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

Xiaoxu Feng,Limin Lv,Hailiang Cheng,Shang Liu,Guoli Song,Qiaolian Wang,Youping Zhang,Dongyun Zuo

doi:10.3390/genes12050753

Xiaoxu Feng, Limin Lv + Show 6 more

Open Access

https://doi.org/10.3390/genes12050753

Copy DOI

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.

Highlights

Trichomes are highly specialized cells originating and extending from the epidermal surface of leaves, stems, petal bases and seeds in plants [1,2]
To capture a global view and the temporal gene expression changes during fiber and fuzz initiation development, a transcriptome profiling experiment was performed from 12 cotton ovule libraries including wild type DPL971 and the fuzzless mutant DPL972 during the fuzz and fiber initiation stage (+1DPA, +3DPA and +5 Days post-anthesis (DPA))
The results demonstrate genes ingenes the MEmagenta module module were enriched in transferase activity and transport protein, in the MEmagenta were enriched in transferase activity and in the MEmagenta module were enriched in transferase activity and transporttransport protein, and the Kyoto Encyclopedia of Genes and Genomes (KEGG)

Summary

Introduction

Trichomes are highly specialized cells originating and extending from the epidermal surface of leaves, stems, petal bases and seeds in plants [1,2]. They contribute to a variety of unessential but important functions for plant growth, including protections against pathogens, insects or even herbivores, water regulation and increasing the tolerance to extreme high temperature and UV irradiation [3,4]. Plenty of functional genes were identified to regulate the mode of epidermal cell development in Arabidopsis, rice, maize, tomato, Artemisia annua, such as MYB-bHLH-WD40(MBW) complex [7,8], OsHL6 [9], OsWOX3 [10], ZmOCL4 [11], ZmSPL10/14/26 [12], SlMYC1 [13], SlWo [14], AaHD1 [15].

Methods

Results

Discussion

Conclusion