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

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

Plant Cell Rep. 2024 Feb 27;43(3):80. doi: 10.1007/s00299-024-03153-7.

Authors

Affiliations

¹ Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
² Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy.
³ Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan.
⁴ Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
⁵ Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
⁶ State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China.
⁷ WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
⁸ Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India.
⁹ Department of Bio-Resources, Amar Singh College Campus, Cluster University Srinagar, Srinagar, JK, India.
¹⁰ Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
¹¹ Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Srinagar, Kashmir, India.
¹² The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia. kadambot.siddique@uwa.edu.au.
¹³ WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia. rajeev.varshney@murdoch.edu.au.

Abstract

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.

Keywords: Artificial intelligence; Bioinformatic tools; Climate change; Defense responses; Environmental pollution; Metal toxicity; Omics approaches.

Publication types

Review

MeSH terms

Artificial Intelligence
Ecosystem*
Gene Expression Profiling
Metals / toxicity
Proteomics*
Soil

Substances

Metals
Soil

Grants and funding

XXXX/Murdoch University