Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis.

Xianyan Zou,Qi Zhang,Ruixian Liu,Yanling Wang,Zhen Zhang,Senmiao Fan,Yulong Feng,Shuya Zhang,Xiao Jiang,Lipeng Zhang,Kang Lei,Tingting Jia,Qún Gě ,Wànkuí Gǒng ,Jǔwǔ Gōng ,Yùzhēn Shí ,Bin Tian ,Àiyīng Liú ,Jùnwén Lǐ ,Yǒulù Yuán ,Hǎihóng Shāng

doi:10.3390/genes10020119

Abstract

Upland cotton (Gossypium hirsutum) is grown for its elite fiber. Understanding differential gene expression patterns during fiber development will help to identify genes associated with fiber quality. In this study, we used two recombinant inbred lines (RILs) differing in fiber quality derived from an intra-hirsutum population to explore expression profiling differences and identify genes associated with high-quality fiber or specific fiber-development stages using RNA sequencing. Overall, 72/27, 1137/1584, 437/393, 1019/184, and 2555/1479 differentially expressed genes were up-/down-regulated in an elite fiber line (L1) relative to a poor-quality fiber line (L2) at 10, 15, 20, 25, and 30 days post-anthesis, respectively. Three-hundred sixty-three differentially expressed genes (DEGs) between two lines were colocalized in fiber strength (FS) quantitative trait loci (QTL). Short Time-series Expression Miner (STEM) analysis discriminated seven expression profiles; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were performed to identify difference in function between genes unique to L1 and L2. Co-expression network analysis detected five modules highly associated with specific fiber-development stages, especially for high-quality fiber tissues. The hub genes in each module were identified by weighted gene co-expression network analysis. Hub genes encoding actin 1, Rho GTPase-activating protein with PAK-box, TPX2 protein, bHLH transcription factor, and leucine-rich repeat receptor-like protein kinase were identified. Correlation networks revealed considerable interaction among the hub genes, transcription factors, and other genes.

Highlights

Cotton (Gossypium spp.) is among the most important crops worldwide and is grown for its natural fiber for the textile industry
To understand the differences in gene expression patterns between two extreme-parent lines derived from an intra-hirsutum recombinant inbred lines (RILs) population of upland cotton and to identify genes associated with elite fiber quality, RNA-seq was performed by constructing 30 libraries from the two lines with three biological replications at five time points that coincided with the stages of fiber initiation, elongation, cell-wall remodeling, and secondary cell wall growth
The 363 genes identified by RNA-seq and colocalized in fiber strength (FS) quantitative trait loci (QTL) were valuable for affecting fiber development

Summary

Introduction

Cotton (Gossypium spp.) is among the most important crops worldwide and is grown for its natural fiber for the textile industry. With the dramatic changes in climate and environment and the reason of the often crosspollinated plant, breeders are focused on the development of new cultivars to improve the fiber quality of upland cotton, which will be highly beneficial for the textile industry. A thorough understanding of the underlying mechanisms of cotton fiber development is crucial to improve fiber quality. Fiber development can be classified into five stages: Fiber initiation (0–3 days post-anthesis (DPA)), elongation (3–15 DPA), transitional cell-wall remodeling (15–20 DPA), secondary wall biosynthesis (20–40 DPA), and maturity (40–50 DPA) [2]. The third and fourth stages are associated with fiber strength and fineness as a result of the development of secondary cell wall thickening

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Results

Discussion

Conclusion