Background: Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li ₂ ) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li ₂ is a model system with which to study fiber elongation. Results: Two near-isogenic lines of Ligon lintless-2 (Li ₂ ) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC₅). An F₂ population was developed from a cross between the two Li ₂ near-isogenic lines and used to develop a linkage map of the Li ₂ locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the Li ₂ locus region with two of the markers flanking the Li ₂ locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the Li ₂ mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li ₂ locus. Conclusions: In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li ₂ locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the Li ₂ gene.

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 (Li 1 ) and Ligon lintless-2 (Li 2 ) 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 Li 1 and Li 2 mutants growing in the field and a greenhouse. 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 Li 1 and Li 2 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. We found that the aquaporins were the most down-regulated gene family in both short fiber mutants. The osmolality and concentrations of soluble sugars were less in saps of Li 1 – Li 2 , whereas the concentrations of malic acid, K+ and other detected ions were significantly higher in saps of mutants than in WT. These results suggest that higher accumulation of ions in fiber cells, reduced osmotic pressure and low expression of aquaporins, may contribute to the cessation of fiber elongation in Li 1 and Li 2 short-fiber mutants. The research presented here provides new insights into osmoregulation of short fiber mutants and the role of aquaporins in cotton fiber elongation.

The length of cotton fiber is an important agronomic trait characteristic that directly affects the quality of yarn and fabric. The cotton (Gossypium hirsutum L.) fiber mutation, Ligon lintless-2, is controlled by a single dominant gene (Li 2 ) and results in extremely shortened lint fibers on mature seeds with no visible pleiotropic effects on vegetative growth and development. The Li 2 mutant phenotype provides an ideal model system to study fiber elongation. To understand metabolic processes involved in cotton fiber elongation, changes in metabolites and transcripts in the Li 2 mutant fibers were compared to wild-type fibers during development.

Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li 1 ) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6 mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li 1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points. Physical and morphological measurements of the Li 1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li 1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li 1 gene. The early termination of fiber elongation in the Li 1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li 1 mutant were identified. Molecular markers closely associated with the Li 1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.