MULTI-OMICS APPROACHES FOR IMPROVING SOIL–PLANT INTERACTIONS IN CROP PRODUCTION: A REVIEW

Abstract

The soil-plant interactions comprise one of the most complex biological systems where plant roots, soil characteristics, roots-derived metabolites and rhizosphere microbes operate to influence nutrient acquisition, growth and productivity of plants. Traditional methods involving analysis of individual parts of this system are often not sufficient to fully understand the molecular and ecological processes taking place in the soil-plant interactions. With the emergence of multi-omics technologies, such as genomics, metagenomics, transcriptomics, metatranscriptomics, proteomics, metaproteomics, metabolomics, ionomics, epigenomics and phenomics, it became possible to study the soil-plant interactions on different biological levels. By applying the mentioned technologies, it is possible to correlate the genetic potential with the gene expression, the protein activity, the metabolites produced and accumulated by the plant, elemental content of the plant as well as its phenotype. Moreover, the investigation of the plant genome-microbiome interactions would allow identifying specific microbial community and plant genes involved in the nutrient-use efficiency, root development and stress resistance. Multi-omics approaches are also applied with the help of artificial intelligence, machine learning and high-throughput phenotyping to produce predictive models for crop production. Recent large-scale field experiments conducted in B. napus have shown the feasibility of integrating host genomics, root transcriptomics, rhizosphere microbiomes and ion omics to explain the natural variation of nitrogen acquisition. However, there still exist the problems related to the cost, data integration, spatial and temporal variability, microbial annotation, standardization and field validation. The future integration of multi-omics with microbiome engineering, precision agriculture, artificial intelligence and climate-smart crop breeding may greatly facilitate the process of sustainable intensification of agricultural production. This review covers the main aspects of multi-omics technologies in improving the soil-plant interactions and crops production.