Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.

/pdf/applications-of-multi-omics-technologies-for-crop-lk15haqwqe.pdf

Applications of Multi-Omics Technologies for Crop Improvement.

Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest. The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca2+ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened. The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.

/pdf/swift-metabolite-changes-and-leaf-shedding-are-milestones-in-103rqd3kl3.pdf

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress

In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants

/pdf/reverse-genetics-and-high-throughput-sequencing-2cqm3w7uf9.pdf

Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

Environmental abiotic stresses limit plant growth, development, and reproduction. This study aims to reveal the response of Brassica napus to salt stress. Here, transcriptomics, metabolomics, and proteomics analysis were performed on 15 Brassica napus leave samples treated with salt at different times. Through functional enrichment analyzing the differentially expressed genes (DEGs), differential metabolites (DMs) and differentially expressed proteins (DEPs), the key factors that dominate Brassica napus response to salt stress were identified. The results showed that the two key hormones responding to salt stress were Abscisic acid (ABA) and jasmonic acid (JA). Salt stress for 24h is an important milestone. Brassica napus adjusted multiple pathways at 24h to avoid over-response to salt stress and cause energy consumption. The increased expression in BnPP2C is tangible evidence. In response to salt stress, JA and ABA work together to reduce the damage caused by salt stress in Brassica napus. The increased expression of all BnJAZs after salt stress highlighted the function of JA that cannot be ignored responding to salt stress. In addition, some metabolites, such as N-acetyl-5-hydroxytryptamine, L-Cysteine and L-(+)-Arginine, play a critical role in maintaining the balance of ROS. Proteins like catalase-3, cysteine desulfurase, HSP90 and P450_97A3 were the most critical differential proteins in response to salt stress. These findings of this study provide data support for Brassica napus breeding.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0262587&type=printable

Transcriptomic, proteomic, metabolomic, and functional genomic approaches of Brassica napus L. during salt stress

The transition from a green, hard, and acidic pericarp to a sweet, soft, coloured, and sugar-rich ripe fruit occurs in many unrelated fruit species. High throughput identification of differentially expressed genes in grape berry has been achieved by the use of 50-mers oligoarrays bearing a set of 3,200 Unigenes from Vitis vinifera to compare berry transcriptome at nine developmental stages. Analysis of transcript profiles revealed that most activations were triggered simultaneously with softening, occurring within only 24 h for an individual berry, just before any change in colouration or water, sugar, and acid content can be detected. Although most dramatically induced genes belong to unknown functional categories, numerous changes occur in the expression of isogenes involved in primary and secondary metabolism during ripening. Focusing on isogenes potentially significant in development regulation (hormonal control of transcription factor) revealed a possible role for several hormones (cytokinin, gibberellin, or jasmonic acid). Transcription factor analysis revealed the induction of RAP2 and WRKY genes at véraison, suggesting increasing biotic and abiotic stress conditions during ripening. This observation was strengthened by an increased expression of multiple transcripts involved in sugar metabolism and also described as induced in other plant organs during stress conditions. This approach permitted the identification of new isogenes as possible control points: a glutathione S-transferase exhibits the same expression profile as anthocyanin accumulation and a new putative sugar transporter is induced in parallel with sugar import.

Isogene specific oligoarrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development

The ability of plants to modify their behavior appropriately in response to salt stress is a major factor in their adaptation to this specific constraint To date, environmental constraints, including salinity, become more and more unfavorable especially for glycophytes such as grapevines Salt tolerance is a complex physiological and multigenic trait Studying the functional networks of transcriptome, proteome and metabolome of grapevine plants subjected to salinity may help to identify candidate genes associated with salt tolerance mechanisms Thus, the integration of omics tools (ie, genomics, proteomics and metabolomics) with physiological approaches allows better understanding of the grapevine plant response and developing efficient markerassisted selection strategies in order to generate salt stress resistant grapevine varieties In this review, research progress in grapevine responses to salt stress is discussed, highlighting the importance of the system biology approach for identifying molecular regulatory networks leading to a better adaptation ability of grapevine to salt stress

/pdf/integration-of-omics-and-system-biology-approaches-to-study-5cv9wb4qt9.pdf

Integration of omics and system biology approaches to study grapevine ( Vitis vinifera L.) response to salt stress: a perspective for functional genomics - A review

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Integration of omics and system biology approaches to study grapevine ( Vitis vinifera L.) response to salt stress: a perspective for functional genomics - A review