Identification of the gene network modules highly associated with the synthesis of phenolics compounds in barley by transcriptome and metabolome analysis

Zhao, Han; Ahsan, Muhammad; Adil, Muhammad Faheem; Chen, Xiaohui; Nazir, Muhammad Mudassir; Shamsi, Imran Haider; Zeng, Fanrong; Zhang, Guoping

doi:10.1016/j.foodchem.2020.126862

Cited by 35 publications

(13 citation statements)

References 37 publications

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“…WGCNA has been used in numerous species to elucidate the interaction between physiological traits and gene expression ( 37 , 43 ). WGCNA was used herein to evaluate transcript expression and trait changes under different light quality treatments, and two modules, namely darkred and cyan, which were highly correlated with anthocyanins and sugars, respectively, were screened out.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptomic and Metabolomic Profiling Reveals the Effect of LED Light Quality on Fruit Ripening and Anthocyanin Accumulation in Cabernet Sauvignon Grape

Zhang

Liu

et al. 2021

Front. Nutr.

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Different light qualities have various impacts on the formation of fruit quality. The present study explored the influence of different visible light spectra (red, green, blue, and white) on the formation of quality traits and their metabolic pathways in grape berries. We found that blue light and red light had different effects on the berries. Compared with white light, blue light significantly increased the anthocyanins (malvidin-3-O-glucoside and peonidin-3-O-glucoside), volatile substances (alcohols and phenols), and soluble sugars (glucose and fructose), reduced the organic acids (citric acid and malic acid), whereas red light achieved the opposite effect. Transcriptomics and metabolomics analyses revealed that 2707, 2547, 2145, and 2583 differentially expressed genes (DEGs) and (221, 19), (254, 22), (189, 17), and (234, 80) significantly changed metabolites (SCMs) were filtered in the dark vs. blue light, green light, red light, and white light, respectively. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, most of the DEGs identified were involved in photosynthesis and biosynthesis of flavonoids and flavonols. Using weighted gene co-expression network analysis (WGCNA) of 23410 highly expressed genes, two modules significantly related to anthocyanins and soluble sugars were screened out. The anthocyanins accumulation is significantly associated with increased expression of transcription factors (VvHY5, VvMYB90, VvMYB86) and anthocyanin structural genes (VvC4H, Vv4CL, VvCHS3, VvCHI1, VvCHI2, VvDFR), while significantly negatively correlated with VvPIF4. VvISA1, VvISA2, VvAMY1, VvCWINV, VvβGLU12, and VvFK12 were all related to starch and sucrose metabolism. These findings help elucidate the characteristics of different light qualities on the formation of plant traits and can inform the use of supplemental light in the field and after harvest to improve the overall quality of fruit.

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Section: Discussionmentioning

confidence: 99%

“…The module eigengene (the first principal component of a given module) value was calculated and used to evaluate the association of modules with fruit physiological indexes in all samples. Regulatory network diagrams were illustrated using Cytoscape 3.7.1 ( 37 ).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic and Metabolomic Profiling Reveals the Effect of LED Light Quality on Fruit Ripening and Anthocyanin Accumulation in Cabernet Sauvignon Grape

Zhang

Liu

et al. 2021

Front. Nutr.

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“…The clean reads were compared with previously assembled transcript sequence using hisat2 software. Count data were acquired using feature Counts software ( Han et al, 2020 ). Transcripts per million (TPM) method was used to estimate gene expression using the Trinity software ( Haas et al, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Effects of Strigolactone on Torreya grandis Gene Expression and Soil Microbial Community Structure Under Simulated Nitrogen Deposition

Wang

Zhang

et al. 2022

Front. Plant Sci.

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Nitrogen enters the terrestrial ecosystem through deposition. High nitrogen levels can affect physical and chemical properties of soil and inhibit normal growth and reproduction of forest plants. Nitrogen modulates the composition of soil microorganisms. Strigolactones inhibits plant branching, promotes root growth, nutrient absorption, and promotes arbuscular fungal mycelia branching. Plants are subjected to increasing atmospheric nitrogen deposition. Therefore, it is imperative to explore the relationship between strigolactone and nitrogen deposition of plants and abundance of soil microorganisms. In the present study, the effects of strigolactone on genetic responses and soil microorganisms of Torreya grandis, under simulated nitrogen deposition were explored using high-throughput sequencing techniques. T. grandis is a subtropical economic tree species in China. A total of 4,008 differentially expressed genes were identified in additional N deposition and GR24 treatment. These genes were associated with multiple GO terms and metabolic pathways. GO enrichment analysis showed that several DEGs were associated with enrichment of the transporter activity term. Both additional nitrogen deposition and GR24 treatment modulated the content of nutrient elements. The content of K reduced in leaves after additional N deposition treatment. The content of P increased in leaves after GR24 treatment. A total of 20 families and 29 DEGs associated with transporters were identified. These transporters may be regulated by transcription factors. A total of 1,402,819 clean reads and 1,778 amplicon sequence variants (ASVs) were generated through Bacterial 16S rRNA sequencing. Random forest classification revealed that Legionella, Lacunisphaera, Klebsiella, Bryobacter, and Janthinobacterium were significantly enriched in the soil in the additional N deposition group and the GR24 treatment group. Co-occurrence network analysis showed significant differences in composition of soil microbial community under different treatments. These results indicate a relationship between N deposition and strigolactones effect. The results provide new insights on the role of strigolactones in plants and composition of soil microorganisms under nitrogen deposition.

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“…Such studies are of special relevance as they can give a picture of the loss of genetic variation due to domestication and provide information for the set-up of breeding applications for phenols-related beer improvement. For example, a network analysis of gene expression and secondary metabolites, induced by the well-known stressor drought [66] in developing grains from several different Tibetan wild barley cultivars, recently allowed the identification of genes whose manipulation is believed to help the development of cultivars with specific contents of phenolic compounds [67]. Less data is available for a role of the genetic background on hop phenols.…”

Section: The Role Of Barley Yeast and Hop Genetics On Beer Phenolsmentioning

confidence: 99%

The Role of Bioactive Phenolic Compounds on the Impact of Beer on Health

2021

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This review reports recent knowledge on the role of ingredients (barley, hop and yeasts), including genetic factors, on the final yield of phenolic compounds in beer, and how these molecules generally affect resulting beer attributes, focusing mainly on new attempts at the enrichment of beer phenols, with fruits or cereals other than barley. An entire section is dedicated to health-related effects, analyzing the degree up to which studies, investigating phenols-related health effects of beer, have appropriately considered the contribution of alcohol (pure or spirits) intake. For such purpose, we searched Scopus.com for any kind of experimental model (in vitro, animal, human observational or intervention) using beer and considering phenols. Overall, data reported so far support the existence of the somehow additive or synergistic effects of phenols and ethanol present in beer. However, findings are inconclusive and thus deserve further animal and human studies.

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Identification of the gene network modules highly associated with the synthesis of phenolics compounds in barley by transcriptome and metabolome analysis

Cited by 35 publications

References 37 publications

Transcriptomic and Metabolomic Profiling Reveals the Effect of LED Light Quality on Fruit Ripening and Anthocyanin Accumulation in Cabernet Sauvignon Grape

Transcriptomic and Metabolomic Profiling Reveals the Effect of LED Light Quality on Fruit Ripening and Anthocyanin Accumulation in Cabernet Sauvignon Grape

Effects of Strigolactone on Torreya grandis Gene Expression and Soil Microbial Community Structure Under Simulated Nitrogen Deposition

The Role of Bioactive Phenolic Compounds on the Impact of Beer on Health

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