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

Abstract

The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the ‘omics’ toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant’s genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence ‘multi-omics’) integrated-omics approaches can decipher the plant’s abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop’s variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

Plant biomarkers as early detection tools in stress management in food crops: a review

“…In recent years, omic technologies have provided a more holistic understanding and aided in identifying plant biomarkers indicative of stress conditions. These include techniques such as genomics to identify significant stress-associated genes, proteomics to study variations in protein abundance relative to induced stress, metabolomics to study variations in cellular metabolites in response to stress, and transcriptomics to analyze gene expression patterns (Roychowdhury et al 2023 ). Furthermore, the advancement of next-generation sequence approaches such as microarrays, RNA sequencing, and single-molecule real-time sequencing have provided high-throughput, sensitive and rapid methods of generating data from omic techniques (Saeed et al 2022 ; Udawat 2023 ).…”

Unravelling Abiotic Stress Physiology in Cotton (Gossypium hirsutum L.): Biotechnological Interventions in Mitigating Abiotic Stress

“…Including signal perception, transduction cascades, activation of transcription factors, gene expression or modulation, and synthesis of functional proteins. Also, enzymes, osmolyte production, antioxidant defense against reactive oxygen species (ROS), and adjustments to biochemical, physiological, and cellular processes [238][239][240][241][242][243][244]. This section explores how altering the expression of single genes via transgenic methods can enhance plant performance under primary abiotic stress conditions.…”

Genetic Diversity and Population Structure of Maize (Zea mays L.) Inbred Lines in Association with Phenotypic and Grain Qualitative Traits Using SSR Genotyping

“…However, such traits are heavily influenced by environmental interaction. To overcome such limitations, DNA-based markers are introduced to identify cultivars and accelerate breeding programs through early selection of maize lines or segregants with the traits of interest [ 11 , 12 ]. A polymerase chain reaction (PCR) leveraging efficient molecular markers, particularly the simple sequence repeats (SSRs) marker, has long been pivotal in maize genetic research and breeding endeavors [ 13 , 14 , 15 ].…”