Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development

Jiasen He; Zhongyang Xu; Muhammad Tehseen Azhar; Zhen Zhang; Pengtao Li; Juwu Gong; Xiao Jiang; Senmiao Fan; Qun Ge; Youlu Yuan; Haihong Shang

doi:10.3389/fpls.2023.1189490

Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development

Front Plant Sci. 2023 Aug 31:14:1189490. doi: 10.3389/fpls.2023.1189490. eCollection 2023.

Authors

Jiasen He¹, Zhongyang Xu¹, Muhammad Tehseen Azhar^{1

2}, Zhen Zhang³, Pengtao Li⁴, Juwu Gong³, Xiao Jiang³, Senmiao Fan³, Qun Ge³, Youlu Yuan³, Haihong Shang^{1

3}

Affiliations

¹ National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China.
² Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
³ National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
⁴ National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang Institute of Technology, Anyang, China.

Abstract

Introduction: Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels.

Methods: Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes.

Results: Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers.

Discussion: Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.

Keywords: DEGs; Gossypium hirsutum; RNA-Seq; WGCNA; fiber development.

Grants and funding

This work was supported by the National Natural Science Foundation of China (No. 3210151266) and the Central Public-interest Scientific Institution Basal Research Fund (No: 1610162021004).