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.

Role of Plant Secondary Metabolites in Defence and Transcriptional Regulation in Response to Biotic Stress

Traditional Chinese Medicine (TCM) has been extensively used as a mainstay for treating various pathologies. Combing the pharmacology and systems biology approaches, the network pharmacology (NP) approach was developed to predict the probable mechanism underlying the therapeutic effect of TCM. However, approaches solely based on NP cannot effectively elucidate the curative mechanism in a holistic and reliable manner due to limitations in NP-based methods and complexity of TCM components. Thus, integration strategies combining NP with other approaches are increasingly being used. Since the interdisciplinary research in TCM has received much attention in the advent of the big data era of which the NP-based integration strategy is broadly used, the strategy is clearly elaborated in the present review. We summarized several NP-based integration strategies and their applications in TCM studies, including multi-omics approach, gut microbiota study, chemical information analysis, data-mining, and network toxicology study.

Integration strategy of network pharmacology in Traditional Chinese Medicine: a narrative review.

The growth and development of maize roots are closely related to drought tolerance. In order to clarify the molecular mechanisms of drought tolerance between different maize (Zea mays L.) varieties at the protein level, the isobaric tags for relative and absolute quantitation (iTRAQ) quantitative proteomics were used for the comparative analysis of protein expression in the seedling roots of the drought-tolerant Chang 7-2 and drought-sensitive TS141 maize varieties under 20% polyethylene glycol 6000 (PEG 6000)-simulated drought stress. We identified a total of 7723 differentially expressed proteins (DEPs), 1243 were significantly differentially expressed in Chang 7-2 following drought stress, 572 of which were up-regulated and 671 were down-regulated; 419 DEPs were identified in TS141, 172 of which were up-regulated and 247 were down-regulated. In Chang 7-2, the DEPs were associated with ribosome pathway, glycolysis/gluconeogenesis pathway, and amino sugar and nucleotide sugar metabolism. In TS141, the DEPs were associated with metabolic pathway, phenylpropanoid biosynthesis pathway, and starch and sucrose metabolism. Compared with TS141, the higher drought tolerance of Chang 7-2 root system was attributed to a stronger water retention capacity; the synergistic effect of antioxidant enzymes; the strengthen cell wall; the osmotic stabilization of plasma membrane proteins; the effectiveness of recycling amino acid; and an improvement in the degree of lignification. The common mechanisms of the drought stress response between the two varieties included: The promotion of enzymes in the glycolysis/gluconeogenesis pathway; cross-protection against the toxicity of aldehydes and ammonia; maintenance of the cell membrane stability. Based on the proteome sequencing information, the coding region sequences of eight DEP-related genes were analyzed at the mRNA level by quantitative real-time PCR (qRT-PCR). The findings of this study can inform the future breeding of drought-tolerant maize varieties.

https://www.mdpi.com/1422-0067/20/11/2793/pdf

Comparative Proteomics Analysis of the Seedling Root Response of Drought-sensitive and Drought-tolerant Maize Varieties to Drought Stress

Arbuscular mycorrhizal fungi (AMF) is an effective way to remove heavy metals' inhibition on plants, however, few relevant research attempts have been made to determine the contribution of AMF to the physiological and biochemical changes related to the enhanced copper tolerance of Phragmites australis under metal-stressed conditions. In this study, the effects of AMF inoculation on P. australis under different concentrations of copper stress were investigated according to the changes in the parameters related to growth and development, and photosynthetic charateristics. Then, differentially expressed proteins (DEPs) were evaluated by the Isobaric Tag for Relative and Absolute Quantification (iTRAQ) system, which could accurately quantify the DEPs by measuring peak intensities of reporter ions in tandem mass spectrometry (MS/MS) spectra. It was found that AMF inoculation may relieve the photosynthesis inhibition caused by copper stress on P. australis and thus promote growth. Proteomic analysis results showed that under copper stress, the inoculation of R. irregularis resulted in a total of 459 differently-expressed proteins (200 up-regulated and 259 down-regulated) in root buds. In addition, the photosynthetic changes caused by AMF inoculation mainly involve the up-regulated expression of transmembrane protein-pigment complexes CP43 (photosystem II) and FNR (ferredoxin-NADP+ oxidoreductase related to photosynthetic electron transport). These results indicate that AMF could effectively improve the growth and physiological activity of P. australis under copper stress, and thus provides a new direction and instructive evidence for determining the mechanisms by which AMF inoculation enhances the copper tolerance of plants.

Arbuscular mycorrhizal fungi effect growth and photosynthesis of Phragmites australis (Cav.) Trin ex. Steudel under copper stress.

KEY MESSAGE: iTRAQ based proteomic identified key proteins and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton. Somatic embryogenesis, which involves cell dedifferentiation and redifferentiation, has been used as a model system for understanding molecular events of plant embryo development in vitro. In this study, we performed comparative proteomics analysis using samples of non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryo (SE) using the isobaric tags for relative and absolute quantitation (iTRAQ) technology. In total, 5892 proteins were identified amongst the three samples. The majority of these proteins (93.4%) were found to have catalytic activity, binding activity, transporter activity or structural molecular activity. Of these proteins, 1024 and 858 were differentially expressed in NEC versus EC and EC versus SE, respectively. Compared to NEC, EC had 452 and 572 down- and up-regulated proteins, respectively, and compared to EC, SE had 647 and 221 down- and up-regulated proteins, respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that genetic information transmission, plant hormone transduction, glycolysis, fatty acid biosynthesis and metabolism, galactose metabolism were the top pathways involved in somatic embryogenesis. Our proteomics results not only confirmed our previous transcriptomic results on the role of the polyamine metabolic pathways and stress responses in cotton somatic embryogenesis, but identified key proteins important for cotton somatic embryogenesis and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton.

/pdf/itraq-based-comparative-proteomic-analysis-provides-insights-19b4xmlwd9.pdf

iTRAQ-based comparative proteomic analysis provides insights into somatic embryogenesis in Gossypium hirsutum L.

This study aimed to compare the differences in the bacterial community structure of Lycium barbarum rhizosphere and elucidate the contribution of rhizosphere bacteria to the active ingredients of L. barbarum fruit.

Elucidating the interaction of rhizosphere bacteria and environmental factors in influencing active ingredient content of Lycium barbarum fruit in China

Abstract There are few studies on denitrification related to the nitrogen cycle in Ebinur Lake wetland. This study aimed to explore the response of the diversity and composition of denitrifying bacteria to the environmental factors in wetland, so as to obtain more information about the community structure of denitrifying bacteria driven by environmental factors. Using the genes encoding nitrite reductase (nirS and nirK) as molecular markers, we analysed the seasonal changes in the diversity of denitrifying bacteria in halophyte soils by high-throughput sequencing technology. The results showed that the diversity of denitrifying bacteria was higher in July and lower in April, showing seasonal changes. The diversity index of denitrifying bacteria in rhizosphere soil was higher than that in non-rhizosphere soil. The diversity of denitrifying bacteria in the Phragmites australis rhizosphere soil was the highest. The diversity of nirK denitrifying bacteria was higher than that of nirS denitrifying bacteria, but the relative abundance was lower than that of nirS denitrifying bacteria. Three-way ANOVA showed that soil types, vegetation types and season had significant effects on the diversity of denitrifying bacteria. Furthermore, redundancy analysis indicated that nitrate was the environmental factor that significantly affected the community structure of nirS denitrifying bacteria in wetland, and electric conductivity, total nitrogen, ammonium and nitrate were the environmental factors that significantly affected the community structure of nirK denitrifying bacteria. These results provide data basis and theoretical support for the dynamic change of diversity of denitrifying bacteria in wetland.

https://www.tandfonline.com/doi/pdf/10.1080/13102818.2022.2070030?needAccess=true

Diversity of nirS and nirK denitrifying bacteria in rhizosphere and non-rhizosphere soils of halophytes in Ebinur Lake Wetland

Integrated application of transcriptomics and metabolomics provides insights into the antifungal activity of α-phenylcinnamic acid against Colletotrichum gloeosporioides

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iTRAQ-based comparative proteomic analysis provides insights into somatic embryogenesis in Gossypium hirsutum L.

Elucidating the interaction of rhizosphere bacteria and environmental factors in influencing active ingredient content of Lycium barbarum fruit in China

Diversity of nirS and nirK denitrifying bacteria in rhizosphere and non-rhizosphere soils of halophytes in Ebinur Lake Wetland

Integrated application of transcriptomics and metabolomics provides insights into the antifungal activity of α-phenylcinnamic acid against Colletotrichum gloeosporioides