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

Comparative Metabolomics and Transcriptome Studies of Two Forms of Rhododendron chrysanthum Pall. under UV-B Stress

Rhododendron chrysanthum Pall. (R. chrysanthum), a plant with UV-B resistance mechanisms that can adapt to alpine environments, has gained attention as an important plant resource with the ability to cope with UV-B stress. In this experiment, R. chrysanthums derived from the same origin were migrated to different culture environments (artificial climate chamber and intelligent artificial incubator) to obtain two forms of R. chrysanthum. After UV-B irradiation, 404 metabolites and 93,034 unigenes were detected. Twenty-six of these different metabolites were classified as UV-B-responsive metabolites. Glyceric acid is used as a potential UV-B stress biomarker. The domesticated Rhododendron chrysanthum Pall. had high amino acid and SOD contents. The study shows that the domesticated Rhododendron chrysanthum Pall. has significant UV-B resistance. The transcriptomics results show that the trends of DEGs after UV-B radiation were similar for both forms of R. chrysanthum: cellular process and metabolic process accounted for a higher proportion in biological processes, cellular anatomical entity accounted for the highest proportion in the cellular component, and catalytic activity and binding accounted for the highest proportion in the molecular function category. Through comparative study, the forms of metabolites resistant to UV-B stress in plants can be reflected, and UV-B radiation absorption complexes can be screened for application in future specific practices. Moreover, by comparing the differences in response to UV-B stress between the two forms of R. chrysanthum, references can be provided for cultivating domesticated plants with UV-B stress resistance characteristics. Research on the complex mechanism of plant adaptation to UV-B will be aided by these results.

Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.

Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.

Multi-omics Analysis of Young Portulaca oleracea L. Plants' Responses to High NaCl Doses Reveals Insights into Pathways and Genes Responsive to Salinity Stress in this Halophyte Species

Soil salinity is among the abiotic stressors that threaten agriculture the most, and purslane (Portulaca oleracea L.) is a dicot species adapted to inland salt desert and saline habitats that hyper accumulates salt and has high phytoremediation potential. Many researchers consider purslane a suitable model species to study the mechanisms of plant tolerance to drought and salt stresses. Here, a robust salinity stress protocol was developed and used to characterize the morphophysiological responses of young purslane plants to salinity stress; then, leaf tissue underwent characterization by distinct omics platforms to gain further insights into its response to very high salinity stress. The salinity stress protocol did generate different levels of stress by gradients of electrical conductivity at field capacity and water potential in the saturation extract of the substrate, and the morphological parameters indicated three distinct stress levels. As expected from a halophyte species, these plants remained alive under very high levels of salinity stress, showing salt crystal-like structures constituted mainly by Na+, Cl-, and K+ on and around closed stomata. A comprehensive and large-scale metabolome and transcriptome single and integrated analyses were then employed using leaf samples. The multi-omics integration (MOI) system analysis led to a data-set of 51 metabolic pathways with at least one enzyme and one metabolite differentially expressed due to salinity stress. These data sets (of genes and metabolites) are valuable for future studies aimed to deepen our knowledge on the mechanisms behind the high tolerance of this species to salinity stress. In conclusion, besides showing that this species applies salt exclusion already in young plants to support very high levels of salinity stress, the initial analysis of metabolites and transcripts data sets already give some insights into other salt tolerance mechanisms used by this species to support high levels of salinity stress.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00061-2.

Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification

Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.

Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress

Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO₄) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts' fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO₄ at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO₄ on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.

Transcriptomic and Metabolic Profiling of Kenaf Stems under Salinity Stress

Kenaf (Hibiscus cannabinus L.) is an indispensable fiber crop that faces increasing salinity stress. In previous studies regarding the molecular mechanisms of how kenaf may respond to salt stress, no metabolic evidences have been reported. Meanwhile, studies regarding kenaf stems under adverse growth conditions have not been conducted. In the present study, multiple-layer evidences including physiological, transcriptomic, and metabolic data regarding how kenaf stems were affected by the salt stress are provided, wherein the stem growth, especially the lignification process, is retarded. Meanwhile, the transcriptomic data indicated genes involved in the photosynthesis are significantly repressed while the multiple flavonoid metabolism genes are enriched. As to the metabolic data, the content variation for the growth-promotion phytohormones such as IAA and the stress-responding ones including ABA are within or without expectations, implying these phytohormones played complicated roles when the kenaf stems encounter salt stress. However, the metabolite variations did not always agree with the expression levels of corresponding key pathway genes, possibly because the metabolite could be biosynthesized or catabolized in multiple pathways. Collectively, our data may enlighten, more specifically, downstream studies on kenaf responses against salinity and other adverse conditions.