A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Abstract

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Changes in Carotenoid Concentration and Expression of Carotenoid Biosynthesis Genes in Daucus carota Taproots in Response to Increased Salinity

“…If plants suffer from inordinate amounts of salt, this will lead to various metabolic perturbations, cutback in water potential (ψw), disordered membrane potential, weaken photosynthesis and diminish nitrogen assimilation [26][27][28]. However, plants have evolved many adaptative mechanisms in response to the condition of high salinity, which involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms [29]. Among them, carotenoids are proved to respond to salt stress [30,31].…”

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

“…Organic acids can form metal–ligand complexes (Tahjib-Ul-Arif et al 2021 ; Vega et al 2022 ) at the root surface or in the cytosol that prevent metal(loid)s from entering vital cellular pathways. Several studies have reported the synthesis and release of low molecular weight organic acids, such as acetic acid and succinate, by roots as an effective strategy for Cd tolerance in the accumulator genotype (Mnasri et al 2015 ; Ubeynarayana et al 2021 ). For example, low-level As increased the secretion of low molecular weight organic acids like citric, oxalic, and malic acid in the rhizosphere of mangroves (Mei et al 2021 ).…”

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses

“…Particularly, proteogenomics is useful for the identification of proteins by integrating genomic, transcriptomic and MS data of the same crop species and/or sample. Thus, the integrative proteogenomics approach has identified novel proteins and provided a hardcore knowledge of the genes’ regulatory expression and cell signalling for abiotic stress tolerance [ 253 ]. Proteogenomics has shed light on the mechanisms of plants’ response to abiotic stress and adaptation to changing the environment.…”