Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated <i>Gossypium hirsutum</i> L.

Upland cotton (<i>Gossypium hirsutum</i> L.) is one of the world’s most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 days postanthesis (DPA), 20 DPA, and mature stages at the morphological level. To explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences, and better inform our efforts to further enhance cotton fiber quality, isobaric tags for relative and absolute protein quantification-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified; among them, 336 were defined as differentially expressed proteins between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in phenylpropanoid biosynthesis, zeatin biosynthesis, fatty acid elongation, and other processes. Association analysis between transcriptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. Differences in proteomics have been verified at the mRNA level by quantitative real-time polymerase chain reaction and have been validated at the physiological and biochemical levels by POD (peroxidase) activity assays and ZA (zeatin) content estimates. This work corroborates the major pathways involved in cotton fiber development and demonstrates that POD activity and zeatin content have a great potential related to fiber elongation and thickening