The Li(2) Mutation Results in Reduced Subgenome Expression Bias in Elongating Fibers of Allotetraploid Cotton (Gossypium hirsutum L.)

Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (Li(2)) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (Gossypium hirsutum L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of Li(2) 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 D(5) genome (G. raimondii) 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 Li(2) fiber transcriptome; 3) Li(2) 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 Li(2) 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.