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

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.

Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin

“…For WGCNA analysis, K ME values indicated the eigengene connectivity based on the assumption that hub genes are identified by sorted K ME values [33]. In this study, several genes with the highest K ME values in each module were selected as hub genes.…”

Identification of TPX2 Gene Family in Upland Cotton and its Functional Analysis in Cotton Fiber Development

“…Two upland cotton genotypes 69307 with longer and stronger cotton fiber and 69362 with short and weaker cotton fiber were cultivated under standard field conditions (10 rows, each 8 m long and 0.8 m) in Zhengzhou, China [32,33]. Cotton fibers at 5, 10, 15, 20, 25, and 30 days post anthesis (DPA) were collected from bolls for extraction of RNA.…”

Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1

“…TFs were obtained from P2TF (Predicted Prokaryotic Transcription Factors) database that contains 372,877 TFs from 1,987 prokaryotes [20]. TFs are ranked based on the correlation of TFs with module hub gene [34][35][36]. The TFs thus obtained in these modules were further confirmed for the presence of DNA binding and other regulatory domain using Conserved Domain Database (CDD) [37].…”

“…It has been previously reported that TFs which are highly correlated with hub gene could be the potential regulators of respective module [34][35][36]. The regulation of darkgreen module PLOS ONE appears to be complex as it possesses multiple TFs.…”