Co-expression networks regulating cotton fiber initiation generated by comparative transcriptome analysis between fiberless XZ142FLM and GhVIN1i

Cotton produces natural fiber as crucial raw material for textile industry and thus is economically one of the most important crops worldwide. Currently the mechanisms that control fiber initiation on ovules are still not well understood. In this study, we performed comparative transcriptome analysis between the natural fiberless mutant XZ142FLM and transgenic fiberless line GhVIN1i generated by RNAi silencing of GhVIN1 to identify molecular regulatory networks controlling fiber initiation. It was found that XZ142FLM and GhVIN1i shared many common differentially expressed genes (DEGs) in ovules during fiber initiation, and their respective DEGs were enriched in several identical pathways related to fiber initiation. Many reported fiber initiation or elongation related genes including GhMML3, GhVIN1, GhMYB25, GhHD-1, GhHOX3 exhibited similar expression patterns in XZ142FLM and GhVIN1i during fiber initiation, suggesting similar mechanisms of fiber initiation operating in the two fiberless lines, which was further verified by comparative temporal expression pattern analysis between TM-1/XZ142FLM and Coker 312/GhVIN1i. Co-expression regulatory networks for controlling fiber initiation were constructed for XZ142FLM and GhVIN1i, respectively, which centered on GhMML3 or GhVIN1 with many known fiber initiation/elongation related genes. Several transcription factors and hub genes were identified in the co-expression networks generated, which may facilitate future research in identification of novel candidate genes regulating fiber initiation and elongation. Overall, the results obtained in this study shed light on the regulatory networks mediated by GhMML3 and GhVIN1 for controlling fiber initiation in cotton.