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.)

Abstract

BackgroundCotton 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.ResultsTwo 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 (SSR) markers were closely mapped around the Li2 locus region with two of the markers flanking the Li2 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 Li2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li2 locus.ConclusionsIn 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.

Comparative Transcriptome Analysis of Short Fiber Mutants Ligon-Lintless 1 And 2 Reveals Common Mechanisms Pertinent to Fiber Elongation in Cotton (Gossypium hirsutum L.)

“…Development of these NILs was described in our earlier reports [18], [19]. For the greenhouse-grown Li 2 plants utilized in this study, growth and sample conditions were described in Hinchliffe et al (2011) [19], and the growing period was between October, 2009 and March, 2010. Each plant was grown in an 18.9 L pot.…”

The Li2 Mutation Results in Reduced Subgenome Expression Bias in Elongating Fibers of Allotetraploid Cotton (Gossypium hirsutum L.)

“…Growth conditions and fiber sampling were previously described [6]. Cotton bolls were harvested at the following time-points during development: day of anthesis (DOA), 1, 3, 5, 8, 12, 16, and 20 days post-anthesis (DPA).…”

Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 mutant cotton (Gossypium hirsutum L.)

“…It has been determined that Li 1 associated with chromosome 22, whereas Li 2 with chromosome 18 [7-9]. Cytological studies did not reveal much difference in seed fiber initiation between mutants and their near-isogenic lines suggesting the effects of the mutation occurs later in development during the elongation stage [9,10]. Kohel et al .…”

“…Our laboratory selected the Li 2 mutant as a model system to study fiber elongation for the reasons mentioned above. An Li 2 mutant cotton line in a near-isogenic state with the Upland cotton variety DP5690 was developed in a backcross program at Stoneville, MS [10]. Morphological evaluation by scanning electron microscopy revealed no visible differences in the appearances of ovules and fibers from Li 2 mutant and WT near-isogenic lines (NILs) during initiation and early elongation up to 5 DPA [10].…”