Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum

Abstract

Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using RNA sequencing. Gene ontology (GO) analysis was conducted and found that DEGs were mainly enriched in the regulation of transcription, metabolic processes and oxidation-reduction-related processes. Weighted gene co-expression network analysis discerned the MEmagenta module highly associated with a fuzz/fuzzless trait, which included a total of 50 hub genes differentially expressed between two materials. GaFZ, which negatively regulates trichome and fuzz formation, was found involved in MEmagenta cluster1. In addition, twenty-eight hub genes in MEmagenta cluster1 were significantly up-regulated and expressed in fuzzless mutant DPL972. It is noteworthy that Ga04G1219 and Ga04G1240, which, respectively, encode Fasciclin-like arabinogalactan protein 18(FLA18) and transport protein, showed remarkable differences of expression level and implied that they may be involved in protein glycosylation to regulate fuzz formation and development. This module and hub genes identified in this study will provide new insights on fiber and fuzz formation and be useful for the molecular design breeding of cotton genetic improvement.

Keywords: WGCNA; fuzz; hub genes; module; transcriptome analysis.

Figure 1

Venn diagram of DEGs identified from two diploid cotton accessions; 1D, 3D, 5D represents 1 Days post-anthesis (DPA), 3 DPA, 5 DPA.

Figure 2

Validation of DEGs identified from transcriptome analysis with qRT-PCR. The heatmap on the top right of figure represents the relative transcription abundances (based on FPKM).

Figure 3

GO enrichment analysis of DEGs at three fiber developmental stages; (A), DEGs detected from 1DPA; (B), DEGs detected from 1DPA; (C) DEGs detected from 1DPA.

Figure 4

Module identification by weighted gene co-expression network analysis (WGCNA). (A,B) represent the soft threshold with scale independence and mean connectivity. (C), Hierarchical dendrogram reveals co-expression modules identified by WGCNA. Each leaf represents one gene. Ten modules were identified based on calculation of eigengenes; each module was decorated with a different color.

Figure 5

The WGCNA showed the MEmagenta module is significantly associated with fuzz formation. Each row means a module, and the correlation coefficient are shown in each square and the p-value was list in Table S4. The names in red in left represent the module highly associated with fuzz development.

Figure 6

The Sankey diagram represents the distributions of DEGs in each module.

Figure 7

K-means clustering of DEGs in the MEmagenta module.

Figure 8

The expression heatmaps of hub genes in the MEmagenta module. The right side of figure represents the relative transcription abundances (based on FPKM). The gene IDs were listed on the left and sample names were displayed on the bottom.