Omics in Major Cereals: Applications, Challenges, and Prospects

Abstract

Omics technologies, viz., genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal breeding program because they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in cereal-omics promise—in combination with time efficiency—the cost benefits. In this review, we provide a comprehensive overview of the established cereal-omics methods in five major cereals, viz., rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants, (2) high-density transcriptomics data to study gene expression patterns, (3) global and targeted proteome profiling to study protein structure and interaction, (4) metabolomic profiling to quantify organ level small-density metabolites and their composition, and (5) high-resolution high-throughput image-based phenomics approaches are surveyed in this review.

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

“…These results suggest that the SA, 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. Thus, transcriptomic analysis has become central in abiotic and biotic stress tolerance studies (Li et al, 2019;Kaur et al, 2021; Table 3), and genes and metabolic pathways identified in these studies can be used as targets in marker assisted breeding programs. With the large amount of data that has been generated and deposited into various public repositories, it is now possible to conduct meta-analysis of transcriptomic responses to abiotic and biotic stresses.…”

“…Thus, GWAS improves the mapping resolution for accurate location of allele/QTL/genes underlying key agronomic traits ( Huang and Han, 2014 ; Pang et al, 2020 ). Unsurprising, large-scale GWAS has become a powerful tool for performing efficient genome-phenotype association analysis and identification of causative QTL/genes for key agronomic traits in diverse crop species ( Sun et al, 2017 ; Jha et al, 2020 ; Berhe et al, 2021 ; Kaur et al, 2021 ; Sinha et al, 2021 ). For instance, using a natural population comprising 713 upland cotton accessions, Sun et al (2018) discovered a total of 10 and 15 SNPs that were significantly associated with relative survival rate and salt tolerance level, respectively, among which two SNPs (i46598Gh and i47388Gh) on genomic region D09 were simultaneously linked with the two traits.…”

“…Different genetic populations have been exploited to identify thousands of QTLs for several agronomic traits, especially recombinant inbred lines, because of their simple development, balanced parental mixture, repeated phenotyping, and relatively high mapping power ( Liang et al, 2021a ). Other mapping population types include introgression lines, advanced backcross populations, F2 populations, double-haploid populations, and backcross populations (reviewed in Kaur et al, 2021 ; Zenda et al, 2021 ).…”

“…Direct infusion mass spectrometry (DIMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) are specialized techniques normally used in direct infusion mode for metabolomics analyses since their high mass accuracy permits for separation to be achieved entirely based on this parameter ( Fraire-Velázquez and Balderas-Hernández, 2013 ; Villate et al, 2021 ). Applicability and limitations of these metabolomics methods and techniques have been extensively discussed in previous articles ( Allwood et al, 2011 ; Razzaq et al, 2019 ; Hamany Djande et al, 2020 ; Kaur et al, 2021 ).…”

Transcriptome Reprogramming of Tomato Orchestrate the Hormone Signaling Network of Systemic Resistance Induced by Chaetomium globosum

“…The mRNA enrichment was performed by using poly-T attached magnetic beads, followed by enzymatic fragmentation. The paired-end (PE) sequencing libraries were prepared by using the Illumina TrueSeq stranded mRNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA) (Kaur et al, 2021). The purification of ds cDNA samples was performed by using Ampure XP beads, followed by A-tailing, adapter ligation, and further enrichment by PCR.…”