Developmental Transcriptional Model describing regulated genes, QTLs and pathways during the primary and secondary cell walls of Pima fibers

Abstract

Gossypium barbadense L. (Egyptian and Pima) produces single celled fiber trichomes that are the longest and richest in cellulosic contents in the plant kingdom. Developmental dissection of fiber at the transcriptional level is crucial to unveiling the genetic mechanisms underpinning fiber morphogenesis. We profiled the transcriptome of developing Pima fibers, as well as genes associated with consensus fiber quality QTLs, at seven developmental time points covering both primary (PCW) and secondary (SCW) cell wall stages. A total of 2,934 genes were differentially expressed at only one (45.19%) or at multiple (54.81%) developmental time points. Based on the coincidence between gene expression dynamics and the time frame of fiber developmental stages, five stage-specific expression profiles were identified. As a link between fiber QTLs and gene expression, 5 potential developmentally regulated QTLs (drQTLs) corresponding to different fiber developmental stages were identified. Genes in the ubiquitin proteolytic pathway, particularly QTL associated genes, appeared to be involved in regulating the transition stage between PCW and SCW; a stage that is crucial to both fiber length and strength in the extra-long staple cotton genotypes. In this respect, Yeast-two-hybrids identified interactions between UBC9 and genes involved in cell and organ elongation, polar cell expansion, microtubule cytoskeleton dynamics and organization, and basic amino acids transportation during the SCW/SCW transition. Altogether, these results were integrated into a proposed model linking fiber developmental stages with the Pima fiber traits.