Identification of An EST-SSR Marker with Complete Linkage to the Ligon Lintless-2 Genetic Locus in Cotton (Gossypium hirsutum L.)

Utilizing a combined approach of functional and structural genomics, an EST-SSR marker was identified with complete linkage to the Ligon lintless-2 (Li₂) genetic locus of cotton (Gossypium hirsutum L.).  Gene expression profiling on selected fiber developmental time-points was conducted using the cotton Affymetrix microarray platform and RT-qPCR on two near-isogenic Li₂ cotton populations, one mutant and one wild-type (WT).  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. Genes that were differentially expressed in mutant and WT fibers were used to search the publically available cotton marker database for existing expressed sequence tag simple sequence repeat (EST-SSR) markers derived from sequences with a high degree of similarity to those used in the database search.  EST-SSR markers that were previously mapped to chromosome 18 or homeologous chromosome 13 were initially selected since the Li₂ gene was previously shown to be located on chromosome 18.  An Li₂ intraspecific F₂ mapping population of 136 individuals was used to screen selected EST-SSR markers.  One marker designated NAU3991 displayed complete linkage to the Li₂ genetic locus in our mapping population suggesting that it may be the Li₂ gene.