Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Ali Raza; Hajar Salehi; Shanza Bashir; Javaria Tabassum; Monica Jamla; Sidra Charagh; Rutwik Barmukh; Rakeeb Ahmad Mir; Basharat Ahmad Bhat; Muhammad Arshad Javed; Dong-Xing Guan; Reyazul Rouf Mir; Kadambot H M Siddique; Rajeev K Varshney

doi:10.1007/s00299-024-03153-7

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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Journal article

Open access

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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Ali Raza, Hajar Salehi, Shanza Bashir, Javaria Tabassum, Monica Jamla, Sidra Charagh, Rutwik Barmukh, Rakeeb Ahmad Mir, Basharat Ahmad Bhat, Muhammad Arshad Javed, …

Plant cell reports, Vol.43(3), 80

2024

DOI: https://doi.org/10.1007/s00299-024-03153-7

PMID: 38411713

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Abstract

Artificial Intelligence

Ecosystem

Gene Expression Profiling

Metals - toxicity

Proteomics

Soil

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

Details

Title: Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity
Authors/Creators: Ali Raza - Oil Crops Research Institute
Hajar Salehi - Università Cattolica del Sacro Cuore
Shanza Bashir - National University of Sciences and Technology
Javaria Tabassum - University of the Punjab
Monica Jamla - Savitribai Phule Pune University
Sidra Charagh - Chinese Academy of Agricultural Sciences
Rutwik Barmukh - Murdoch University, Centre for Crop and Food Innovation
Rakeeb Ahmad Mir - Central University of Kashmir
Basharat Ahmad Bhat - Cluster University Srinagar
Muhammad Arshad Javed - University of the Punjab
Dong-Xing Guan - Zhejiang University
Reyazul Rouf Mir - Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir
Kadambot H M Siddique - The University of Western Australia
Rajeev K Varshney - Murdoch University, Food Futures Institute
Publication Details: Plant cell reports, Vol.43(3), 80
Publisher: Springer
Grant note: XXXX / Murdoch University
Identifiers: 991005641569807891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.91 Contamination & Phytoremediation; 3.91.172 Phytoremediation Mechanisms
Web Of Science research areas: Plant Sciences
ESI research areas: Plant & Animal Science