RNA-Seq Analysis of Short Fiber Mutants Ligon-Lintless-1 (Li1) and - 2 (Li2) Revealed Important Role of Aquaporins in Cotton (Gossypium hirsutum L.) Fiber Elongation

Cotton fiber length is a key determinant of fiber quality for the textile industry.  Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon lintless-1 (Li₁) and Ligon lintless-2 (Li₂) are monogenic and dominant mutations, that result in an extreme reduction in the length of lint fiber to approximately 6 mm on mature seeds. In a near-isogenic state with wild type (WT) cotton these two short fiber mutants provide an excellent model system to study mechanisms of fiber elongation.

We used next generation sequencing (RNA-seq) to identify common fiber elongation related genes in developing fibers of Li₁ and Li₂ mutants independent of environmental conditions. We found a large number of differentially expressed genes common to both mutants, including 531 up-regulated genes and 652 down-regulated genes. Major intrinsic proteins or aquaporins were one of the most significantly over-represented gene families among common down-regulated genes in Li₁ and Li₂ fibers. The members of three subfamilies of aquaporins, including plasma membrane intrinsic proteins, tonoplast intrinsic proteins and NOD26-like intrinsic proteins were down-regulated in short fiber mutants. The osmotic concentration and the concentrations of soluble sugars were lower in fiber cells of both short fiber mutants than in WT, whereas the concentrations of K⁺ and malic acid were significantly higher in mutants during rapid cell elongation.

These results suggest that higher accumulation of ions in fiber cells of Li₁ and Li₂ may be the result of limited uptake of water due to a combination of factors, such as reduced osmotic pressure and low expression of aquaporins, causing cessation of fiber elongation. The research presented here provides new insights into osmoregulation of short fiber mutants and the role of aquaporins in cotton fiber elongation.