Research Article

Identification of Rice Blast Resistance-related Co-expression Modules in Near Iso-genic Lines by WGCNA  

Xiang Li1,2 , Linna Ma1,2 , Liwei Guo1,2 , Yixiang Liu1,2 , Min Yang1,2 , Shusheng Zhu1,2 , Xiahong He2,3 , Youyong Zhu1,2 , Huichuan Huang1,2
1 College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
2 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
3 Southwest Forestry University, Kunming, 650233, China
Author    Correspondence author
Molecular Pathogens, 2022, Vol. 13, No. 1   doi: 10.5376/mp.2022.13.0001
Received: 17 Jan., 2022    Accepted: 25 Jan., 2022    Published: 14 Mar., 2022
© 2022 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Li X., Ma L.N., Guo L.W., Liu Y.X., Yang M., Zhu S.S., He X.H., Zhu Y.Y., and Huang H.C., 2022, Identification of rice blast resistance-related co-expression modules in near iso-genic lines by WGCNA, Molecular Pathogens, 13(1): 1-10 (doi: 10.5376/mp.2022.13.0001)

Abstract

Weighted gene co-expression network analysis (WGCNA) is often used to analyze multi-sample (>15) data, identify co-expressed gene modules, and explore the relationship between co-expression modules and target traits in systematic biology. In order to explore the gene co-expression network in response to Magnaporthe oryzae infection in rice near iso-genic lines (NIL) carrying different broad-spectrum resistance genes. We analyzed the expression pattern of genes by WGCNA based on the data of GSE117030 form the GEO database and identified 23 co-expression modules. Combining expression patterns with phenotypes, we chose tan module and midnightblue module as target modules. GO enrichment analysis showed that most of the genes in the target module were related to cell components. A co-expression network was constructed for the genes in the target module, and some hub genes were screened out. These results provide new insights into further understanding the mechanism of broad-spectrum resistance genes and breeding rice varieties with disease resistance.

Keywords
WGCNA; Rice; Rice blast; Broad-spectrum resistance gene; Near isogenic lines

Rice (Oryza sativa L.) is an important food crop in the world, especially in Asia. About 1/3 of the world's population relies on rice as the staple food (Wang et al., 2018; Zhao et al., 2018), among which Oryza sativa ssp. japonica and Oryza sativa ssp. indica are the most widely planted. (Zhang et al., 1992; Wang et al., 2018). With the continuous growth of world population, human's demand for rice yield and quality is also increasing (Seck et al., 2012). Rice yield and quality are affected by various biotic and abiotic factors in the external environment, among which Rice blast caused by Magnaporthe oryzae is one of the most important biotic factors. Under suitable environmental conditions, rice is affected by Magnaporthe oryzae from seedling stage to grain filling stage. In resistance to M. oryzae infection, resistant varieties (Sharma et al., 2012; Li et al., 2016) and fungicides (Skamnioti and Gurr, 2009) are usually used. However, these two methods have certain deficiencies and limitations. On the one hand, rice varieties carrying species-specific resistance genes will gradually lose their resistance in the face of M. oryzae with the rapid evolution and mutation. On the other hand, the use of fungicides also presents potential environmental safety risks (Ma et al., 2019). Therefore, the application of broad-spectrum resistance gene is very important in the prevention and control of M. oryzae. At present, many broad-spectrum resistance genes have been identified in rice (Li et al., 2019), such as Pi1 (Hua et al., 2012), Pi9 (Liu et al., 2002; Qu et al., 2006), Pi21 (Fukuoka et al., 2001), Pi54 (Sharma et al., 2010), Pita (Jia et al., 2000), bsr-d1 (Li et al., 2017), etc. Most of the changes in gene expression occurred at the transcriptional stage when plants were infected by pathogenic bacteria (Jain et al., 2017). Therefore, using transcriptomics to study the infection of M. oryzae to rice can effectively identify potential candidate genes with resistance function (Jain et al., 2017). Near Iso-genic lines (NIL) are one of the ideal genetic materials for studying the resistance mechanism of rice to M. oryzae (Mackill et al., 1992). Usually, NIL carrying a broad-spectrum resistance gene is constructed for study, and the corresponding analysis method is usually also simple pairwise comparison. Few studies used the same parents to construct NIL containing different broad-spectrum resistance genes to compare the resistance differences of different broad-spectrum resistance genes (Jain et al., 2019).

 

With the rapid development of high-throughput sequencing technology, researchers have begun to use multi-sample sequencing to study systems biology. The traditional difference comparison analysis method can only compare two samples and cannot effectively deal with the multi-sample high-dimensional data. The emergence and development of network analysis algorithm has changed this dilemma. Network analysis can effectively process high-dimensional data and extract biologically significant differential expression profiles. Weighted gene co-expression network analysis (WGCNA) is a widely used network analysis method. WGCNA is an unsupervised learning method, which is based on the expression spectrum data of different samples for clustering and can identify co-expression modules, screen candidate biomarkers and identify potential target sites among different samples (Langfelder et al., 2008). WGCNA has been used in many plant studies. Mao et al. (2009) used 1 094 gene chip data to construct Arabidopsis gene co-expression network, and identified 382 core genes. Greenham et al. (2017) applied WGCNA to the transcriptional data of Brassica rapa and constructed the gene co-expression network at different time points under drought stress, revealing the physiological and transcriptional characteristics of Brassica rapa at the early stage under drought stress. Shang and Gao (2020) used WGCNA to analyze transcriptional differences in Arabidopsis thaliana infected with powdery mildew. Qin et al. (2020) identified 15 co-expression modules of genes closely related to potato root drought resistance based on WGCNA, and gene annotation found that most of these core genes were related to drought stress regulation. Chang et al. (2020) identified the co-expression genes related to endogenous abscisic acid in response to the stress of Sclerospora graminicola by WGCNA in foxtail millet. Ma et al. (2019) used WGCNA to identify co-expression modules of plant height and ear height in maize. Thirunavukkarasu et al. (2013) used WGCNA to analyze 528 gene chip data of maize (Zea Mays L.) under waterlogging stress and identified 7 functional modules. Ju et al. (2019) used WGCNA to identify co-expression modules of genes related to internode elongation of cotton fruiting branches. Tai et al. (2018) used WGCNA to analyze transcriptomic data from different tissues of tea (Camellia sinensis) and identified 35 co-expression modules, of which 20 modules were significantly associated with the biosynthesis of catechins, theanine and caffeine. And identified hub genes that regulate the metabolism of the three substances. In addition to gene expression profile data, WGCNA can also be used for other high-throughput data. Pei et al. (2017) slightly improved WGCNA and successfully applied it to proteomics and metabolomics data, obtaining a biologically meaningful explanation. DiLeo et al. (2011) compared the performance of principal component analysis (PCA), batch learning self-organizing maps (BL-SOM), and weighted gene co-expression network analysis (WGCNA) on the data of tomato fruit metabolism. Compared with the previous two methods, WGCNA also provided information about co-expression of metabolites while clustering metabolites based on expression quantity, and successfully identified three co-expression modules related to tomato fruit ripening.

 

Based on RNA-seq data GSE117030 (Jain et al. 2019) from GEO database, this study used WGCNA to construct gene co-expression network, and conducted correlation analysis between gene co-expression module and processing mode. In order to provide new ideas and clues for further study on the molecular mechanism of rice resistance to M. oryzae infection, NIL carrying different broad-spectrum resistance genes were excavated and co-expression network was constructed.

 

1 Results and Analysis

1.1 Construction of a weighted gene co-expression network

After the soft threshold β=16 is calculated, the similarity matrix is transformed into adjacency matrix, and then the adjacency matrix is transformed into topological overlap matrix (TOM). In order to eliminate the errors caused by background noise and false correlation, the formula dissTom=1-Tom is used to transform the topological matrix into a heterogeneous matrix. Finally, the clustering generated by function hcluster() is cut by dynamic cutting method. Genes with similar expression patterns are clustered on the same branch, and each branch represents a co-expression module. Different colors represent different modules, among which gray modules represent genes that cannot be assigned to any module, so gray modules are not counted as identified co-expression modules.  Differential genes were clustered by correlation according to their expression levels, and genes with higher correlation were assigned to the same module (Figure 1). Turquoise module gene was the most abundant with 1 779 genes. The number of white module genes was the least, with 104 genes (Table 1).

 

 

Figure 1 Gene co-expression network gene clustering and module cutting

 

 

Table 1 Distribution of gene number in co-expression module

 

1.2 Specific module identification

After the different treatments were regarded as quality traits and converted into continuous traits, association analysis was conducted with the modules and correlation heat map was made (Figure 2). It was found that the correlation between the tan and the treatment of PB1+Pi1 inoculated with M. oryzae Mo-nwi-53 24 h was 0.83 (P=6e-07). The correlation between the midnightblue module and treatment of PB1+Pi54 inoculated with M. oryzae Mo-nwi-53 24 h was 0.97 (P=2e-14). Similar expression characteristics can also be seen from the gene expression heat map (Figure 3). Tan module and midnightblue module were selected as target modules for subsequent analysis.

 

 

Figure 2 Correlation heat map of gene co-expression network module and different processes

Note: The leftmost color indicates different co-expression modules; The numbers in the figure indicate the correlation between the modules and different processes; The numbers in parentheses indicate the correlation P value

 

 

Figure 3 Heat map of gene expression in the tan module and midnightblue module

Note: a: Tan module; b: Midnightblue module

 

1.3 GO enrichment analysis of the target module

To further explore the function of genes in the target module, agriGO was used to perform GO enrichment analysis on tan module and midnightblue. The results showed (Figure 4) that GO items significantly enriched by genes in tan module were mainly related to cell components such as GO:0005829: cytoplasmic solution; GO:0009579: thylakoid; GO:0005856: cytoskeleton; GO:0044444: cytoplasmic part; GO:0005737: cytoplasm.

 

 

Figure 4 GO enrichment analysis of tan modules and midnightblue module

Note: The color depth indicates the significant enrichment degree of GO compression (white if there is no significant, and the color is deepened by increasing the significant degree). The solid line, the dashed line, and the dotted line respectively indicate that there are two, one, or no significant enrichment entries at both ends of the line

 

1.4 Mining of hub genes and construction of interaction network

According to the network structure results generated by WGCNA, the associated nodes with connectivity (weight value)>0.80 were screened for the construction of weighted gene co-expression network and hub gene mining. After data were imported into Cytoscape, the network was analyzed, and the nodes with the top 10 Outdegree values were screened out as the hub genes of the weighted gene co-expression network (Figure 5). Through functional query, it was found that some hub genes of the weighted gene co-expression network were related to plant disease resistance. For example, LOC_Os01g08710.1 was a WRKY transcription factor (Table 2).

 

 

Figure 5 Gene co-expression network of tan module and midnightblue module and their hub genes

 

 

Table 2 Hub gene and its function

 

2 Discussion

Life science studies tend to be more and more large-sample studies. Groen et al. (2020) used 15 635 transcripts to study the adaptive mechanisms of rice under natural selection. Traditional analysis methods can not effectively classify genes in large samples and can not dig out the biological significance hidden in the data. The advent of network analysis has changed that. Network analysis can classify complex data, efficiently explore the overall gene expression rules between different samples, and calculate the interaction patterns between genes in samples. WGCNA presents the global expression pattern of genes in the samples by modularizing the classification of genes. In addition, the function of unknown genes can be predicted by using known genes to provide ideas and clues for subsequent biological experiments. Therefore, WGCNA plays an important role in gene chip and transcriptome data of multi-samples, and also has important applications in other omics data processing (DiLeo et al., 2011; Pei et al., 2017).

 

In this study, based on RNA-seq data of rice near-isogenic lines carrying different broad-spectrum resistance genes, a total of 23 specific modules were identified and 2 modules highly correlated with traits were selected for further study. Jain et al. (2019) used the transcriptome data to pally compare rice near-isogenic lines carrying different broad-spectrum resistance genes and analyze their signal network, and found that the combination of broad-spectrum resistance genes Pi9 and Pi54 can maximize rice blast resistance. R genes such as Pi9, Pita, Pi21 and Pi54 play important roles in rice blast broad-spectrum resistance. The near-isogenic lines constructed based on these R genes could effectively cope with the infection of rapidly mutating M. oryzae. Jain et al. (2019) compared the transcriptional differences between different NILs and susceptible varieties by comparative transcriptome, and found that rice plants with different near-isogenic lines had different SDEL (Significant differentially expressed loci) in the face of M. oryzae infection. These SDEL regulate the metabolism of rice plants, such as starch synthesis and degradation, fatty acid synthesis, phospholipid hydrolysis, phenylpropane synthesis, jasmonic acid metabolism, etc. They did not identify a gene interaction network for M. oryza infection, only pairwise comparisons were made. On this basis, WGCNA was used to analyze the transcriptional differences of different near-isogenic lines after infection with M. oryzae, and the co-expression network of highly related genes with different near-isogenic lines was constructed. Two specific modules were identified by constructing a weighted gene co-expression network, and these two specific modules were highly correlated with NIL carrying different broad-spectrum resistance genes in response to M. oryzae infection, and the corresponding biological significance was revealed. Using connectivity as an indicator, the potential hub genes in specific modules were revealed. The results of this study provide new ideas and theoretical guidance for further understanding the molecular mechanism of rice broad-spectrum resistance genes.

 

3 Materials and Methods

3.1 Data acquisition

Log in GEO to download transcriptome expression profile data of GSE117030 (Jain et al., 2019), and extract FPKM values using R (Version 3.6.3) software as gene expression profile data.

 

3.2 Module division

R-package WGCNA (Langfelder et al., 2008) was used for weighted gene co-expression network analysis.  Before WGCNA analysis, genes need to be filtered. goodSamplesGenes(), a function provided by R-package WGCNA, was used for gene and sample filtering to improve the accuracy of the co-expression network. The soft thresholding power was determined according to the principle of scale-free networks. The soft thresholding power provided by software was usually used for subsequent analysis. The clustering tree was constructed according to the correlation of gene expression levels, and the co-expression patterns were identified by dynamic pruning method. The minimum number of genes in modules was set to 50, and the modules with similar expression patterns were merged according to the similarity of module eigenvalues (0.75).

 

Correlation analysis was conducted between traits and each module, and module-trait heat map was drawn. The closer the absolute value of correlation between a trait and a module is to 1, the more the gene of the module is related to the trait. Co-expression modules with biological significance can be found through the heat map for subsequent analysis.

 

3.3 Functional enrichment of module genes

agriGO (V 2.0) (Du et al., 2010) was used for GO function analysis of genes in candidate modules. With FDR≤0.05 as the threshold, GO terms that meet this condition are considered as differential enrichment GO terms.

 

3.4 Construction and visualization of gene co-expression networks

Cytoscape_3.7.2 (Shannon et al., 2003) was used to process the gene co-expression network output by WGCNA to screen out the hub genes and visualize them. Each node in the network represents a gene, and the edge represents the mutual regulatory relationship between genes. Gene co-expression network can help us accurately screen out possible hub genes and make functional prediction of genes with unknown functions by using genes with known functions.

 

3.5 Data statistics

All statistical analyses in this study are based on R 3.6.3. R software packages ggplot2 and pheatmap were used to draw part of the diagrams, and R software package VennDiagram (Chen et al., 2011) was used to draw Venn diagram.

 

Authors’ contributions

LX and MLN are the experimental designer and executor of this study. They have completed data analysis and written the first draft of the paper. GLW, LYX, YM, ZSS, HXH, ZYY participated in experimental design and analysis of experimental results; HHC is the architect and principal of the project, directing experimental design, data analysis, paper writing and revision. All authors read and approved the final manuscript.

 

Acknowledgement

This study was supported by the National Natural Science Foundation of China (31801792, 31960554), the International Cooperative Research Center for Yunnan Green Food (2019ZG00901) and Yunnan Academician Workstation of the Chinese Academy of Engineering of Yunnan Province (2018IC063).

 

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Zhao Q., Feng Q., Lu H.Y., Li Y., Wang A., Tian Q.L., Zhan Q.L., Lu Y.Q., Zhang L., Huang T., Wang Y.C., Fan D.L., Zhao Y., Wang Z.Q., Zhou C.C., Chen J.Y., Zhu C.R., Li W.J., Weng Q.J., Xu Q., Wang Z.X., Wei X.H., Han B., and Huang X.H., 2018, Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice, Nat. Genet., 50(2): 278-284.
https://doi.org/10.1038/s41588-018-0041-z
PMid:29335547

Molecular Pathogens
• Volume 13
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