The <i>Li₂</i> Mutation Results in Reduced Subgenome Expression Bias in Elongating Fibers of Allotetraploid Cotton (<i>Gossypium hirsutum</i> L.)

<div><p>Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (<i>Li₂</i>) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (<i>Gossypium hirsutum</i> L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of <i>Li₂</i> mutant and wild type near-isogenic lines at the peak of elongation followed by mapping and PolyCat categorization of RNA-seq data to the reference D₅ genome (<i>G. raimondii</i>) for homeologous gene expression analysis. The majority of homeologous genes, 83.6% according to the reference genome, were expressed during fiber elongation. Our results revealed: 1) approximately two times more genes were induced in the A_T subgenome comparing to the D_T subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in the <i>Li₂</i> fiber transcriptome; 3) <i>Li₂</i> had a significantly greater effect on the D_T than on the A_T subgenome. Transcriptional regulators and cell wall homeologous genes significantly affected by the <i>Li₂</i> mutation were reviewed in detail. This is the first report to explore the effects of a single mutation on homeologous gene expression in allotetraploid cotton. These results provide deeper insights into the evolution of allotetraploid cotton gene expression and cotton fiber development.</p>