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.)

Authors: Hinchliffe, Doug; Turley, Rickie; Naoumkina, Marina; Kim, Hee-Jin; TANG, YUHONG - Samuel Roberts Noble Foundation, Inc; Yeater, Kathleen; Li, Ping; Fang, David

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2011
Publication Date: 9/9/2011
Citation: Hinchliffe, D.J., Turley, R.B., Naoumkina, M.A., Kim, H.J., Tang, Y., Yeater, K.M., Li, P., Fang, D.D. 2011. 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.). Biomed Central (BMC) Genomics. 12:445.

Interpretive Summary: The seed fibers of cultivated cottons represent a globally important agronomic crop utilized by the textile industries. 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. Varieties of cultivated upland cotton that display fiber mutation phenotypes including short fibers and lintless and fuzzless seeds were first described in the early twentieth century. The cotton fiber mutation Ligon lintless-2 has significantly shorter fibers than normal cotton and provides a unique and powerful model system to study what controls the length of cotton fibers as they develop. 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 main objective of this research was to identify the genes responsible for the short fiber mutation in Ligon lintless-2 cotton plants. In the field of cotton genomics, we report the first successful conversion of gene expression data into a genetic marker that is extremely close to the gene, or is the gene responsible for a commercially important fiber trait.

Technical Abstract: 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 (Li2) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation. Two near-isogenic lines of Ligon lintless-2 (Li2) 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 Li2 near-isogenic lines and used to develop a linkage map of the Li2 locus on chromosome 18. Five simple sequence repeat markers (SSR) were closely mapped around the Li2 locus region with two of the markers flanking the Li2 locus at 0.87 and 0.52 centimorgans. 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 Li2 mutant phenotype. Microarray gene expression data lead to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li2 locus. 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 Li2 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 Li2 gene.