maps full response chains (e.g., drought-induced TF → pathway enzymes → osmoprotectants) and highlights cross-omics “hub” nodes via co-expression and network modeling. The result is more robust biomarkers and selection indices than either layer alone. In breeding, multi-omics profiles enable early, data-driven screening for stress tolerance, yield stability, and quality, reducing cycle time and field dependency. For systems and synthetic biology, integrated datasets reveal bottlenecks and control points to rationally engineer pathways—whether for flavonoid enrichment, nutrient fortification, or stress hardening. Practically, multi-omics turns complex traits into measurable signatures and manipulable modules, accelerating crop improvement programs and de-risking decisions from discovery to pre-breeding and line advancement.

Applications and Case Studies in Plant Omics Research

To illustrate the power of proteomics and metabolomics in agriculture, here we highlight five application areas with recent multi-omics case studies that demonstrate real-world impacts. Each case underscores how an integrated omics approach has provided actionable insights – from unraveling stress defense mechanisms to guiding breeding and bioengineering of crops.

Crop Stress Response (Abiotic & Biotic): MYB-Driven Flavonoid Defense Under Drought

Drought and salinity rapidly elevate reactive oxygen species (ROS), damaging membranes and photosystems. An integrated proteomics–metabolomics study in Chinese chive pinpointed AtuMYB306 as a central drought-responsive regulator that transcriptionally activates flavonoid biosynthesis. Proteome data showed higher levels of key enzymes (e.g., 4CL, F3H, F3′H), while metabolomics confirmed a coordinated surge of antioxidant flavonoids that quench ROS and stabilize cellular homeostasis. Functional validation in Arabidopsis demonstrated that overexpressing AtuMYB306 increases flavonoid accumulation and significantly improves osmotic/drought tolerance—clear evidence that tuning this network converts stress cues into a protective chemical phenotype. Mechanistically, AtuMYB306 binds promoters of flavonoid-pathway genes to drive flux toward ROS-scavenging metabolites, providing a tractable axis for breeding or engineering stress-hardy crops. For programs targeting resilience, this multi-omics signature—upstream MYB activation, enzyme induction, and downstream flavonoid build-up—offers measurable markers for early selection and a rational route to bolster antioxidant capacity without compromising growth. These findings illustrate how integrated omics links regulatory proteins to defense metabolites, turning complex stress responses into actionable, trait-level levers for crop improvement.

Figure 1. Drought-induced AtuMYB306 activates flavonoid biosynthesis to scavenge ROS

Source: Li T, Wang Z, Chen Y, et al. Plant Stress. 2024;14:100591. Proposed mechanism figure (e.g., Fig. 9G). DOI: 10.1016/j.stress.2024.100591.

Nutritional & Flavor Quality Analysis: Metabolomic Fingerprints Differentiate Sugar–Acid Balance in Tomato

Metabolomics explains why tomatoes taste sweet, tart, or balanced. A survey of Greek tomato germplasm profiled non-volatile/volatile metabolites alongside transcriptomes and postharvest traits. Sweet-leaning accessions accumulated more sugars; tart genotypes showed higher citric/malic acid, while volatiles and phenolics modulated aroma and antioxidant value. Integrating omics with shelf-life revealed that long-shelf-life (LSL) types favored ABA catabolism and polyamine flux, whereas short-shelf-life (SSL) lines upregulated ethylene biosynthesis—molecular levers that align with slower softening and lower decay in LSL fruit. Practically, breeders can screen lines using metabolite “fingerprints” (sugar–acid ratio, key volatiles, carotenoids) and pathway markers (ABA/ethylene nodes) to select flavor and storability together, cutting cycle time versus sensory-only selection. This provides actionable quality markers for early-stage triage and supports simultaneous improvement of taste, nutrition, and shelf stability.

Figure 2. Ethylene/ABA pathway shifts underlying shelf-life divergence (SSL vs. LSL)

Source: Figure 5 in Mellidou I, Kanellis AK, et al. Front Plant Sci. 2023;14:1267340.

Plant Development & Growth Regulation: ABA–GA–Ethylene Crosstalk Drives Seed Dormancy Release

Dormancy release hinges on hormone rebalancing and metabolic readiness. In Paris polyphylla, widely-targeted metabolomics and transcriptomics showed sharp ABA decline with rising bioactive 13-hydroxylated GA₄, alongside increased lyso-phospholipids and PLA₂ expression—signals of membrane remodeling and energy mobilization. Network analysis indicated that ethylene counters ABA while promoting GA pathways, tipping seeds toward germination. The joint omics readout links enzyme transcripts (CYP707A, GA20ox/GA3ox, UGTs) to measured hormone pools, clarifying sequence and directionality. For seed technologies and nursery operations, these markers guide treatment choices (e.g., GA type/dose) and identify candidate regulators for uniform germination. The proposed model—ABA conjugation, selective GA biosynthesis, and ethylene facilitation—offers concrete levers to manipulate dormancy in medicinal and crop species.

Figure 3. Model of hormone–lipid reprogramming during dormancy breaking

Source: Figure 6 in Zheng G, Li W, Xu F, et al. BMC Plant Biol. 2023;23:247.

Crop Improvement & Trait Selection: Multi-Omics Markers for Drought-Tolerant Rice

Root-tip metabolomics in contrasting rice genotypes (tolerant Azucena vs. sensitive IR64) revealed distinct stress chemistries and performance. Under drought, Azucena expanded root length/surface and accumulated compatible solutes and antioxidants (e.g., trehalose, mannitol, proline), while pathway enrichment highlighted purine metabolism and TCA cycle activity; markers such as allantoin, galactaric and gluconic acids correlated with drought traits. These metabolite signatures, coupled with morphological metrics, enable early selection without multi-season field screens. Deployed as a targeted panel, they flag resilient root chemotypes and suggest engineering targets (e.g., purine→allantoin flux). Integrating proteome or transcript proxies can further stabilize predictive indices across environments, turning below-ground resilience into measurable, lab-screenable endpoints for breeding pipelines.

Figure 4. PCA/PLS-DA of root-tip metabolomes under drought vs. control

Source: Figure 1A–B in Ghorbanzadeh Z, Hamid R, Jacob F, et al. BMC Genomics. 2023;24:152.

Metabolic Engineering & Synthetic Biology: Rewiring Flavonoid Biosynthesis via MYB Activation

Mapping regulatory control points enables rational pathway design. In Chinese chive, multi-omics prioritized AtuMYB306 as a central flavonoid regulator. Functional assays in Arabidopsis confirmed that overexpression elevates key enzymes (4CL, F3H, F3′H), boosts flavonoid accumulation, and improves osmotic/drought tolerance—establishing a transferable control knob for antioxidant flux. ChIP/activation evidence shows direct promoter binding and transcriptional activation, providing a clean handle for stacking strategies or promoter engineering. For bioactive enrichment or stress-hardening, MYB-guided modules offer predictable gains while omics monitoring guards against off-target trade-offs. This closes the loop from discovery to design-build-test, illustrating how regulatory TFs can reconstruct a target metabolome in planta.

Figure 5. AtuMYB306 directly binds and activates flavonoid-pathway genes

Source: Figure 8 in Li T, Wang Z, Chen Y, et al. Plant Stress. 2024;14:100591.

Plant Omics Services for Crop Improvement

From illuminating stress-response networks to accelerating trait improvement, proteomics and metabolomics are transforming plant science and crop development. The case studies above show how a multi-omics strategy delivers breakthroughs—whether uncovering a drought-protective flavonoid circuit in maize or decoding flavor chemistry in tomatoes—and ultimately enables smarter, more resilient agriculture under climate and market pressures. If you’re ready to apply these approaches to your research or breeding program, our team can help you design and execute a fit-for-purpose workflow. Get in touch to leverage multi-omics for your project’s success.

Unlock stress resilience, flavor, and nutrition with an integrated omics workflow tailored to plant tissues and complex matrices.

Widely-Targeted Plant Metabolomics (LC–MS/MS): Large-scale profiling across primary and secondary metabolites (sugars, organic acids, flavonoids, alkaloids, terpenoids). Curated plant libraries enable confident IDs and pathway coverage for discovery and benchmarking.

Targeted Plant Panels:

• Phytohormones (ABA, IAA, GA, CKs, SA/JA): quantitative tracking of signaling dynamics across tissues and time points.
• Carotenoids (β-carotene, lutein, zeaxanthin, etc.): precise quantification for nutrition, color, and photoprotection traits.

DIA Proteomics for Plants: Deep, reproducible protein quantification in leaves, roots, seeds, and fruits; robust for pigmented/polyphenol-rich matrices. Optional PRM validation for sentinel enzymes and TFs.

Integrated Analysis: KEGG/GO enrichment, protein–metabolite networks, and trait-linked signatures to prioritize candidate genes, pathways, and selection markers.

Request a Custom Omics Plan

Share your crop, tissue, and target traits. We’ll design a fit-for-purpose workflow—from sampling and LC–MS/MS method selection to DIA design and cross-omics interpretation—to deliver publication-ready results and actionable markers for breeding and metabolic engineering.

Reference

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3. Li J, Zhang H, Fan J, et al. Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return. Front Plant Sci. 2022;13:997557. doi:10.3389/fpls.2022.997557.
4. Mellidou I, Kanellis AK, et al. A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm. Front Plant Sci. 2023;14:1267340. doi:10.3389/fpls.2023.1267340.
5. Li T, Wang Z, Chen Y, et al. Multi-omics analysis reveals the transcription factor AtuMYB306 improves drought tolerance by regulating flavonoid metabolism in Chinese chive (Allium tuberosum). Plant Stress. 2024;14(4):100591. doi:10.1016/j.stress.2024.100591.
6. Ghorbanzadeh Z, Hamid R, Jacob F, et al. Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice. BMC Genomics. 2023;24(1):152. doi:10.1186/s12864-023-09246-z.
7. Zheng G, Su H, Tan Q, et al. Multiomics strategies for decoding seed dormancy breakdown in Paris polyphylla. BMC Plant Biol. 2023;23(1):247. doi:10.1186/s12870-023-04262-3.
8. Nakabayashi R, Yonekura-Sakakibara K, Urano K, et al. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of flavonoids. Plant J. 2014;77(3):367–379. doi:10.1111/tpj.12388.