pubmed.ncbi.nlm.nih.gov

Gene coexpression network analysis combined with metabonomics reveals the resistance responses to powdery mildew in Tibetan hulless barley - PubMed

  • ️Mon Jan 01 2018

Gene coexpression network analysis combined with metabonomics reveals the resistance responses to powdery mildew in Tibetan hulless barley

Hongjun Yuan et al. Sci Rep. 2018.

Abstract

Powdery mildew is a fungal disease that represents a ubiquitous threat to crop plants. Transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in Tibetan hulless barley in response to powdery mildew. There were 3418 genes and 405 metabolites differentially expressed between the complete resistance cultivar G7 and the sensitive cultivar Z13. Weighted gene coexpression network analysis was carried out, and the differentially expressed genes were enriched in five and four major network modules in G7 and Z13, respectively. Further analyses showed that phytohormones, photosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways were altered during Qingke-Blumeria graminis (DC.) f.sp. hordei (Bgh) interaction. Comparative analyses showed a correspondence between gene expression and metabolite profiles, and the activated defenses resulted in changes of metabolites involved in plant defense response, such as phytohormones, lipids, flavone and flavonoids, phenolamides, and phenylpropanoids. This study enabled the identification of Bgh responsive genes and provided new insights into the dynamic physiological changes that occur in Qingke during response to powdery mildew. These findings greatly improve our understanding of the mechanisms of induced defense response in Qingke and will provide new clues for the development of resistant Tibetan hulless barley varieties.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Differential gene expression of Tibetan hulless barley in response to powdery mildew. (A) Numbers of genes up-regulated (red) and down-regulated (green) in G7 and Z13 after inoculation with powdery mildew over time. (B) Heatmap of differentially expressed genes in G7. The columns show the 15 samples G7-0 hpi_1, G7-0 hpi_2, G7-0 hpi_3, G7-168 hpi_1, G7-168 hpi_2, G7-168 hpi_3, G7-6 hpi_1, G7-6 hpi_2, G7-6 hpi_3, G7-72 hpi_1, G7-72 hpi_2, G7-72 hpi_3, G7-36 hpi_1, G7-36 hpi_2, G7-36 hpi_3; while the rows show the TPM values scaled by the z-score algorithm. (C) Heatmap of differentially expressed genes in Z13. The columns show the 15 samples Z13-0 hpi_1, Z13-0 hpi_2, Z13-0 hpi_3, Z13-6 hpi_1, Z13-6 hpi_2, Z13-6 hpi_3, Z13-72 hpi_1, Z13-72 hpi_2, Z13-72 hpi_3, Z13-36 hpi_1, Z13-36 hpi_2, Z13-36 hpi_3, Z13-168 hpi_1, Z13-168 hpi_2, Z13-168 hpi_3; while the rows show the TPM values scaled by the z-score algorithm. Hierarchical clustering of expression pattern for genes in was shown at the left of the heatmap figure. (D) Clustering and classification of differentially expressed genes of G7 in response to Bgh over time (0, 6, 36, 72, 168 hpi). Twenty trends were determined, and the profiles of genes significantly enriched (P-value < 0.05) are colored. The number of genes in the trend is shown above each profile. (E) Clustering and classification of differentially expressed genes of Z13 in response to Bgh over time (0, 6, 36, 72, 168 hpi). Twenty trends were determined, and the profiles of genes significantly enriched (P-value < 0.05) are colored. The number of genes in the trend is shown above each profile.

Figure 2
Figure 2

Venn diagram showing overlap of up-regulated and down-regulated genes of Tibetan hulless barley in response to powdery mildew. (A) Venn diagram showing overlap of up-regulated genes of G7 in response to powdery mildew. (B) Down-regulated genes of G7 in response to powdery mildew. (C) Venn diagram of the up-regulated genes of G7 and Z13 in response to powdery mildew. (D) Venn diagram of the down-regulated genes of G7 and Z13 in response to powdery mildew. (E) Venn diagram depicting intersections of up-regulated genes of Z13 in response to powdery mildew. (F) Down-regulated genes of Z13 in response to powdery mildew. Area of overlap is not proportional to the degree of overlap. The numbers of genes and their percentage in each region of the diagram are indicated.

Figure 3
Figure 3

Weighted gene coexpression network of differentially expressed genes of G7 and Z13 in response to powdery mildew. (A) Weighted gene coexpression network of DEGs of G7 in response to powdery mildew. (B) Weighted gene coexpression network of DEGs of Z13 in response to powdery mildew. All adjacency values plotted are greater than 0.35. (C) Cluster of gene dendrogram in G7. Gene dendrogram and heatmap of the DEGs, showing 5 modules depicted with different colors. (D) Cluster of gene dendrogram in Z13. Gene dendrogram and heatmap of the DEGs, showing 4 modules depicted with different colors.

Figure 4
Figure 4

(A) Module-trait correlation of G7 in response to powdery mildew. Each row corresponds to a module. Each column corresponds to a specific time point. The color of each box at the row-column intersection indicates the correlation coefficient between the module and the time point. A high degree of correlation between a specific module and the time point is indicated by dark red or dark blue. (B–F) Scatterplots of gene significance versus each module membership.

Figure 5
Figure 5

(A) Module-trait correlation of Z13 in response to powdery mildew. Each row corresponds to a module. Each column corresponds to a specific time point. The color of each box at the row-column intersection indicates the correlation coefficient between the module and the time point. A high degree of correlation between a specific module and the time point is indicated by dark red or dark blue. (B–E) Scatterplots of gene significance versus each module membership.

Figure 6
Figure 6

Expression patterns of genes and metabolites involved in the biosynthesis of jasmonates. (A) Schematic pathway. Uppercase letters indicate genes that encode enzymes. Solid arrows represent established biosynthesis steps, while broken arrows indicate the involvement of multiple enzymatic reactions. (B) Metabolite accumulation after Bgh inoculation; values are the means ± SE. The asterisk (*) indicates a significant difference in G7 versus Z13 (p < 0.05).

Similar articles

Cited by

References

    1. Dodds PN, Rathjen JP. Plant immunity: towards an integrated view of plant-pathogen interactions. Nature Reviews Genetics. 2010;11:539. doi: 10.1038/nrg2812. - DOI - PubMed
    1. Zhang J, et al. Coexpression network analysis of the genes regulated by two types of resistance responses to powdery mildew in wheat. Scientific Reports. 2016;6:23805. doi: 10.1038/srep23805. - DOI - PMC - PubMed
    1. Naumann M, Somerville S, Voigt C. Differences in early callose deposition during adapted and non-adapted powdery mildew infection of resistant Arabidopsis lines. Plant signaling & behavior. 2013;8:e24408. doi: 10.4161/psb.24408. - DOI - PMC - PubMed
    1. Huang XQ, Röder MS. Molecular mapping of powdery mildew resistance genes in wheat: A review. Euphytica. 2004;137:203–223. doi: 10.1023/B:EUPH.0000041576.74566.d7. - DOI
    1. Cheng Y, Yao J, Zhang H, Huang L, Kang Z. Cytological and molecular analysis of nonhost resistance in rice to wheat powdery mildew and leaf rust pathogens. Protoplasma. 2015;252:1167. doi: 10.1007/s00709-014-0750-9. - DOI - PubMed

Publication types

MeSH terms

Substances