Molecular analysis of late-stage fiber development in upland cotton

Cotton is the world's most important textile and the number one value-added crop. It plays a crucial role in the economy of Texas – supporting close to 50,000 jobs and supplying $2 billion to the state economy. Its role is even more evident in the South Plains of Texas, which supplies approximately 10% of the world's cotton. Understanding molecular events associated with the developing fiber could provide candidate targets for genetic improvement. Such modifications could lead to substantial crop enhancements, in terms of either yield or fiber quality or both, signifying considerable economic ramifications for the industry. Late-stage (21 and 24 days post-anthesis, dpa) fiber samples of the Upland cotton cultivar, TM1, were subjected to transcriptomic analysis using RNA Sequencing technology (Illumina MiSeq). Using de novo assembly in DNASTAR NGen software, the sequence reads with a quality score greater than 30 (9.2 million reads from 21 dpa and 7.5 million reads from 24 dpa) were assembled into 23942 contigs and 19750 contigs, respectively. RNA-Seq analysis using DNASTAR Array Star revealed 2928 differentially expressed transcripts. Differential expression was defined as those transcripts with 99% confidence and greater than 2.0-fold expression change between 21 and 24 dpa samples. Additionally, the proteomes from these two time-points were analyzed using nano liquid chromatography tandem mass spectrometry. The proteins were identified using a proteome created from transcriptomic data using The GPM search engine with a 1% false discovery rate. Proteins present in all replicates of each stage were annotated with the Mercator tool from Max Planck Institute. MapMan software was employed to visualize expression profiles at the pathway level of both transcriptomic and proteomic data. This mapping revealed up-regulation of pectinesterases and chromatin remodeling factors, such as DNA methyltransferases and histone deacetylases, and down-regulation of components of cell-signaling. Additionally, changes indicative of dormancy, prior to dehydration and final maturation appear to begin during this critical phase of fiber development. A complete analysis of this key transition in fiber development will be discussed.