A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

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 F-2 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.