The Cotton Fiber Transcriptome: A Single-Celled Genomics Platform for Studying Plant Cell Walls.

Cotton fibers are economically important seed trichomes that are among the longest and fastest growing single cells in the plant kingdom. Fibers possess a thin primary cell wall (PCW) typical of dicots and a thick cellulosic secondary cell wall (SCW) that is not lignified. Developmental switches that control dynamic re-modeling of the cotton fiber transcriptome control stage-specific gene expression and the temporal regulation of cell wall biogenesis during fiber morphogenesis. Developing cotton fibers therefore offer a unique single-celled model system for investigating the genetic mechanisms underlying biogenesis of plant cell walls. Of the ~28,000 genes represented in the cotton fiber transcript, more than 1000 SCW-specific gene transcripts have been identified as candidate genes for important fiber quality traits. Data mining of expression data by double feature selection analysis identified a subset of fiber genes of interest involved in carbohydrate metabolism that is also mis-expressed in a SCW-defective mutant exhibiting a significant decrease in crystalline cellulose and poor fiber quality. A strong correlation between the genes, genotype and fiber phenotype suggests this group of genes serve as prime candidates for regulating carbohydrate flux and cell wall structure and composition. A genetical genomics approach also correlates these genes with QTL for fiber quality that can be readily categorized as PCW or SCW based on developmental expression profiles. Mutant analysis played a major role in the identification of candidate genes that play crucial roles in fiber quality, and are targets of opportunity for genetic improvement programs.