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A chromosome substitution line, CS-B25, was developed by the substitution of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbadense, a double haploid Pima 3-79 line. CS-B25 has improved fiber traits compared to its parent TM-1. To explore the molecule mechanisms underlying improved fiber traits, deep sequencing of total RNA was used to compare gene expression in fibers of CS-B25 and TM-1 at 10 days post anthesis (10-DPA). A total of 1872 differentially expressed genes (DEGs) were detected between the two lines, with 1175 up-regulated and 697 down-regulated in CS-B25. Gene Ontology (GO) enrichment analysis of the expression data by Generally Applicable Gene-set Enrichment (GAGE) and ReviGO indicated that the most prevalent Biological Process GO terms associated with DEGs included DNA-templated transcription, response to oxidative stress, and cellulose biosynthesis. Enriched Molecular Function GO terms included structural constituents of cytoskeleton, peroxidase activity, cellulose synthase (UDP-forming) activity, and transcription regulatory region sequence-specific DNA binding factors. GAGE was also used to find enriched KEGG pathways, and the highly represented pathways were Biosynthesis of Amino Acids, Starch and Sucrose Metabolism, Phenylpropanoid Biosynthesis, Protein Processing in Endoplasmic Reticulum, and Plant Hormone Signal Transduction. Many of the identified DEGs are involved in cytoskeleton and cell wall metabolism. The results of gene expression data have provided new insight into the molecular mechanisms of fiber development during the fiber elongation stage and would offer novel candidate genes that may be utilized in cotton fiber quality improvement.

Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms that govern fiber development with positive fiber traits, a study of global gene expression profiling of 10-DPA fibers in a PHYA1 RNAi line and its parent Coker 312 was conducted by high-throughput RNA sequencing. A comparative analysis of transcriptomes between the two lines had identified 142 genes that were differentially expressed in the 10-DPA fiber of the RNAi line. Gene Ontology analysis showed that these differentially expressed genes were mainly involved in metabolic pathways, heterocyclic/organic cyclic compound binding and multiple enzyme activities, and cell structures which were reported to play important roles in fiber development. Twenty-eight KEGG pathways were mapped for the 142 genes, and the pathways related to glycolysis/gluconeogenesis and pyruvate metabolism were the most abundant and followed by cytochrome P450-involved pathways, suggesting that fiber improvement could be through the regulation of proteins involved in cytochrome P450 pathways. Genes encoding WRKY transcription factors, sucrose synthase, xyloglucan endotransglucosylase hydrolase, udp-glucuronate: xylan alpha-glucuronosyltransferase, and genes involved in lipid metabolism and ABA/brassinosteroid signal transduction pathways were found differentially expressed in the RNAi line. These genes have direct impacts on cotton fiber quality. The results of this study elucidate molecular signatures and possible mechanisms of fiber improvement in the background of PHYA1 RNAi in cotton and should help for future fine-tuning and programming of cotton fiber development.