Integrated Transcriptomics and Metabolomics Between 10 – 28 Days Post Anthesis in Two Species of Commercial Cotton Fiber

Cotton fiber is a tissue comprised of a single cell type that develops from the seed epidermis in discrete stages including: initiation, elongation, a transition from primary to secondary wall deposition, and secondary wall thickening. Most cotton fiber produced comes from the species Gossypium hirsutum, but Gossypium barbadense cotton fibers are longer, stronger, and finer leading to a higher value yarn. We characterized fiber development in these two allotetraploid cotton species under controlled growth conditions and used RNAseq and metabolomics (Metabolon Inc., Durham, NC) to identify differences at 10, 15, 18 21, and 28 days post anthesis. The Gossypium raimondii genome was used in combination with Gossypium arboretum ESTs as a mapping reference. 37,937 transcripts (reads per kilobases per million reads >2) were identified of which 8,842 transcripts were differentially expressed (fold change>2) between the two species during development. Metabolic profiling of the cotton fiber showed that 186 of 206 identified metabolites were differentially accumulated between the two species during fiber development. KEGG ontology was used to map both datasets to metabolic pathways. Our results indicate that the two species differ most significantly in protein biosynthesis and turnover for all timepoints and in ROS management during the transition stage and secondary cell wall deposition. Other pathways that are differentially regulated between the two species include: glutathione metabolism, nitrogen metabolism, galactose metabolism, phenylpropanoid biosynthesis, amino and nucleotide sugar metabolism, starch and sucrose metabolism, and glycolysis. This work was funded by the National Science Foundation (award #1025947).