Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops

Abstract

Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

“…Moreover, it turned out that the beneficial effects of biochar amendments could be evaluated by measuring the parameters used for monitoring water shortage and nutrient deprivation stress [123]. In summary, biochar primarily improves the reliability of water and nutrient supply, which allows plants to grow efficiently, while the window of stress resistance remains narrow [125]. Additional recent research indicated that the positive effect of biochar is not restricted to the water and nutrient supply to plant roots, but extends to soil microorganisms, as well [121,126].…”

A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises

“…CRISPR/Cas9 has been used to modify any sequence and to bring any character to crops. Molecular breeders discovered many genes related to abiotic stress tolerance and engineered them into crops [180]. CRISPR/Cas9 generated slmapk3 protein gene mutants improved defense response to drought stress in tomatoes [181].…”

“…These studies indicate that the CRISPR/Cas9 technique has enormous potential for developing climate-adapted crops. The above studies showed that Cas9 could alter genes to facilitate resistance against many abiotic stresses, e.g., drought, high temperatures, heavy metals, as well as nutrient deficiencies [180]. A list of climate-smart crops is shown in Table 6.…”

An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics

“…The process of gene regulatory dynamism in various cellular, physiological and biochemical mechanisms in plants was altered by environmental factors. Therefore, to analyze the processes involved in this regulatory mechanism, several functional omics projects, have been initiated across the world in recent years [ 49 , 73 , 74 ]. Moreover, multiple omics and bioinformatics approaches have been used for developing crop plants that are tolerant to AbS through molecular breeding and genetic engineering and also through advancements and increasing knowledge in genetics, genomics, and molecular physiology [ 75 , 76 ].…”