Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Abstract

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the “omics” technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

Integrated Metabolomic and Transcriptomic Analyses Reveal Novel Insights of Anthocyanin Biosynthesis on Color Formation in Cassava Tuberous Roots

“…With the availability of cassava genome, the members derived from a gene family or involved in a biological pathway are identified ( 31 ). However, it is still hard to systematically determine the key players without an assistance of other omics approaches (e.g., transcriptome and metabolome), which define a biosystem at distinct molecular layers ( 32 ). Multi-omics studies have been performed to identify candidate genes and pathways controlling pigment accumulation in many plants ( 13 , 15 , 16 ).…”

Reproductive-Stage Heat Stress in Cereals: Impact, Plant Responses and Strategies for Tolerance Improvement

“…Over the past decade, flourishing development in omics technologies has revolutionized the way plant biologists dissect diverse mechanisms underlying plant tolerance to different environmental stresses [189]. These omics (see Box 1) approaches have necessitated the identification of key differentially expressed genes (DEGs), proteins (DEPs) and metabolites (DEMs) underpinning plant biotic and abiotic stress tolerance, using contrasting (tolerant and sensitive) genotypes in comparative transcriptomic, proteomic and metabolomic studies, respectively [130,189]. With regard to HS tolerance, comparative transcriptomics [190] and proteomics [191,192] analyses have revealed HS-responsive genes and proteins, as well as mechanisms regulating thermotolerance at the R stage in cereals.…”

“…Therefore, more studies targeting the R stages are needed to provide much insight into RSHS response in cereals. Fortunately, we can now leverage omics technologies to perform comparative analyses of different crop genotypes' responses to HS and identify key candidate genes or proteins underpinning those responses [189].…”

Transcriptomic and Metabolomic Analysis of Seedling-Stage Soybean Responses to PEG-Simulated Drought Stress

“…In general, omics technology, which includes genomics, transcriptomics, proteomics, and metabolomics, is utilized for further molecular research, allowing for a better understanding of the gene, protein, and metabolite activities in plant responses to abiotic stress. These methods are critical for identifying crucial genes, proteins, and metabolic pathways that underpin many important agronomic features and for marker-assisted crop breeding [ 18 ].…”