scRNA-seq and scATAC-seq reveal dual transcriptional and translational regulation in fiber cells in Upland and Pima cotton

Fiber cell initiation and development affect cotton fiber yield and quality. Cotton fiber develops from the ovular epidermis of a seed, and approximately 25-30% of protodermal cells in each cotton ovule develop into fiber. However, the molecular basis for fiber cell development remains elusive. Here, we analyzed single-cell RNA-seq (scRNA-seq) data from over 40,000 cells during early stages of fiber cell development in Upland and Pima cotton and in a naked seed mutant. We found concerted expression changes of 900-1,700 genes in fiber-cell clusters involving gene expression, translation, and peptide biosynthesis, which were substantially delayed or absent in the mutant. Expression of ∼500 and ∼300 genes in Upland and Pima cotton, respectively, was distinguishably different and consistent with overrepresentation of the genes in transcriptional and translational regulation, implying their roles in fiber yield and quality traits. Gene co-expression network analysis (GCNA) of scRNA-seq and scATAC-seq data revealed two modules of fiber gene co-expression networks. One module of the fiber co-expressed genes was associated with elevated chromatin accessibility for transcriptional regulation, whereas the other module of the genes was related to translational regulation and ribosome biogenesis. Indeed, expression of cotton putative translation factor genes was elevated in fiber cell clusters in both Upland and Pima cotton. Finally, cotton transgenic plants expressing promoter::GFP confirmed expression patterns of fiber-expressed GhRDL2_D5 during fiber cell initiation. These single-cell genomic resources provide insights into fiber cell development for breeding and biotechnological improvement of fiber yield and quality in Upland and Pima cotton.