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.
Highlights
Optimizing climate-change adaptation, agricultural productivity, food security and environmental protection is the grand challenge confronting scientists in this 21st century
Several ROS scavenging enzymes such as POD (TraesCS2B01G125200, TraesCS2A01G107500, etc.), SOD (TraesCS2D01G123300) and CAT (TraesCS6A01G041700), as well as mitogen-activated protein kinases (Novel11623, TraesCS4D01G198600, etc.) and WRKY TF genes (Novel00700, Novel01914, etc.) were up-regulated in response to aphid attack (Zhang Y. et al, 2020). These results suggest that the salicylic acid (SA), jasmonic acid (JA), protein phosphatases and MAPK-WRKY signaling pathways are the central metabolic pathways activated in response to aphid attack and can be targeted for aphid tolerance breeding
We have cited several relevant examples to highlight how various omics approaches have anchored the crop improvement programs. Deployment of these omics techniques, genomics, transcriptomics, proteomics, metabolomics and phenomics to study plant responses to numerous abiotic and biotic stresses has been vital in revealing several key genes, proteins and metabolic pathways underlying several quantitative and quality traits of agronomic importance in major crop species
Summary
Optimizing climate-change adaptation, agricultural productivity, food security and environmental protection is the grand challenge confronting scientists in this 21st century. Recent advances in genome sequencing techniques, coupled with omics-platforms generated data, have facilitated the availability of enormous genomic and transcriptomic data for various crop species, and have significantly improved gene discovery, gene expression profiling, marker-assisted selection, domestication of underutilized species, and introgression of unique and key traits into desired crops (Pathak et al, 2018; Muthamilarasan et al, 2019; Cortés and López-Hernández, 2021) This is permitting us to routinely delineate the molecular and genetic underpinnings to the several phenotypic traits of agricultural importance (Scossa et al, 2021). Citing some relevant examples, we appraise our knowledge on the recent progress in omics approaches and how these developments, integrated with other modern plant breeding, data analysis, and gene editing technologies, are altering the crop improvement landscape related to abiotic and biotic stress tolerance, higher nutritional quality and other key agronomic traits, thereby facilitating global food and nutrition security
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